diff --git a/CHANGELOG b/CHANGELOG
index 619737659da8ef4cd3c21a798cbbf784ec44b50d..dadb7279143d82cfb84765018ce6256269aeee10 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -8,6 +8,7 @@ minerva (19.0.0~alpha.0) stable; urgency=medium
* Backward incompatible: custom annotation validation on project upload
removed (#2101)
* Improvement: new API (#1594)
+ * Improvement: allow to download generated ZIP (#2233)
* Small improvement: layers have images (#2156)
* Small improvement: when exporting to SBML provide annotation as
identifiers.org uri (#2202)
@@ -23,6 +24,7 @@ minerva (19.0.0~alpha.0) stable; urgency=medium
* Bug fix: when removing project the layer texts/rectangles/ovals were not
removed
* Bug fix: index.html has been cached but should not (#2210)
+ * Bug fix: export to SBGN-ML could generate invalid notes node for the file
-- Piotr Gawron <piotr.gawron@uni.lu> Wed, 18 Sep 2024 13:00:00 +0200
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
index 9df84096a223608d427ade3d813d1f81972c91c0..ab44805c4f56d44a82e9b083a89561abf543346c 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java
@@ -1,24 +1,22 @@
package lcsb.mapviewer.cdplugin.copypaste;
-import java.util.HashSet;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.HashSet;
+import java.util.Set;
/**
* This abstract class defines common function for {@link CopyAction} and
* {@link PasteAction}.
- *
+ *
* @author Piotr Gawron
- *
*/
public class CopyPasteAbstractAction {
/**
@@ -35,9 +33,8 @@ public class CopyPasteAbstractAction {
/**
* Serializes {@link MiriamData} into string that will be stored into system
* clipboard.
- *
- * @param md
- * object to serialize
+ *
+ * @param md object to serialize
* @return string representation of {@link MiriamData}
*/
protected String serialize(final MiriamData md) {
@@ -48,9 +45,8 @@ public class CopyPasteAbstractAction {
/**
* Deserialize {@link MiriamData} from string creted by
* {@link #serialize(MiriamData)} method.
- *
- * @param string
- * string representation of {@link MiriamData}
+ *
+ * @param string string representation of {@link MiriamData}
* @return {@link MiriamData} obtained from input string
*/
protected MiriamData deserialize(final String string) {
@@ -77,14 +73,11 @@ public class CopyPasteAbstractAction {
/**
* Returns serialized string of annotations and notes.
- *
- * @param annotationString
- * xml string representing annotations in CellDesigner
- * @param notesString
- * flat notes String
+ *
+ * @param annotationString xml string representing annotations in CellDesigner
+ * @param notesString flat notes String
* @return serialized string
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
+ * @throws InvalidXmlSchemaException thrown when xmlString is invalid
*/
protected String getCopyString(final String annotationString, final String notesString) throws InvalidXmlSchemaException {
XmlAnnotationParser xap = new XmlAnnotationParser();
@@ -100,10 +93,8 @@ public class CopyPasteAbstractAction {
/**
* Deserialize string created by {@link #getCopyString(String, String)}
* method. Used to create {@link MiriamData} set and notes from clipboard.
- *
- * @param value
- * string for deserialization
- *
+ *
+ * @param value string for deserialization
* @return {@link Pair} of {@link MiriamData} set and notes string
*/
protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(final String value) {
@@ -112,7 +103,7 @@ public class CopyPasteAbstractAction {
}
String[] rows = value.split("\n");
- StringBuilder sb = new StringBuilder("");
+ StringBuilder sb = new StringBuilder();
boolean miriam = true;
diff --git a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
index 7d0ba23e86e11f8ebf654512c007c39b769ee27c..332181c519a78009a04f6e6a02fefbe472ab08a1 100644
--- a/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
+++ b/CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java
@@ -1,25 +1,23 @@
package lcsb.mapviewer.cdplugin.copypaste;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import jp.sbi.celldesigner.plugin.PluginListOf;
import jp.sbi.celldesigner.plugin.PluginReaction;
import jp.sbi.celldesigner.plugin.PluginSBase;
import jp.sbi.celldesigner.plugin.PluginSpecies;
import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.Set;
/**
* CD Plugin action responsible for translating annotation stored in notes to
* xml format stored in annotations.
- *
+ *
* @author Piotr Gawron
- *
*/
public class PasteAction extends CopyPasteAbstractAction {
/**
@@ -30,11 +28,9 @@ public class PasteAction extends CopyPasteAbstractAction {
/**
* Method that perform annotation of a CellDesigner species listed in
* speciesList.
- *
- * @param plug
- * - a plugin object
- * @param speciesList
- * - list of species to annotate
+ *
+ * @param plug - a plugin object
+ * @param speciesList - list of species to annotate
*/
public void performAnnotation(final CopyPastePlugin plug, final PluginListOf speciesList) {
XmlAnnotationParser xap = new XmlAnnotationParser();
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java
index fcf345ef25ea6ea9c898b2fe16b20de7fd018877..39cb26152ee23c5b4fd1e8cf06c68a428bc5dd30 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MiriamConnectorImpl.java
@@ -4,9 +4,9 @@ import lcsb.mapviewer.annotation.cache.CachableInterface;
import lcsb.mapviewer.annotation.cache.QueryCacheInterface;
import lcsb.mapviewer.annotation.cache.SourceNotAvailable;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.http.HttpStatus;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
index 445af6b389d760cc97dfa5b80d83a966fe130ee9..5eb873865a98980b9ec6b4f492bcd09ff834a727 100644
--- a/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
+++ b/annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java
@@ -48,7 +48,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test
- public void testGoUri() throws Exception {
+ public void testGoUri() {
assertNotEquals(1, MiriamType.GO.getUris().size());
}
@@ -60,7 +60,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test
- public void testGetUrl() throws Exception {
+ public void testGetUrl() {
MiriamData md = TaxonomyBackend.HUMAN_TAXONOMY;
String url = miriamConnector.getUrlString(md);
@@ -68,30 +68,30 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test(expected = InvalidArgumentException.class)
- public void testGetUrlForInvalidMiriam() throws Exception {
+ public void testGetUrlForInvalidMiriam() {
miriamConnector.getUrlString(new MiriamData());
}
@SuppressWarnings("deprecation")
@Test(expected = InvalidArgumentException.class)
- public void testGetUrlForInvalidMiriam2() throws Exception {
+ public void testGetUrlForInvalidMiriam2() {
miriamConnector.getUrlString(new MiriamData(MiriamType.UNKNOWN, ""));
}
@Test
- public void testGetUrlForInvalidMiriam3() throws Exception {
+ public void testGetUrlForInvalidMiriam3() {
String url = miriamConnector.getUrlString(new MiriamData(MiriamType.ENTREZ, "abc"));
assertNull(url);
}
@Test
- public void testIsValidIdentifier() throws Exception {
+ public void testIsValidIdentifier() {
assertTrue(miriamConnector.isValidIdentifier(MiriamType.ENTREZ.getCommonName() + ":" + "1234"));
- assertFalse(miriamConnector.isValidIdentifier("blablabla"));
+ assertFalse(miriamConnector.isValidIdentifier("blah"));
}
@Test
- public void testResolveUrl() throws Exception {
+ public void testResolveUrl() {
for (final MiriamType mt : MiriamType.values()) {
boolean deprecated = false;
try {
@@ -100,6 +100,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
deprecated = true;
}
} catch (final NoSuchFieldException | SecurityException e) {
+ logger.error(e, e);
}
if (!deprecated) {
@@ -109,7 +110,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test
- public void testGetUrlForDoi() throws Exception {
+ public void testGetUrlForDoi() {
// exclude first cached value
MiriamData md = new MiriamData(MiriamType.DOI, "10.1038/npjsba.2016.20");
@@ -118,7 +119,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test
- public void testMiriamDataToUri() throws Exception {
+ public void testMiriamDataToUri() {
assertNotNull(miriamConnector.miriamDataToUri(TaxonomyBackend.HUMAN_TAXONOMY));
}
@@ -128,7 +129,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
when(mockDownloader.getFromNetwork(anyString(), anyString(), nullable(String.class)))
.thenThrow(new IOException());
ReflectionTestUtils.setField(miriamConnector, "webPageDownloader", mockDownloader);
- miriamConnector.refreshCacheQuery("http://google.pl/");
+ miriamConnector.refreshCacheQuery("https://google.pl/");
}
@Test(expected = InvalidArgumentException.class)
@@ -142,7 +143,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test
- public void testCheckValidyOfUnknownMiriamType() throws Exception {
+ public void testCheckValidityOfUnknownMiriamType() {
// user connector without cache
@SuppressWarnings("deprecation")
boolean value = miriamConnector.isValidMiriamType(MiriamType.UNKNOWN);
@@ -155,7 +156,7 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
}
@Test
- public void testGetUrlWithNewLine() throws Exception {
+ public void testGetUrlWithNewLine() {
MiriamData md = new MiriamData(MiriamType.HGNC_SYMBOL, "test\name");
String url = miriamConnector.getUrlString(md);
diff --git a/commons/src/main/java/lcsb/mapviewer/common/Comparator.java b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
index b096d920c8e7605a246ae94b07dc2476656d7268..e908c2846bb1cf95bfe3c2ccd7e0b1939f81329c 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/Comparator.java
@@ -1,21 +1,18 @@
package lcsb.mapviewer.common;
-import java.util.ArrayList;
-import java.util.List;
-
+import lcsb.mapviewer.common.exception.NotImplementedException;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
-import lcsb.mapviewer.common.exception.NotImplementedException;
+import java.util.ArrayList;
+import java.util.List;
public abstract class Comparator<T extends Object> implements java.util.Comparator<T> {
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger();
- private Class<T> comparatorClazz;
- private boolean exactClassMatch;
- private List<Comparator<? extends T>> subClassComparatorList = new ArrayList<>();
+ protected static Logger logger = LogManager.getLogger();
+
+ private final Class<T> comparatorClazz;
+ private final boolean exactClassMatch;
+ private final List<Comparator<? extends T>> subClassComparatorList = new ArrayList<>();
protected Comparator(final Class<T> clazz) {
this(clazz, false);
@@ -26,7 +23,7 @@ public abstract class Comparator<T extends Object> implements java.util.Comparat
this.exactClassMatch = exactClassMatch;
}
- @SuppressWarnings({ "rawtypes", "unchecked" })
+ @SuppressWarnings({"rawtypes", "unchecked"})
@Override
public final int compare(final T arg0, final T arg1) {
if (arg0 == null) {
@@ -68,7 +65,7 @@ public abstract class Comparator<T extends Object> implements java.util.Comparat
return null;
}
- @SuppressWarnings({ "rawtypes", "unchecked" })
+ @SuppressWarnings({"rawtypes", "unchecked"})
private int compareParents(final T arg0, final T arg1) {
Comparator parentComparator = getParentComparator();
while (parentComparator != null) {
diff --git a/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java b/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
index 1f178fbfcba7f136d27714a3c4b215b3800db79b..f237a1a15d4d738fc0956e1a508b459119cfb419 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/comparator/SetComparator.java
@@ -1,22 +1,21 @@
package lcsb.mapviewer.common.comparator;
-import java.util.Comparator;
-import java.util.Set;
-
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
+import java.util.Comparator;
+import java.util.Set;
+
/**
* Comparator used for comparing sets of strings.
- *
+ *
* @author Piotr Gawron
- *
*/
public class SetComparator<T> implements Comparator<Set<T>> {
/**
* Default class logger.
*/
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
private Comparator<T> objectComparator;
@@ -41,6 +40,7 @@ public class SetComparator<T> implements Comparator<Set<T>> {
for (final T objectInList0 : arg0) {
if (objectComparator.compare(objectInList0, objectInList1) == 0) {
found = true;
+ break;
}
}
if (!found) {
@@ -54,11 +54,11 @@ public class SetComparator<T> implements Comparator<Set<T>> {
for (final T objectInList1 : arg1) {
if (objectComparator.compare(objectInList0, objectInList1) == 0) {
found = true;
+ break;
}
}
if (!found) {
- new Exception().printStackTrace();
- logger.debug("Cannot find object " + objectInList0 + " in set: " + arg1);
+ logger.debug("Cannot find object {} in set: {}", objectInList0, arg1);
return 1;
}
}
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 5a0a9c557ede768a9cef891c3184b0f93c179118..4327db604ea35a7039064dd0f65ad81edea825ce 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -1,86 +1,92 @@
<project xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>19.0.0~alpha.0</version>
- </parent>
- <artifactId>converter-CellDesigner</artifactId>
- <name>CellDesigner converter</name>
- <description>CellDesigner converter for model</description>
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </parent>
+ <artifactId>converter-CellDesigner</artifactId>
+ <name>CellDesigner converter</name>
+ <description>CellDesigner converter for model</description>
- <dependencies>
+ <dependencies>
- <!-- dependency from the MapViewer model -->
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>19.0.0~alpha.0</version>
- </dependency>
+ <!-- dependency from the MapViewer model -->
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </dependency>
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter</artifactId>
- <version>19.0.0~alpha.0</version>
- </dependency>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model-command</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </dependency>
- <!-- Log4J2 -->
- <dependency>
- <groupId>org.apache.logging.log4j</groupId>
- <artifactId>log4j-api</artifactId>
- <version>${log4j2.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.logging.log4j</groupId>
- <artifactId>log4j-core</artifactId>
- <version>${log4j2.version}</version>
- </dependency>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>converter</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </dependency>
- <!-- mockito used for testing -->
- <dependency>
- <groupId>org.mockito</groupId>
- <artifactId>mockito-core</artifactId>
- <version>${mockito.version}</version>
- <scope>test</scope>
- </dependency>
+ <!-- Log4J2 -->
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-api</artifactId>
+ <version>${log4j2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-core</artifactId>
+ <version>${log4j2.version}</version>
+ </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
+ <!-- mockito used for testing -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-core</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
- <!-- Utils used for connection via http for SBML validation -->
- <dependency>
- <groupId>org.apache.httpcomponents</groupId>
- <artifactId>httpclient</artifactId>
- <version>${apache.httpcomponents.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>org.apache.httpcomponents</groupId>
- <artifactId>httpmime</artifactId>
- <version>${apache.httpcomponents.version}</version>
- <scope>compile</scope>
- </dependency>
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
- <!-- https://mvnrepository.com/artifact/org.springframework/spring-context -->
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-context</artifactId>
- <version>${springframework.version}</version>
- </dependency>
+ <!-- Utils used for connection via http for SBML validation -->
+ <dependency>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpclient</artifactId>
+ <version>${apache.httpcomponents.version}</version>
+ <scope>test</scope>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.httpcomponents</groupId>
+ <artifactId>httpmime</artifactId>
+ <version>${apache.httpcomponents.version}</version>
+ <scope>compile</scope>
+ </dependency>
- <!-- spring module used for testing -->
- <dependency>
- <groupId>org.springframework</groupId>
- <artifactId>spring-test</artifactId>
- <version>${springframework.version}</version>
- </dependency>
+ <!-- https://mvnrepository.com/artifact/org.springframework/spring-context -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-context</artifactId>
+ <version>${springframework.version}</version>
+ </dependency>
- </dependencies>
+ <!-- spring module used for testing -->
+ <dependency>
+ <groupId>org.springframework</groupId>
+ <artifactId>spring-test</artifactId>
+ <version>${springframework.version}</version>
+ </dependency>
+
+ </dependencies>
</project>
\ No newline at end of file
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 545ba73da2660a8636cd896dcd46a06c12b603f6..6f6a521c4dca37c62dde398460987229211a6947 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -8,10 +8,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ZIndexPopulator;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.compartment.CompartmentCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.function.FunctionCollectionXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.parameter.ParameterCollectionXmlParser;
@@ -41,6 +38,9 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.LogFormatter;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
+import lcsb.mapviewer.utils.ZIndexPopulator;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.LogManager;
@@ -406,7 +406,7 @@ public class CellDesignerXmlParser extends Converter {
private void processModelRdfNode(final Model model, final Node node) throws InvalidXmlSchemaException {
final XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
- CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
model.addMiriamData(xmlAnnotationParser.parseRdfNode(node, null));
model.addAuthors(xmlAnnotationParser.getAuthorsFromRdf(node));
model.setCreationDate(xmlAnnotationParser.getCreateDateFromRdf(node));
@@ -734,12 +734,12 @@ public class CellDesignerXmlParser extends Converter {
result.append(speciesCollectionXmlParser.geneCollectionToXmlString(genes));
result.append(speciesCollectionXmlParser.rnaCollectionToXmlString(rnas));
result.append(speciesCollectionXmlParser.antisenseRnaCollectionToXmlString(antisenseRnas));
- result.append(layerParser.layerCollectionToXml(model.getLayers()));
+ result.append(layerParser.layerCollectionToXml(model.getLayers(), model.getCompartments()));
result.append("</celldesigner:extension>\n");
final XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
- CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(),
model.getCreationDate(), model.getModificationDates(), model.getIdModel()));
result.append("</annotation>\n");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
index 0eef92bcf220686a13c3f3815768ff28140e45cc..a10c2acd55c3478b5e87a96fd4de1061f9292f10 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CommonXmlParser.java
@@ -1,56 +1,34 @@
package lcsb.mapviewer.converter.model.celldesigner;
-import java.awt.Color;
-import java.awt.geom.Dimension2D;
-import java.awt.geom.Point2D;
-import java.io.ByteArrayInputStream;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.Set;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-
+import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.geometry.DoubleDimension;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine;
+import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
import org.apache.commons.lang3.StringUtils;
import org.w3c.dom.Node;
import org.xml.sax.ErrorHandler;
import org.xml.sax.SAXException;
import org.xml.sax.SAXParseException;
-import lcsb.mapviewer.common.XmlParser;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.common.geometry.DoubleDimension;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine;
-import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
-import lcsb.mapviewer.model.map.MiriamRelationType;
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import java.awt.Color;
+import java.awt.geom.Dimension2D;
+import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
/**
* Class with parsers for common CellDesigner objects.
- *
+ *
* @author Piotr Gawron
- *
*/
public class CommonXmlParser {
- public static final Set<MiriamRelationType> RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER;
-
- static {
- Set<MiriamRelationType> types = new HashSet<>();
- types.addAll(Arrays.asList(MiriamRelationType.values()));
- types.remove(MiriamRelationType.BQ_MODEL_IS_DERIVED_FROM);
- types.remove(MiriamRelationType.BQ_BIOL_HAS_PROPERTY);
- types.remove(MiriamRelationType.BQ_BIOL_IS_PROPERTY_OF);
- types.remove(MiriamRelationType.BQ_MODEL_IS_INSTANCE_OF);
- types.remove(MiriamRelationType.BQ_MODEL_HAS_INSTANCE);
- types.remove(MiriamRelationType.BQ_BIOL_HAS_TAXON);
- RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER = Collections.unmodifiableSet(types);
- }
-
- private DocumentBuilderFactory dbFactory;
- private DocumentBuilder documentBuilder;
+ private final DocumentBuilderFactory dbFactory;
+ private final DocumentBuilder documentBuilder;
public CommonXmlParser() {
try {
@@ -59,7 +37,6 @@ public class CommonXmlParser {
documentBuilder.setErrorHandler(new ErrorHandler() {
@Override
public void warning(final SAXParseException e) throws SAXException {
- ;
}
@Override
@@ -80,9 +57,8 @@ public class CommonXmlParser {
/**
* Parse xml representation of position into Poin2D object.
- *
- * @param node
- * xml node to parse
+ *
+ * @param node xml node to parse
* @return Point2D object
*/
public Point2D getPosition(final Node node) {
@@ -94,9 +70,8 @@ public class CommonXmlParser {
/**
* Parse xml representation of dimension.
- *
- * @param node
- * xml node to parse
+ *
+ * @param node xml node to parse
* @return dimension (with width and height fields)
*/
public Dimension2D getDimension(final Node node) {
@@ -108,9 +83,8 @@ public class CommonXmlParser {
/**
* Parse xml representation of CellDesigner SingleLine.
- *
- * @param node
- * xml node to parse
+ *
+ * @param node xml node to parse
* @return single line object (with width field)
*/
public SingleLine getSingleLine(final Node node) {
@@ -121,9 +95,8 @@ public class CommonXmlParser {
/**
* Parse xml representation of CellDesigner color.
- *
- * @param node
- * xml node to parse
+ *
+ * @param node xml node to parse
* @return Color value stored in xml
*/
public Color getColor(final Node node) {
@@ -137,9 +110,8 @@ public class CommonXmlParser {
/**
* Parse xml representation of CellDesigner view.
- *
- * @param node
- * xml node to parse
+ *
+ * @param node xml node to parse
* @return view parsed from xml
* @see View
*/
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
index 59a5aaf0a588b7adc470a1c4d5be1e085fb27f55..f6b0188e76a0db963f316887da82ea2c6891edc2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java
@@ -1,20 +1,25 @@
package lcsb.mapviewer.converter.model.celldesigner;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.geometry.ColorParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.BlockDiagram;
import lcsb.mapviewer.model.map.layout.ElementGroup;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerImage;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.utils.RestAnnotationParser;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -23,9 +28,12 @@ import org.w3c.dom.NodeList;
import java.awt.Color;
import java.awt.geom.Point2D;
+import java.io.File;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
/**
* Parser used for parsing CellDesigner xml to get {@link Layer} object.
@@ -78,7 +86,7 @@ public class LayerXmlParser {
* @param layers collection of layers
* @return xml node representing layers collection
*/
- public String layerCollectionToXml(final Collection<Layer> layers) {
+ public String layerCollectionToXml(final Collection<Layer> layers, final Collection<Compartment> compartments) {
for (final Layer layer : layers) {
if (NumberUtils.isParsable(layer.getLayerId())) {
problematicIdCounter = Math.max(problematicIdCounter, Integer.parseInt(layer.getLayerId()));
@@ -86,8 +94,25 @@ public class LayerXmlParser {
}
StringBuilder result = new StringBuilder();
result.append("<celldesigner:listOfLayers>");
+ boolean compartmentsAdded = false;
+ Set<PathwayCompartment> pathways = new HashSet<>();
+ for (Compartment compartment : compartments) {
+ if (compartment instanceof PathwayCompartment) {
+ pathways.add((PathwayCompartment) compartment);
+ }
+ }
for (final Layer layer : layers) {
- result.append(layerToXml(layer));
+ if (layer.getName().equals(CreateHierarchyCommand.PATHWAY_LAYER_NAME)) {
+ compartmentsAdded = true;
+ result.append(layerToXml(layer, pathways));
+ } else {
+ result.append(layerToXml(layer, new HashSet<>()));
+ }
+ }
+ if (!compartmentsAdded && pathways.size() > 0) {
+ Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
+ result.append(layerToXml(layer, pathways));
}
result.append("</celldesigner:listOfLayers>\n");
return result.toString();
@@ -272,21 +297,27 @@ public class LayerXmlParser {
* @param layer object to be transformed into xml
* @return CellDesigner xml representation for the layer
*/
- String layerToXml(final Layer layer) {
+ String layerToXml(final Layer layer, final Set<PathwayCompartment> pathways) {
StringBuilder result = new StringBuilder();
String id = layer.getLayerId();
if (!NumberUtils.isParsable(id)) {
id = (problematicIdCounter++) + "";
}
- result.append("<celldesigner:layer id =\"" + id + "\" ");
- result.append(" name =\"" + XmlParser.escapeXml(layer.getName()) + "\" ");
- result.append(" locked =\"" + layer.isLocked() + "\" ");
- result.append(" visible =\"" + layer.isVisible() + "\">\n");
+ result.append("<celldesigner:layer id =\"").append(id).append("\" ");
+ result.append(" name =\"").append(XmlParser.escapeXml(layer.getName())).append("\" ");
+ result.append(" locked =\"").append(layer.isLocked()).append("\" ");
+ result.append(" visible =\"").append(layer.isVisible()).append("\">\n");
result.append("<celldesigner:listOfTexts>\n");
for (final LayerText layerText : layer.getTexts()) {
result.append(layerTextToXml(layerText));
}
+ for (final LayerImage layerImage : layer.getImages()) {
+ result.append(layerImageToXml(layerImage));
+ }
+ for (final PathwayCompartment pathway : pathways) {
+ result.append(pathwayToXml(pathway));
+ }
result.append("</celldesigner:listOfTexts>\n");
result.append("<celldesigner:listOfSquares>\n");
@@ -553,4 +584,54 @@ public class LayerXmlParser {
return result.toString();
}
+ String layerImageToXml(final LayerImage layer) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layerSpeciesAlias>");
+ result.append("<celldesigner:layerNotes>\n");
+ String notes = "";
+ if (layer.getGlyph() != null) {
+ notes += "\n" + ComplexZipConverter.GLYPH_PREFIX + "glyphs/" + new File(layer.getGlyph().getFile().getOriginalFileName()).getName();
+ }
+ result.append(notes);
+ result.append("\n</celldesigner:layerNotes>");
+ result.append("<celldesigner:paint color=\"" + XmlParser.colorToString(Color.BLACK) + "\"/>");
+ result.append("<celldesigner:bounds x=\"" + layer.getX() + "\" ");
+ result.append(" y=\"" + layer.getY() + "\" ");
+ result.append(" w=\"" + layer.getWidth() + "\" ");
+ result.append(" h=\"" + layer.getHeight() + "\"/>");
+ result.append("<celldesigner:font size=\"" + ((int) LayerText.DEFAULT_LAYER_FONT_SIZE) + "\"/>");
+ result.append("</celldesigner:layerSpeciesAlias>\n");
+ return result.toString();
+ }
+
+ String pathwayToXml(final PathwayCompartment pathway) {
+ StringBuilder result = new StringBuilder();
+ result.append("<celldesigner:layerSpeciesAlias>");
+ result.append("<celldesigner:layerNotes>\n");
+ String notes = pathway.getName();
+ if (notes == null) {
+ notes = "";
+ }
+ if (commonParser.getNotesXmlContent(pathway.getNotes()) != null) {
+ notes += "\n" + commonParser.getNotesXmlContent(pathway.getNotes());
+ }
+ if (pathway.getFillColor() != null && !pathway.getFillColor().equals(Color.WHITE)) {
+ notes += "\nBackgroundColor:" + new ColorParser().colorToHtml(pathway.getFillColor());
+ }
+ if (!pathway.getBorderColor().equals(Color.LIGHT_GRAY)) {
+ notes += "\nBorderColor:" + new ColorParser().colorToHtml(pathway.getBorderColor());
+ }
+ result.append(notes);
+ result.append("\n</celldesigner:layerNotes>");
+ result.append("<celldesigner:paint color=\"" + XmlParser.colorToString(pathway.getFontColor()) + "\"/>");
+ result.append("<celldesigner:bounds x=\"" + pathway.getX() + "\" ");
+ result.append(" y=\"" + pathway.getY() + "\" ");
+ result.append(" w=\"" + pathway.getWidth() + "\" ");
+ result.append(" h=\"" + pathway.getHeight() + "\"/>");
+ result.append("<celldesigner:font size=\"" + pathway.getFontSize().intValue() + "\"/>");
+ result.append("</celldesigner:layerSpeciesAlias>\n");
+ return result.toString();
+ }
+
+
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
index f5804daed339ff43d3f609ab7613fe5ec2b5179b..1d3414215079be80c51b6869aefebf912ca88e01 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/alias/AliasCollectionXmlParser.java
@@ -1,31 +1,29 @@
package lcsb.mapviewer.converter.model.celldesigner.alias;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
/**
* This class contains function to parse CellDesigner xml nodes containing
* collection of aliases. It also contains functionality to do reverse operation
* - transform set of aliases into xml node.
- *
+ *
* @author Piotr Gawron
- *
*/
public class AliasCollectionXmlParser {
@@ -33,7 +31,7 @@ public class AliasCollectionXmlParser {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
/**
* Single SpeciesAlias parser for CellDesigner node.
@@ -53,19 +51,17 @@ public class AliasCollectionXmlParser {
/**
* Annotation parser.
*/
- private RestAnnotationParser rap = new RestAnnotationParser();
+ private final RestAnnotationParser rap = new RestAnnotationParser();
/**
- * Default parser. As an parameter model object for which parsing is done is
+ * Default parser. As a parameter model object for which parsing is done is
* required. This is due to the fact that CellDesigner model is very tangled and
* very often data are distributed in many different places and in other places
* they are missing...
- *
- * @param model
- * map model for which parsing is performed
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
+ *
+ * @param model map model for which parsing is performed
+ * @param elements collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public AliasCollectionXmlParser(final CellDesignerElementCollection elements, final Model model) {
speciesAliasParser = new SpeciesAliasXmlParser(elements, model);
@@ -76,12 +72,10 @@ public class AliasCollectionXmlParser {
/**
* Parses xml node containing list of species aliases into collection of
* SpeciesAlias.
- *
- * @param aliasListNode
- * xml node to be parsed
+ *
+ * @param aliasListNode xml node to be parsed
* @return collection of SpeciesAlias obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
+ * @throws InvalidXmlSchemaException thrown when there is a problem with xml
*/
public List<Species> parseXmlSpeciesAliasCollection(final Node aliasListNode) throws InvalidXmlSchemaException {
List<Species> result = new ArrayList<Species>();
@@ -104,9 +98,8 @@ public class AliasCollectionXmlParser {
/**
* Creates xml string representing collection of SpeciesAlias.
- *
- * @param collection
- * collection of SpeciesAlias
+ *
+ * @param collection collection of SpeciesAlias
* @return xml string representing collection of SpeciesAlias
*/
public String speciesAliasCollectionToXmlString(final Collection<Species> collection) {
@@ -121,12 +114,10 @@ public class AliasCollectionXmlParser {
/**
* Parses xml node containing list of complex aliases into collection of
* ComplexAlias.
- *
- * @param aliasListNode
- * xml node to be parsed
+ *
+ * @param aliasListNode xml node to be parsed
* @return collection of ComplexAlias obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
+ * @throws InvalidXmlSchemaException thrown when xmlString is invalid
*/
public List<Complex> parseXmlComplexAliasCollection(final Node aliasListNode) throws InvalidXmlSchemaException {
List<Complex> result = new ArrayList<Complex>();
@@ -151,9 +142,8 @@ public class AliasCollectionXmlParser {
/**
* Creates xml string representing collection of ComplexAlias.
- *
- * @param collection
- * collection of ComplexAlias
+ *
+ * @param collection collection of ComplexAlias
* @return xml string representing collection of ComplexAlias
*/
public String complexAliasCollectionToXmlString(final Collection<Complex> collection) {
@@ -168,12 +158,10 @@ public class AliasCollectionXmlParser {
/**
* Parses xml node containing list of compartment aliases into collection of
* CompartmentAlias.
- *
- * @param aliasListNode
- * xml node to be parsed
+ *
+ * @param aliasListNode xml node to be parsed
* @return collection of CompartmentAlias obtained from xml node
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
+ * @throws InvalidXmlSchemaException thrown when xmlString is invalid
*/
public List<Compartment> parseXmlCompartmentAliasCollection(final Node aliasListNode) throws InvalidXmlSchemaException {
List<Compartment> result = new ArrayList<>();
@@ -197,9 +185,8 @@ public class AliasCollectionXmlParser {
/**
* Assing compartment parents for list of compartments.
- *
- * @param compartments
- * compartments that are looking for parents
+ *
+ * @param compartments compartments that are looking for parents
*/
private void assignParents(final List<Compartment> compartments) {
Compartment nullParent = new Compartment("null");
@@ -225,9 +212,8 @@ public class AliasCollectionXmlParser {
/**
* Creates xml string representing collection of CompartmentAlias.
- *
- * @param collection
- * collection of CompartmentAlias
+ *
+ * @param collection collection of CompartmentAlias
* @return xml string representing collection of CompartmentAlias
*/
public String compartmentAliasCollectionToXmlString(final Collection<Compartment> collection) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
index 826126c06146feffa985ea54aaf44c6df21823f2..64ae60ab255f61b51cde8a2324c5fbbd29c8edb7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java
@@ -1,15 +1,9 @@
package lcsb.mapviewer.converter.model.celldesigner.compartment;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
@@ -17,41 +11,43 @@ import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
/**
* Parser of CellDesginer xml nodes for compartment elements.
- *
+ *
* @author Piotr Gawron
- *
*/
public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerCompartment, Compartment> {
/**
* Parser used to retrieve Miriam data for the element.
*/
- private XmlAnnotationParser xmlAnnotationParser;
+ private final XmlAnnotationParser xmlAnnotationParser;
/**
* Collection of {@link CellDesignerElement cell designer elements} parsed
* from xml.
*/
- private CellDesignerElementCollection elements;
+ private final CellDesignerElementCollection elements;
/**
* Xml parser used for processing notes into structured data.
*/
- private RestAnnotationParser rap = new RestAnnotationParser();
+ private final RestAnnotationParser rap = new RestAnnotationParser();
/**
* Default constructor.
- *
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
+ *
+ * @param elements collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public CompartmentXmlParser(final CellDesignerElementCollection elements) {
this.elements = elements;
- xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ xmlAnnotationParser = new XmlAnnotationParser(lcsb.mapviewer.utils.RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
}
@Override
@@ -83,7 +79,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
@Override
public String toXml(final Compartment compartment) {
- StringBuilder sb = new StringBuilder("");
+ StringBuilder sb = new StringBuilder();
sb.append("<compartment ");
sb.append("metaid=\"" + elements.getElementId(compartment) + "\" ");
sb.append("id=\"" + elements.getElementId(compartment) + "\" ");
@@ -125,12 +121,9 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
/**
* Process annotation part of the xml node.
*
- * @param compartment
- * object that we create
- * @param xmlNode
- * annotation xml node
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
+ * @param compartment object that we create
+ * @param xmlNode annotation xml node
+ * @throws InvalidXmlSchemaException thrown when there is a problem with xml
*/
private void parseAnnotationNode(final CellDesignerCompartment compartment, final Node xmlNode) throws InvalidXmlSchemaException {
NodeList annotationNodes = xmlNode.getChildNodes();
@@ -156,12 +149,9 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
/**
* Process extension part of the xml node.
*
- * @param compartment
- * object that we create
- * @param xmlNode
- * annotation xml node
- * @throws InvalidXmlSchemaException
- * thrown when xmlNode is invalid
+ * @param compartment object that we create
+ * @param xmlNode annotation xml node
+ * @throws InvalidXmlSchemaException thrown when xmlNode is invalid
*/
private void parseExtensionNode(final CellDesignerCompartment compartment, final Node xmlNode) throws InvalidXmlSchemaException {
NodeList annotationNodes = xmlNode.getChildNodes();
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
index 3cd4a8e5263ddbe456f74a65c06ee41f3a853368..c144284b07413796ecaf99673c8c3663486f94e1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -1,22 +1,19 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
+import lcsb.mapviewer.commands.layout.ModifierType;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
@@ -49,6 +46,8 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
@@ -81,60 +80,60 @@ public class ReactionFromXml {
* Product lines in cell designer starts in the 3/5 of the center line.
*/
private static final double PRODUCT_START_RATIO = 0.6;
- private CellDesignerElementCollection elements;
+ private final CellDesignerElementCollection elements;
/**
* Stores information about {@link CellDesignerAnchor} for a node.
*/
- private Map<ReactionNode, CellDesignerAnchor> anchorsByNodes = new HashMap<>();
+ private final Map<ReactionNode, CellDesignerAnchor> anchorsByNodes = new HashMap<>();
/**
* Stores information about operator type that should be used for a modifier
* node.
*/
- private Map<ReactionNode, String> typeByModifier = new HashMap<>();
+ private final Map<ReactionNode, String> typeByModifier = new HashMap<>();
/**
* Stores information to which point on the central rectangle modifier should
* be connected.
*/
- private Map<ReactionNode, String> lineTypeByModifier = new HashMap<>();
+ private final Map<ReactionNode, String> lineTypeByModifier = new HashMap<>();
/**
* Stores information about list of points that create line describing
* modifier.
*/
- private Map<ReactionNode, List<Point2D>> pointsByModifier = new HashMap<>();
+ private final Map<ReactionNode, List<Point2D>> pointsByModifier = new HashMap<>();
/**
* Stores information about list of points that create line describing
* modifier.
*/
- private Map<ReactionNode, LineProperties> linePropertiesByModifier = new HashMap<>();
+ private final Map<ReactionNode, LineProperties> linePropertiesByModifier = new HashMap<>();
/**
* Helps to determine if the key Modifier should be treats as part of
* NodeOperator (value in the map).
*/
- private Map<Modifier, Modifier> modifierParentOperator = new HashMap<>();
+ private final Map<Modifier, Modifier> modifierParentOperator = new HashMap<>();
/**
* Identifies central line segment in {@link TwoProductReactionInterface} and
* {@link TwoReactantReactionInterface} reactions.
*/
- private Map<ReactionNode, Integer> indexByComplexReaction = new HashMap<>();
+ private final Map<ReactionNode, Integer> indexByComplexReaction = new HashMap<>();
/**
* Default class logger.
*/
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
/**
* Xml parser used for processing notes into structured data.
*/
- private RestAnnotationParser rap = new RestAnnotationParser();
+ private final RestAnnotationParser rap = new RestAnnotationParser();
/**
* Helper object used for manipulation on the point coordinates in
* CellDesigner format.
*/
- private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
+ private final CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
/**
* Should SBGN standard be used.
*/
- private boolean sbgn;
+ private final boolean sbgn;
- private boolean oldCellDesignerVersion;
+ private final boolean oldCellDesignerVersion;
/**
* Default constructor.
@@ -217,7 +216,7 @@ public class ReactionFromXml {
// with reversible flag (even though it cannot be reversible)
if (result.isReversible()) {
logger.warn(
- new ElementUtils().getElementTag(result) + "Reacion was marked as reversible but it cannot be reversible");
+ new ElementUtils().getElementTag(result) + "Reacion was marked as reversible but it cannot be reversible");
result.setReversible(false);
}
}
@@ -328,7 +327,7 @@ public class ReactionFromXml {
* @throws InvalidXmlSchemaException thrown when annotationNode is invalid xml
*/
private Reaction parseReactionAnnotation(final Node annotationNode, final Reaction reaction, final Model model)
- throws ReactionParserException {
+ throws ReactionParserException {
Reaction result = reaction;
NodeList nodes = annotationNode.getChildNodes();
if (oldCellDesignerVersion) {
@@ -342,9 +341,9 @@ public class ReactionFromXml {
} else if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
try {
XmlAnnotationParser xmlParser = new XmlAnnotationParser(
- CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
result.addMiriamData(xmlParser.parseRdfNode(node, new LogMarker(ProjectLogEntryType.PARSING_ISSUE,
- result.getClass().getSimpleName(), result.getElementId(), model.getName())));
+ result.getClass().getSimpleName(), result.getElementId(), model.getName())));
} catch (final InvalidXmlSchemaException e) {
throw new ReactionParserException("Problem with parsing RDF", result, e);
}
@@ -394,7 +393,7 @@ public class ReactionFromXml {
result.addReactant(parseBaseReactant(reactantNode, model));
} else {
throw new ReactionParserException(
- "Unknown element of celldesigner:baseReactants: " + node.getNodeName(), result);
+ "Unknown element of celldesigner:baseReactants: " + node.getNodeName(), result);
}
}
}
@@ -407,7 +406,7 @@ public class ReactionFromXml {
result.addProduct(parseBaseProduct(model, reactantNode));
} else {
throw new ReactionParserException(
- "Unknown element of celldesigner:baseProducts: " + node.getNodeName(), result);
+ "Unknown element of celldesigner:baseProducts: " + node.getNodeName(), result);
}
}
}
@@ -429,7 +428,7 @@ public class ReactionFromXml {
gateMembers = nodeReaction;
} else {
throw new ReactionParserException(
- "Unknown element of reaction/celldesigner:extension: " + nodeReaction.getNodeName(), result);
+ "Unknown element of reaction/celldesigner:extension: " + nodeReaction.getNodeName(), result);
}
}
}
@@ -456,7 +455,7 @@ public class ReactionFromXml {
createOperatorsForTwoProductReaction(result);
} else {
throw new ReactionParserException(
- "Problem with parsing lines. Unknown reaction: " + type + "; " + result.getClass().getName(), result);
+ "Problem with parsing lines. Unknown reaction: " + type + "; " + result.getClass().getName(), result);
}
for (final AbstractNode reactionNode : result.getNodes()) {
@@ -503,7 +502,7 @@ public class ReactionFromXml {
if (result.isReversible()) {
for (final Reactant reactant : result.getReactants()) {
reactant.getLine().getBeginAtd()
- .setArrowType(result.getProducts().get(0).getLine().getEndAtd().getArrowType());
+ .setArrowType(result.getProducts().get(0).getLine().getEndAtd().getArrowType());
}
}
@@ -559,7 +558,7 @@ public class ReactionFromXml {
* schema
*/
private EditPoints gateMembersToPoints(final Reaction reaction, final Node gateMembers)
- throws InvalidXmlSchemaException, ReactionParserException {
+ throws InvalidXmlSchemaException, ReactionParserException {
Node lastMember = null;
EditPoints result = new EditPoints();
for (int i = 0; i < gateMembers.getChildNodes().getLength(); i++) {
@@ -622,9 +621,9 @@ public class ReactionFromXml {
ModifierTypeUtils modifierTypeUtils = new ModifierTypeUtils();
Point2D p = modifierTypeUtils.getAnchorPointOnReactionRect(modifier.getReaction(),
- lineTypeByModifier.get(modifier));
+ lineTypeByModifier.get(modifier));
PolylineData line = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, p,
- pointsByModifier.get(modifier));
+ pointsByModifier.get(modifier));
startPoint = converter.getAnchorPointCoordinates(element, anchorsByNodes.get(modifier), line);
line.setStartPoint(startPoint);
@@ -690,14 +689,14 @@ public class ReactionFromXml {
reactant.setLine(reactant.getLine().reverse());
reactant.getLine().addLine(p2, p);
- reactant.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
- operator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ reactant.getLine().trimEnd(ReactionData.RECT_SIZE / 2 - 1);
+ operator.getLine().trimEnd(ReactionData.RECT_SIZE / 2 - 1);
result.addNode(operator);
PolylineData centerLine = new PolylineData(
- pointTransformation.copyPoint(reactant.getLine().getEndPoint()),
- pointTransformation.copyPoint(operator.getLine().getEndPoint()));
+ pointTransformation.copyPoint(reactant.getLine().getEndPoint()),
+ pointTransformation.copyPoint(operator.getLine().getEndPoint()));
centerLine.setType(reactant.getLine().getType());
result.setLine(centerLine);
@@ -711,7 +710,7 @@ public class ReactionFromXml {
private void createOperators(final Reaction result) {
// central line points
Point2D p1 = result.getReactants().get(0).getLine().getLines()
- .get(result.getReactants().get(0).getLine().getLines().size() - 1).getP1();
+ .get(result.getReactants().get(0).getLine().getLines().size() - 1).getP1();
Point2D p2 = result.getProducts().get(0).getLine().getLines().get(0).getP2();
Point2D tmp = result.getProducts().get(0).getLine().getStartPoint();
Point2D productSplitOperatorBeginPoint = new Point2D.Double(tmp.getX(), tmp.getY());
@@ -743,7 +742,7 @@ public class ReactionFromXml {
double dy = p2.getY() - p1.getY();
Point2D reactantAndOperatorBeginPoint = new Point2D.Double(p1.getX() + dx * REACTANT_END_RATIO,
- p1.getY() + dy * REACTANT_END_RATIO);
+ p1.getY() + dy * REACTANT_END_RATIO);
PolylineData ld = new PolylineData(reactantAndOperatorBeginPoint, reactantAndOperatorEndPoint);
@@ -787,7 +786,7 @@ public class ReactionFromXml {
}
Point2D productSplitOperatorEndPoint = new Point2D.Double(p1.getX() + dx * PRODUCT_START_RATIO,
- p1.getY() + dy * PRODUCT_START_RATIO);
+ p1.getY() + dy * PRODUCT_START_RATIO);
ld = new PolylineData(productSplitOperatorEndPoint, productSplitOperatorBeginPoint);
@@ -812,7 +811,7 @@ public class ReactionFromXml {
if (!toExclude.contains(product)) {
// outputOperator.addOutput(product);
product.getLine().setStartPoint(productSplitOperatorEndPoint.getX(),
- productSplitOperatorEndPoint.getY());
+ productSplitOperatorEndPoint.getY());
}
}
if (lineType != null) {
@@ -890,7 +889,7 @@ public class ReactionFromXml {
andOperator.getLine().addLine(product.getLine().getLines().get(i));
}
andOperator.getLine().setEndPoint(p);
- andOperator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ andOperator.getLine().trimEnd(ReactionData.RECT_SIZE / 2 - 1);
p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
@@ -898,14 +897,14 @@ public class ReactionFromXml {
product.getLine().removeLine(0);
}
product.getLine().setStartPoint(p);
- product.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ product.getLine().trimBegin(ReactionData.RECT_SIZE / 2 - 1);
product.getLine().getEndAtd().setArrowType(ArrowType.FULL);
result.addNode(andOperator);
PolylineData centerLine = new PolylineData(pointTransformation.copyPoint(andOperator.getLine().getEndPoint()),
- pointTransformation.copyPoint(product.getLine().getStartPoint()));
+ pointTransformation.copyPoint(product.getLine().getStartPoint()));
centerLine.setType(product.getLine().getType());
result.setLine(centerLine);
@@ -939,7 +938,7 @@ public class ReactionFromXml {
types += string + ", ";
}
throw new ReactionParserException(
- "Couldn't find type of BOOLEAN_LOGIC_GATE. Unknown types identified: " + types, result);
+ "Couldn't find type of BOOLEAN_LOGIC_GATE. Unknown types identified: " + types, result);
}
operator.addInputs(andOperator.getInputs());
@@ -947,18 +946,18 @@ public class ReactionFromXml {
// operator line
Point2D secondPoint = pointTransformation.getPointOnLine(product.getLine().getLines().get(0).getP1(),
- product.getLine().getLines().get(0).getP2(), 0.4);
+ product.getLine().getLines().get(0).getP2(), 0.4);
Point2D thirdPoint = pointTransformation.getPointOnLine(product.getLine().getLines().get(0).getP1(),
- product.getLine().getLines().get(0).getP2(), 0.6);
+ product.getLine().getLines().get(0).getP2(), 0.6);
PolylineData line = new PolylineData(pointTransformation.copyPoint(
- product.getLine().getStartPoint()),
- pointTransformation.copyPoint(secondPoint));
+ product.getLine().getStartPoint()),
+ pointTransformation.copyPoint(secondPoint));
line.setType(product.getLine().getType());
operator.setLine(line);
// center line
PolylineData centerLine = new PolylineData(pointTransformation.copyPoint(secondPoint),
- pointTransformation.copyPoint(thirdPoint));
+ pointTransformation.copyPoint(thirdPoint));
centerLine.setType(product.getLine().getType());
result.setLine(centerLine);
@@ -1022,7 +1021,7 @@ public class ReactionFromXml {
Point2D p3 = product2Converter.getPointCoordinates(product2.getElement(), anchorsByNodes.get(product2));
Point2D centerPoint = pointTransformation.getCoordinatesInNormalBase(product1.getElement().getCenter(),
- product2.getElement().getCenter(), reactant.getElement().getCenter(), p);
+ product2.getElement().getCenter(), reactant.getElement().getCenter(), p);
int startId0 = 0;
int num0 = points.getLineStartingPoints().get(0);
@@ -1041,15 +1040,15 @@ public class ReactionFromXml {
PolylineData reactantLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint, p1, linePoints1);
p1 = product2Converter.getAnchorPointCoordinates(product2.getElement(), anchorsByNodes.get(product2),
- product2Line.reverse());
+ product2Line.reverse());
product2Line.setEndPoint(p1);
p1 = product1Converter.getAnchorPointCoordinates(product1.getElement(), anchorsByNodes.get(product1),
- product1Line.reverse());
+ product1Line.reverse());
product1Line.setEndPoint(p1);
p1 = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant),
- reactantLine.reverse());
+ reactantLine.reverse());
reactantLine.setEndPoint(p1);
product2Line.getEndAtd().setArrowType(ArrowType.FULL);
@@ -1071,7 +1070,7 @@ public class ReactionFromXml {
* @throws ReactionParserException thrown when data for reaction is invalid
*/
private void createLinesForTwoReactantReaction(final Reaction reaction, final EditPoints points)
- throws ReactionParserException {
+ throws ReactionParserException {
ReactionLineData rld = null;
if (!(reaction instanceof HeterodimerAssociationReaction)) {
rld = ReactionLineData.getByReactionType(reaction.getClass());
@@ -1129,7 +1128,7 @@ public class ReactionFromXml {
}
p1 = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant),
- reactantLine.reverse());
+ reactantLine.reverse());
reactantLine.setEndPoint(p1);
reactantLine = reactantLine.reverse();
@@ -1138,9 +1137,9 @@ public class ReactionFromXml {
int productEndId = productStartId + points.getLineStartingPoints().get(reaction.getReactants().size());
List<Point2D> linePoints3 = new ArrayList<>(points.getPoints().subList(productStartId, productEndId));
PolylineData productLine = PolylineDataFactory.createPolylineDataFromEditPoints(centerPoint,
- productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product)), linePoints3);
+ productConverter.getPointCoordinates(product.getElement(), anchorsByNodes.get(product)), linePoints3);
Point2D p1 = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
- productLine.reverse());
+ productLine.reverse());
productLine.setEndPoint(p1);
if (rld != null) {
productLine.setType(rld.getLineType());
@@ -1171,7 +1170,7 @@ public class ReactionFromXml {
Point2D startPoint = reactantConverter.getPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant));
PolylineData ld = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
- editPoints.getPoints());
+ editPoints.getPoints());
// first place where the index of rectangle is kept
Integer index = editPoints.getReactionCenterLineIndex();
@@ -1194,7 +1193,7 @@ public class ReactionFromXml {
}
startPoint = reactantConverter.getAnchorPointCoordinates(reactant.getElement(), anchorsByNodes.get(reactant), ld);
endPoint = productConverter.getAnchorPointCoordinates(product.getElement(), anchorsByNodes.get(product),
- ld.reverse());
+ ld.reverse());
ld.setStartPoint(startPoint);
ld.setEndPoint(endPoint);
@@ -1211,11 +1210,11 @@ public class ReactionFromXml {
Point2D p2 = ld.getLines().get(ld.getLines().size() - index - 1).getP2();
Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
reactantLine.setEndPoint(p);
- reactantLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ reactantLine.trimEnd(ReactionData.RECT_SIZE / 2 - 1);
p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
productLine.setStartPoint(p);
- productLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ productLine.trimBegin(ReactionData.RECT_SIZE / 2 - 1);
productLine.getEndAtd().setArrowType(ArrowType.FULL);
@@ -1229,7 +1228,7 @@ public class ReactionFromXml {
productLine.trimEnd(rld.getProductLineTrim());
PolylineData reactionLine = new PolylineData(pointTransformation.copyPoint(reactantLine.getEndPoint()),
- pointTransformation.copyPoint(productLine.getStartPoint()));
+ pointTransformation.copyPoint(productLine.getStartPoint()));
reactionLine.setType(reactantLine.getType());
reaction.setLine(reactionLine);
}
@@ -1294,7 +1293,7 @@ public class ReactionFromXml {
Point2D point = new Point2D.Double(posX, posY);
if (!pointTransformation.isValidPoint(point)) {
throw new InvalidArgumentException(
- "Invalid point parsed from input string: " + string + ". Result point: " + point);
+ "Invalid point parsed from input string: " + string + ". Result point: " + point);
}
points2.add(point);
}
@@ -1323,7 +1322,7 @@ public class ReactionFromXml {
result.addReactant(newReactant);
} else {
throw new ReactionParserException(
- "Unknown element of celldesigner:listOfReactantLinks: " + node.getNodeName(), result);
+ "Unknown element of celldesigner:listOfReactantLinks: " + node.getNodeName(), result);
}
}
}
@@ -1366,7 +1365,7 @@ public class ReactionFromXml {
points = parseEditPoints(node);
} else {
throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
- reaction);
+ reaction);
}
}
}
@@ -1402,7 +1401,7 @@ public class ReactionFromXml {
// central line points
Point2D p1 = reaction.getReactants().get(0).getLine().getLines()
- .get(reaction.getReactants().get(0).getLine().getLines().size() - 1).getP1();
+ .get(reaction.getReactants().get(0).getLine().getLines().size() - 1).getP1();
Point2D p2 = reaction.getProducts().get(0).getLine().getLines().get(0).getP2();
Set<AbstractNode> toExclude = new HashSet<AbstractNode>();
@@ -1446,7 +1445,7 @@ public class ReactionFromXml {
result.addProduct(link);
} else {
throw new ReactionParserException("Unknown element of celldesigner:listOfProductLinks: " + node.getNodeName(),
- result);
+ result);
}
}
}
@@ -1490,7 +1489,7 @@ public class ReactionFromXml {
points = parseEditPoints(node);
} else {
throw new ReactionParserException("Unknown element of celldesigner:reactantLink: " + node.getNodeName(),
- reaction);
+ reaction);
}
}
}
@@ -1547,7 +1546,7 @@ public class ReactionFromXml {
parseModificationReaction(result, node, model);
} else {
throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
- result);
+ result);
}
}
}
@@ -1593,7 +1592,7 @@ public class ReactionFromXml {
ModifierType modifierType = modifierTypeUtils.getModifierTypeForStringType(type);
if (modifierType == null) {
String errorInfo = "[" + reaction.getClass().getSimpleName() + "\t" + reaction.getIdReaction()
- + "]\tUnknown modifier type: " + type;
+ + "]\tUnknown modifier type: " + type;
if (ReactionLineData.getByCellDesignerString(type) != null) {
errorInfo += ".\tThis type can be applied to reaction type only, not modifier.";
}
@@ -1630,7 +1629,7 @@ public class ReactionFromXml {
}
} else {
throw new ReactionParserException("Unknown element of celldesigner:listOfModification: " + node.getNodeName(),
- reaction);
+ reaction);
}
}
@@ -1666,7 +1665,7 @@ public class ReactionFromXml {
startPoint = reactantConverter.getPointCoordinates(param.getElement(), anchorsByNodes.get(param));
PolylineData polyline = PolylineDataFactory.createPolylineDataFromEditPoints(startPoint, endPoint,
- pointsByModifier.get(param));
+ pointsByModifier.get(param));
startPoint = reactantConverter.getAnchorPointCoordinates(param.getElement(), anchorsByNodes.get(param), polyline);
polyline.setStartPoint(startPoint);
@@ -1723,7 +1722,7 @@ public class ReactionFromXml {
result.setLineDirections(getlineDirectionMapForReactions(reactantNode));
} else {
throw new InvalidXmlSchemaException(
- "Unknown element of celldesigner:connectScheme: " + nodeReaction.getNodeName());
+ "Unknown element of celldesigner:connectScheme: " + nodeReaction.getNodeName());
}
}
}
@@ -1750,7 +1749,7 @@ public class ReactionFromXml {
result.put(index, value);
} else {
throw new InvalidXmlSchemaException(
- "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
+ "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
}
}
}
@@ -1781,7 +1780,7 @@ public class ReactionFromXml {
anchorsByNodes.put(reactant, CellDesignerAnchor.valueOf(XmlParser.getNodeAttr("position", node)));
} else {
throw new InvalidXmlSchemaException(
- "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
+ "Unknown element of reaction/celldesigner:baseReactant: " + node.getNodeName());
}
}
}
@@ -1812,7 +1811,7 @@ public class ReactionFromXml {
anchorsByNodes.put(product, CellDesignerAnchor.valueOf(XmlParser.getNodeAttr("position", node)));
} else {
throw new InvalidXmlSchemaException(
- "Unknown element of reaction/celldesigner:baseProduct: " + node.getNodeName());
+ "Unknown element of reaction/celldesigner:baseProduct: " + node.getNodeName());
}
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index 7e7311cbadb7eddf565d240108f7660f3365cc6c..f51028bd81c02857009bc0302226e719ac5d9208 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -1,32 +1,16 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerLineTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
@@ -47,60 +31,70 @@ import lcsb.mapviewer.model.map.reaction.type.TwoReactantReactionInterface;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
/**
* This is a part of {@link ReactionXmlParser} class functionality that allows
* to export reaction into CellDesigner xml node.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ReactionToXml {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Helper object used for manipulation on the point coordinates in
* CellDesigner format.
*/
- private CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
+ private final CellDesignerPointTransformation pointTransformation = new CellDesignerPointTransformation();
/**
* Helper object used for manipulation on the line structures in CellDesigner
* format.
*/
- private CellDesignerLineTransformation lineTransformation = new CellDesignerLineTransformation();
+ private final CellDesignerLineTransformation lineTransformation = new CellDesignerLineTransformation();
/**
* Collection of {@link CellDesignerElement cell designer elements} parsed
* from xml.
*/
- private CellDesignerElementCollection elements;
+ private final CellDesignerElementCollection elements;
/**
* Helps in providing human readable identifiers of elements for logging.
*/
- private ElementUtils eu = new ElementUtils();
-
- private int metaIdCounter = 0;
-
+ private final ElementUtils eu = new ElementUtils();
/**
* Defines if SBGN standard should be used.
*/
- private boolean sbgn;
+ private final boolean sbgn;
+ private int metaIdCounter = 0;
/**
* Default constructor. Model is required because some nodes require access to
* other parts of the model.
- *
- * @param sbgn
- * Should the converter use SBGN standard
- * @param elements
- * collection of {@link CellDesignerElement cell designer elements}
- * parsed from xml
+ *
+ * @param sbgn Should the converter use SBGN standard
+ * @param elements collection of {@link CellDesignerElement cell designer elements}
+ * parsed from xml
*/
public ReactionToXml(final CellDesignerElementCollection elements, final boolean sbgn) {
this.elements = elements;
@@ -109,9 +103,8 @@ public class ReactionToXml {
/**
* Transform reaction into CellDesigner xml representation.
- *
- * @param reaction
- * reaction to transform
+ *
+ * @param reaction reaction to transform
* @return xml representation of reaction
*/
public String toXml(final Reaction reaction) throws InconsistentModelException {
@@ -160,9 +153,8 @@ public class ReactionToXml {
/**
* Returns xml node with list of modification.
- *
- * @param reaction
- * reaction for which list is generated
+ *
+ * @param reaction reaction for which list is generated
* @return xml node with list of modification
*/
private String getListOfModificationsXmlStringForReaction(final Reaction reaction) throws InconsistentModelException {
@@ -202,9 +194,8 @@ public class ReactionToXml {
/**
* Returns SBML node with list of modifications.
- *
- * @param reaction
- * reaction for which list is generated
+ *
+ * @param reaction reaction for which list is generated
* @return SBML node with list of modifications
*/
private String getSbmlListOfModificationsXmlStringForReaction(final Reaction reaction) {
@@ -222,9 +213,8 @@ public class ReactionToXml {
/**
* Creates modifierSpeciesReference SBML node for given modifier.
- *
- * @param modifier
- * modifier to be transformed
+ *
+ * @param modifier modifier to be transformed
* @return modifierSpeciesReference SBML node for given modifier
*/
private String getModifierReferenceXmlString(final Modifier modifier) {
@@ -258,9 +248,8 @@ public class ReactionToXml {
/**
* Creates xml node for given modifier operator.
- *
- * @param modifierOperator
- * modifier operator to be transformed
+ *
+ * @param modifierOperator modifier operator to be transformed
* @return xml node for given modifier operator
*/
private String getModifierXmlString(final NodeOperator modifierOperator) {
@@ -306,7 +295,7 @@ public class ReactionToXml {
sb.append("\"");
sb.append(">\n");
- PolylineData[] lines = new PolylineData[] { modifierOperator.getLine() };
+ PolylineData[] lines = new PolylineData[]{modifierOperator.getLine()};
sb.append(getConnectSchemeXmlStringForLines(lines));
sb.append(getLineXmlStringForLines(modifierOperator.getLine()));
@@ -317,11 +306,9 @@ public class ReactionToXml {
/**
* Creates xml node for given modifier.
- *
- * @param modifier
- * modifier to be transformed
- * @param gate
- * operator to which modifier is connected (if any)
+ *
+ * @param modifier modifier to be transformed
+ * @param gate operator to which modifier is connected (if any)
* @return xml node for given modifier
*/
private String getModifierXmlString(final Modifier modifier, final NodeOperator gate) throws InconsistentModelException {
@@ -367,7 +354,7 @@ public class ReactionToXml {
}
sb.append(">\n");
- PolylineData[] lines = new PolylineData[] { modifier.getLine() };
+ PolylineData[] lines = new PolylineData[]{modifier.getLine()};
sb.append(getConnectSchemeXmlStringForLines(lines));
sb.append(getLinkTargetXmlString(modifier));
@@ -378,37 +365,34 @@ public class ReactionToXml {
}
private String getLineXmlStringForLines(final PolylineData line) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:line ");
- sb.append("width=\"" + line.getWidth() + "\" ");
- sb.append("color=\"" + XmlParser.colorToString(line.getColor()) + "\" ");
- sb.append("type=\"Straight\" ");
- sb.append("/>\n");
- return sb.toString();
+ String sb = "<celldesigner:line "
+ + "width=\"" + line.getWidth() + "\" "
+ + "color=\"" + XmlParser.colorToString(line.getColor()) + "\" "
+ + "type=\"Straight\" "
+ + "/>\n";
+ return sb;
}
/**
* Gets target link string for given modifier.
- *
- * @param modifier
- * modifier to be transformed
+ *
+ * @param modifier modifier to be transformed
* @return anchor xml node representing modifier connection to reaction
*/
private String getLinkTargetXmlString(final ReactionNode modifier) {
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:linkTarget species=\"" + elements.getElementId(modifier.getElement()) + "\" alias=\""
- + modifier.getElement().getElementId() + "\">\n");
- sb.append(getAnchorXml(modifier.getElement(), modifier.getLine().getStartPoint()));
- sb.append("</celldesigner:linkTarget>\n");
+ String sb = "<celldesigner:linkTarget species=\""
+ + elements.getElementId(modifier.getElement()) + "\" alias=\""
+ + modifier.getElement().getElementId() + "\">\n"
+ + getAnchorXml(modifier.getElement(), modifier.getLine().getStartPoint())
+ + "</celldesigner:linkTarget>\n";
- return sb.toString();
+ return sb;
}
/**
* Creates SBML node for list of products.
- *
- * @param reaction
- * reaction from which products are taken
+ *
+ * @param reaction reaction from which products are taken
* @return SBML node representing list of products
*/
private String getListOfProductsXmlStringForReaction(final Reaction reaction) {
@@ -449,9 +433,8 @@ public class ReactionToXml {
/**
* Creates sbml node for list of reactants.
- *
- * @param reaction
- * reaction from which products are taken
+ *
+ * @param reaction reaction from which products are taken
* @return sbml node representing list of reactants
*/
private String getListOfReactantsXmlStringForReaction(final Reaction reaction) {
@@ -490,34 +473,31 @@ public class ReactionToXml {
/**
* Creates annotation xml node for reaction.
- *
- * @param reaction
- * reaction to be processed
+ *
+ * @param reaction reaction to be processed
* @return xml node representing annotation part
*/
private String getAnnotationXmlStringForReaction(final Reaction reaction) throws InconsistentModelException {
String reactionClassString = getCellDesignerReactionTypeString(reaction);
- StringBuilder sb = new StringBuilder();
- sb.append("<annotation>\n");
- sb.append("<celldesigner:extension>\n");
- sb.append("<celldesigner:reactionType>" + reactionClassString + "</celldesigner:reactionType>\n");
- sb.append(getBaseReactantsXmlStringForReaction(reaction));
- sb.append(getBaseProductsXmlStringForReaction(reaction));
- sb.append(getListOfReactantLinksXmlStringForReaction(reaction));
- sb.append(getListOfProductLinksXmlStringForReaction(reaction));
- sb.append(getConnectSchemeXmlStringForReaction(reaction));
- sb.append(getEditPointsXmlStringForReaction(reaction));
- sb.append(getListOfModificationsXmlStringForReaction(reaction));
- sb.append(getListOfGateMembersXmlStringForReaction(reaction));
-
- sb.append(getLineXmlStringForLines(reaction.getLine()));
XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
- CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
- sb.append("</celldesigner:extension>\n");
- sb.append(xmlAnnotationParser.dataSetToXmlString(reaction.getMiriamData(), reaction.getIdReaction()));
- sb.append("</annotation>\n");
- return sb.toString();
+ RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ String sb = "<annotation>\n"
+ + "<celldesigner:extension>\n"
+ + "<celldesigner:reactionType>" + reactionClassString + "</celldesigner:reactionType>\n"
+ + getBaseReactantsXmlStringForReaction(reaction)
+ + getBaseProductsXmlStringForReaction(reaction)
+ + getListOfReactantLinksXmlStringForReaction(reaction)
+ + getListOfProductLinksXmlStringForReaction(reaction)
+ + getConnectSchemeXmlStringForReaction(reaction)
+ + getEditPointsXmlStringForReaction(reaction)
+ + getListOfModificationsXmlStringForReaction(reaction)
+ + getListOfGateMembersXmlStringForReaction(reaction)
+ + getLineXmlStringForLines(reaction.getLine())
+ + "</celldesigner:extension>\n"
+ + xmlAnnotationParser.dataSetToXmlString(reaction.getMiriamData(), reaction.getIdReaction())
+ + "</annotation>\n";
+ return sb;
}
String getCellDesignerReactionTypeString(final Reaction reaction) {
@@ -564,9 +544,8 @@ public class ReactionToXml {
/**
* Returns xml node with a list of gate members for reaction. For now only
* {@link TwoReactantReactionInterface} is supported.
- *
- * @param reaction
- * reaction for which the xml will be returned
+ *
+ * @param reaction reaction for which the xml will be returned
* @return xml string with list of gate members for reaction
*/
private StringBuilder getListOfGateMembersXmlStringForReaction(final Reaction reaction) {
@@ -645,9 +624,8 @@ public class ReactionToXml {
/**
* Creates xml node (listOfProductLinks) with list of products.
- *
- * @param reaction
- * reaction for which list of products is created
+ *
+ * @param reaction reaction for which list of products is created
* @return xml node (listOfProductLinks) with list of products
*/
private String getListOfProductLinksXmlStringForReaction(final Reaction reaction) {
@@ -666,9 +644,8 @@ public class ReactionToXml {
/**
* Creates xml node (listOfReactantLinks) with list of reactants.
- *
- * @param reaction
- * reaction for which list of reactants is created
+ *
+ * @param reaction reaction for which list of reactants is created
* @return xml node (listOfReactantLinks) with list of reactants
*/
private String getListOfReactantLinksXmlStringForReaction(final Reaction reaction) {
@@ -689,63 +666,54 @@ public class ReactionToXml {
/**
* Creates rectantLink xml node for reactant.
- *
- * @param reactant
- * reactant to be transformed
+ *
+ * @param reactant reactant to be transformed
* @return xml node describing reactantLink
*/
private String getReactantLinkXmlString(final Reactant reactant) {
Element alias = reactant.getElement();
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:reactantLink ");
- sb.append("reactant=\"" + elements.getElementId(alias) + "\" ");
- sb.append("alias=\"" + alias.getElementId() + "\" ");
- // targetLineIndex is missing (maybe it's unimportant :))
- sb.append(">\n");
-
- sb.append(getAnchorXml(alias, reactant.getLine().getStartPoint()));
- sb.append(getConnectSchemeXmlStringForLines(new PolylineData[] { reactant.getLine() }));
- sb.append(getEditPointsXmlStringForLine(new PolylineData[] { reactant.getLine() }, 0));
- sb.append(getLineXmlStringForLines(reactant.getLine()));
- sb.append("</celldesigner:reactantLink>\n");
- return sb.toString();
+ String sb = "<celldesigner:reactantLink "
+ + "reactant=\"" + elements.getElementId(alias) + "\" "
+ + "alias=\"" + alias.getElementId() + "\" "
+ // targetLineIndex is missing (maybe it's unimportant :))
+ + ">\n"
+ + getAnchorXml(alias, reactant.getLine().getStartPoint())
+ + getConnectSchemeXmlStringForLines(new PolylineData[]{reactant.getLine()})
+ + getEditPointsXmlStringForLine(new PolylineData[]{reactant.getLine()}, 0)
+ + getLineXmlStringForLines(reactant.getLine())
+ + "</celldesigner:reactantLink>\n";
+ return sb;
}
/**
* Creates productLink xml node for product.
- *
- * @param product
- * product to be transformed
+ *
+ * @param product product to be transformed
* @return xml node describing productLink
*/
private String getProductLinkXmlString(final Product product) {
Element alias = product.getElement();
- PolylineData[] lines = new PolylineData[] { getLineBeforeTrimming(product) };
-
- StringBuilder sb = new StringBuilder();
- sb.append("<celldesigner:productLink ");
- sb.append("product=\"" + elements.getElementId(alias) + "\" ");
- sb.append("alias=\"" + alias.getElementId() + "\" ");
- // targetLineIndex is missing (maybe it's unimportant :))
- sb.append(">\n");
-
- sb.append(getAnchorXml(alias, getLineBeforeTrimming(product).getEndPoint()));
-
- sb.append(getConnectSchemeXmlStringForLines(lines));
-
- sb.append(getEditPointsXmlStringForLine(lines, 0));
- sb.append(getLineXmlStringForLines(product.getLine()));
- sb.append("</celldesigner:productLink>\n");
- return sb.toString();
+ PolylineData[] lines = new PolylineData[]{getLineBeforeTrimming(product)};
+
+ String sb = "<celldesigner:productLink "
+ + "product=\"" + elements.getElementId(alias) + "\" "
+ + "alias=\"" + alias.getElementId() + "\" "
+ // targetLineIndex is missing (maybe it's unimportant :))
+ + ">\n"
+ + getAnchorXml(alias, getLineBeforeTrimming(product).getEndPoint())
+ + getConnectSchemeXmlStringForLines(lines)
+ + getEditPointsXmlStringForLine(lines, 0)
+ + getLineXmlStringForLines(product.getLine())
+ + "</celldesigner:productLink>\n";
+ return sb;
}
/**
* Creates valid xml node with connectScheme for the set of lines.
- *
- * @param lines
- * list of lines to be included in connectScheme. As far as I
- * remember only one or three lines could be provided.
+ *
+ * @param lines list of lines to be included in connectScheme. As far as I
+ * remember only one or three lines could be provided.
* @return xml node with connectScheme
*/
String getConnectSchemeXmlStringForLines(final PolylineData[] lines) {
@@ -774,13 +742,11 @@ public class ReactionToXml {
* Creates
* {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure representing lines in CellDesigner.
- *
- * @param lines
- * lines to be transformed into single
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure
- * @param centerIndex
- * where the central line is positioned
+ *
+ * @param lines lines to be transformed into single
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure
+ * @param centerIndex where the central line is positioned
* @return xml node
*/
private String getEditPointsXmlStringForLine(final PolylineData[] lines, final Integer centerIndex) {
@@ -791,15 +757,12 @@ public class ReactionToXml {
* Creates
* {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure representing lines in CellDesigner.
- *
- * @param lines
- * lines to be transformed into single
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure
- * @param centerPoint
- * central point when list of lines is greater than 1
- * @param centerIndex
- * where the central line is positioned
+ *
+ * @param lines lines to be transformed into single
+ * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
+ * structure
+ * @param centerPoint central point when list of lines is greater than 1
+ * @param centerIndex where the central line is positioned
* @return xml node
*/
private String getEditPointsXmlStringForLine(final PolylineData[] lines, final Point2D centerPoint, final Integer centerIndex) {
@@ -851,12 +814,9 @@ public class ReactionToXml {
* Returns xml node representing
* {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
* structure.
- *
- * @param reaction
- * reaction for which xml node is generated
- * @return xml node representing
- * {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints}
- * structure
+ *
+ * @param reaction reaction for which xml node is generated
+ * @return xml node representing {@link lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints} structure
*/
String getEditPointsXmlStringForReaction(final Reaction reaction) {
if (getCellDesignerReactionTypeString(reaction).equals("BOOLEAN_LOGIC_GATE")) {
@@ -896,6 +856,7 @@ public class ReactionToXml {
for (final AbstractNode node : operator.getOutputs()) {
if (!(node instanceof Product)) {
process = false;
+ break;
}
}
if (process) {
@@ -920,7 +881,7 @@ public class ReactionToXml {
Point2D centerPoint = pointTransformation.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
- return getEditPointsXmlStringForLine(new PolylineData[] { line1.reverse(), line2, line3 }, centerPoint, index);
+ return getEditPointsXmlStringForLine(new PolylineData[]{line1.reverse(), line2, line3}, centerPoint, index);
}
private String getEditPointsXmlStringForTwoReactantReaction(final Reaction reaction) {
@@ -935,6 +896,7 @@ public class ReactionToXml {
for (final AbstractNode node : operator.getInputs()) {
if (!(node instanceof Reactant)) {
process = false;
+ break;
}
}
if (process) {
@@ -970,7 +932,7 @@ public class ReactionToXml {
Point2D centerPoint = pointTransformation.getCoordinatesInCellDesignerBase(pointA, pointB, pointC, pointO);
return getEditPointsXmlStringForLine(
- new PolylineData[] { line1.reverse(), line2.reverse(), line3.reverse().reverse() }, centerPoint,
+ new PolylineData[]{line1.reverse(), line2.reverse(), line3.reverse().reverse()}, centerPoint,
line3.getLines().size() - product.getLine().getLines().size());
}
@@ -978,7 +940,7 @@ public class ReactionToXml {
Reactant r = reaction.getReactants().get(0);
Point2D centerPoint = r.getLine().getEndPoint();
return getEditPointsXmlStringForLine(
- new PolylineData[] { reaction.getProducts().get(0).getLine() }, centerPoint,
+ new PolylineData[]{reaction.getProducts().get(0).getLine()}, centerPoint,
0);
}
@@ -1012,7 +974,7 @@ public class ReactionToXml {
PolylineData pd = new PolylineData(points);
pd.setStartPoint(getAnchorPoint(reactant.getElement(), reactant.getLine().getStartPoint()));
pd.setEndPoint(getAnchorPoint(product.getElement(), productLine.getEndPoint()));
- return getEditPointsXmlStringForLine(new PolylineData[] { pd }, centerPosition);
+ return getEditPointsXmlStringForLine(new PolylineData[]{pd}, centerPosition);
}
private Point2D getAnchorPoint(final Element element, final Point2D originalPoint) {
@@ -1024,9 +986,8 @@ public class ReactionToXml {
/**
* Creates valid xml node with connectScheme for the reaction.
- *
- * @param reaction
- * reaction for which the connectSchema is going to be created
+ *
+ * @param reaction reaction for which the connectSchema is going to be created
* @return xml node with connectScheme
*/
String getConnectSchemeXmlStringForReaction(final Reaction reaction) {
@@ -1086,9 +1047,8 @@ public class ReactionToXml {
/**
* Returns xml node with list of base products.
- *
- * @param reaction
- * reaction for which the node is created
+ *
+ * @param reaction reaction for which the node is created
* @return xml node with list of base products
*/
private String getBaseProductsXmlStringForReaction(final Reaction reaction) {
@@ -1116,9 +1076,8 @@ public class ReactionToXml {
/**
* Returns xml node with list of base reactants.
- *
- * @param reaction
- * reaction for which the node is created
+ *
+ * @param reaction reaction for which the node is created
* @return xml node with list of base reactants
*/
private String getBaseReactantsXmlStringForReaction(final Reaction reaction) {
@@ -1150,12 +1109,10 @@ public class ReactionToXml {
/**
* Returns xml node that describes anchor point.
- *
- * @param alias
- * alias on which we are looking for anchor
- * @param point
- * point on the alias that should be aligned to the closest anchor
- * point
+ *
+ * @param alias alias on which we are looking for anchor
+ * @param point point on the alias that should be aligned to the closest anchor
+ * point
* @return xml node with anchor point
*/
private String getAnchorXml(final Element alias, final Point2D point) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
index 0ca1fe6f736a47c20bd4478da6c9ad7d1ebdae99..afd8025635db0f2e16ab4c89eeae20a7a1bbd3a9 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/AbstractElementXmlParser.java
@@ -1,32 +1,28 @@
package lcsb.mapviewer.converter.model.celldesigner.species;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerParserException;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.Document;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+
+import java.util.ArrayList;
+import java.util.List;
/**
* Abstract class with the interface to parse element in CellDesigner file.
- *
+ *
+ * @param <T> type of the CellDesigner object to parse
+ * @param <S> type of the model object to be obtained
* @author Piotr Gawron
- *
- * @param <T>
- * type of the CellDesigner object to parse
- * @param <S>
- * type of the model object to be obtained
*/
public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>, S extends Element> {
@@ -36,13 +32,13 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* List of special strings in CellDesigner that should be translated into some
* UTF characters.
*/
- private List<Pair<String, String>> encodedStrings = new ArrayList<>();
+ private final List<Pair<String, String>> encodedStrings = new ArrayList<>();
/**
* Parser of the notes that allows to extract additional structured data for
* the object.
*/
- private RestAnnotationParser rap = new RestAnnotationParser();
+ private final RestAnnotationParser rap = new RestAnnotationParser();
/**
* Default constructor.
@@ -110,29 +106,21 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
* Returns a {@link Pair} containing CellDesigner identifier in
* {@link Pair#getLeft()} and element in {@link Pair#getRight()}.
*
- * @param node
- * xml node be parsed
- * @return {@link Pair} containing CellDesigner identifier in
- * {@link Pair#getLeft()} and element parsed from xml node in
- * {@link Pair#getRight()}.
- * @throws InvalidXmlSchemaException
- * thrown when xml is invalid
+ * @param node xml node be parsed
+ * @return {@link Pair} containing CellDesigner identifier in {@link Pair#getLeft()} and element parsed from xml node in {@link Pair#getRight()}.
+ * @throws InvalidXmlSchemaException thrown when xml is invalid
*/
public abstract Pair<String, T> parseXmlElement(final Node node)
throws InvalidXmlSchemaException, CellDesignerParserException;
/**
- * Parses CellDEsigner xml node that is given as a plain text into element.
+ * Parses CellDesigner xml node that is given as a plain text into element.
* Returns a {@link Pair} containing CellDesigner identifier in
* {@link Pair#getLeft()} and element in {@link Pair#getRight()}.
- *
- * @param xmlString
- * node to parse
- * @return {@link Pair} containing CellDesigner identifier in
- * {@link Pair#getLeft()} and element parsed from xml node in
- * {@link Pair#getRight()}.
- * @throws InvalidXmlSchemaException
- * thrown when xmlString is invalid
+ *
+ * @param xmlString node to parse
+ * @return {@link Pair} containing CellDesigner identifier in {@link Pair#getLeft()} and element parsed from xml node in {@link Pair#getRight()}.
+ * @throws InvalidXmlSchemaException thrown when xmlString is invalid
*/
public Pair<String, T> parseXmlElement(final String xmlString)
throws InvalidXmlSchemaException, CellDesignerParserException {
@@ -143,22 +131,19 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
/**
* Method transforms element into CellDesigner xml string.
- *
- * @param element
- * object to be transformed
+ *
+ * @param element object to be transformed
* @return CellDesigner xml string representing element
- * @throws InconsistentModelException
- * thrown when xml cannot be generated because structure of objects
- * is invalid
+ * @throws InconsistentModelException thrown when xml cannot be generated because structure of objects
+ * is invalid
*/
public abstract String toXml(S element) throws InconsistentModelException;
/**
* This method decodes CellDesigner string with all known CellDesigner special
* tokens.
- *
- * @param name
- * string to be decoded
+ *
+ * @param name string to be decoded
* @return decoded string
*/
protected String decodeName(final String name) {
@@ -171,9 +156,8 @@ public abstract class AbstractElementXmlParser<T extends CellDesignerElement<?>,
/**
* This method encodes {@link String} using CellDesigner special tokens.
- *
- * @param name
- * string to be decoded
+ *
+ * @param name string to be decoded
* @return decoded string
*/
protected String encodeName(final String name) {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
index 7ee2005cbe94302f2790577c68fbfd5d00aa0cba..4c1da26a41ce8bee754ab09b10d2216cb7899b36 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesCollectionXmlParser.java
@@ -4,10 +4,7 @@ import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerGene;
@@ -23,6 +20,8 @@ import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.w3c.dom.Node;
@@ -128,7 +127,7 @@ public class SpeciesCollectionXmlParser {
rnaParser = new RnaXmlParser(elements);
geneParser = new GeneXmlParser(elements);
antisenseRnaParser = new AntisenseRnaXmlParser(elements);
- xap = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ xap = new XmlAnnotationParser(lcsb.mapviewer.utils.RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
}
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
index 6edd9a584bec1e01505d29e118f4943f3b4d953a..77d3d0a6e5a35866896f2921fa16fa5be8304da0 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java
@@ -6,10 +6,7 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerAntisenseRna;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerComplexSpecies;
@@ -37,6 +34,8 @@ import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
+import lcsb.mapviewer.utils.RestAnnotationParser;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
@@ -234,7 +233,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
if (rdfNode != null) {
final XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
- CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
species.addMiriamData(xmlAnnotationParser.parseRdfNode(rdfNode, new LogMarker(ProjectLogEntryType.PARSING_ISSUE,
species.getClass().getSimpleName(), species.getElementId(), "")));
}
@@ -325,7 +324,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
builder.append("</celldesigner:extension>\n");
final XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
- CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ RestAnnotationParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
builder.append(xmlAnnotationParser.dataSetToXmlString(species.getMiriamData(), elements.getElementId(species)));
builder.append("</annotation>\n");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
index d6a906b736987999c73cb3c42e66422c4de62422..21059567562f7f82932a4031607d576e1220d8b2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
@@ -1,15 +1,10 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
+import lcsb.mapviewer.commands.layout.ModifierType;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -19,26 +14,29 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
/**
* Util class that helps in transformation of CellDesigner modifiers into
* {@link Modifier} object in our model.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ModifierTypeUtils {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Returns {@link ModifierType} that reference to the clazz.
- *
- * @param clazz
- * class type for which result is returned
+ *
+ * @param clazz class type for which result is returned
* @return {@link ModifierType} that reference to the clazz
*/
public ModifierType getModifierTypeForClazz(final Class<? extends Modifier> clazz) {
@@ -53,9 +51,8 @@ public class ModifierTypeUtils {
/**
* Returns {@link ModifierType} that reference to the CellDesigner string
* 'type'.
- *
- * @param type
- * CellDesigner string defining modifier type
+ *
+ * @param type CellDesigner string defining modifier type
* @return {@link ModifierType} that reference to the CellDesigner 'type'
*/
public ModifierType getModifierTypeForStringType(final String type) {
@@ -69,11 +66,9 @@ public class ModifierTypeUtils {
/**
* Creates {@link Modifier} for the CellDesigner type.
- *
- * @param type
- * CellDesigner type of the modifier
- * @param alias
- * alias to which modifier point to
+ *
+ * @param type CellDesigner type of the modifier
+ * @param alias alias to which modifier point to
* @return {@link Modifier} for the CellDesigner type
*/
public Modifier createModifierForStringType(final String type, final Species alias) {
@@ -91,9 +86,8 @@ public class ModifierTypeUtils {
/**
* Returns CellDesigner string used for modifier creation.
- *
- * @param modifier
- * modifier for which CellDesigner string is looked for
+ *
+ * @param modifier modifier for which CellDesigner string is looked for
* @return CellDesigner string used for modifier creation
*/
public String getStringTypeByModifier(final Modifier modifier) {
@@ -108,9 +102,8 @@ public class ModifierTypeUtils {
* Returns string that identfies TargetLine index for the modifier. TargetLine
* index is a CellDesigner String that identifies to which point on the
* rectangle in the center line modifier line is connected.
- *
- * @param modifier
- * modifier for target line
+ *
+ * @param modifier modifier for target line
* @return string that identfies TargetLine index for the modifier
*/
public String getTargetLineIndexByModifier(final Modifier modifier) {
@@ -130,9 +123,8 @@ public class ModifierTypeUtils {
* Returns string that identfies TargetLine index for the modifier operator.
* TargetLine index is a CellDesigner String that identifies to which point on
* the rectangle in the center line modifier line is connected.
- *
- * @param modifier
- * modifier operator for target line
+ *
+ * @param modifier modifier operator for target line
* @return string that identfies TargetLine index for the modifier
*/
public String getTargetLineIndexByModifier(final NodeOperator modifier) {
@@ -157,21 +149,17 @@ public class ModifierTypeUtils {
* Returns string that identfies TargetLine index for the modifier line
* connected to reaction (target line index is explained here:
* {@link #getTargetLineIndexByModifier(Modifier)}).
- *
- *
- * @param modType
- * type of modifier for the line
- * @param reaction
- * reaction on which target line index is looked for
- * @param originalLine
- * line that connects modifier to the reaction
+ *
+ * @param modType type of modifier for the line
+ * @param reaction reaction on which target line index is looked for
+ * @param originalLine line that connects modifier to the reaction
* @return string that identifies TargetLine index for modifier line
*/
private String getTragteLineIndex(final ModifierType modType, final Reaction reaction, final PolylineData originalLine) {
PolylineData line = new PolylineData(originalLine);
line.trimEnd(-modType.getTrimLength());
- String[] possibleValues = new String[] { "0,2", "0,3", "0,4", "0,5", "0,6", "0,7" };
+ String[] possibleValues = new String[]{"0,2", "0,3", "0,4", "0,5", "0,6", "0,7"};
Point2D closestPoint = new Point2D.Double(Double.MAX_VALUE, Double.MAX_VALUE);
Point2D checkedPoint = line.getEndPoint();
String result = "0,0";
@@ -189,11 +177,9 @@ public class ModifierTypeUtils {
* This method get anchor point on the reaction line (the center point of this
* line is given as a parameter). The anchor point depends on the line and
* lineConnectionType associated with the modification.
- *
- * @param reaction
- * reaction on which we are looking for a point
- * @param lineConnectionType
- * point of connection to the reaction center rectangle
+ *
+ * @param reaction reaction on which we are looking for a point
+ * @param lineConnectionType point of connection to the reaction center rectangle
* @return coordinates of point on the center rectangle
*/
public Point2D getAnchorPointOnReactionRect(final Reaction reaction, final String lineConnectionType) {
@@ -212,34 +198,34 @@ public class ModifierTypeUtils {
if (spr.length > 1) {
id = spr[1];
if (id.equals("2")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y -= ReactionData.RECT_SIZE / 2;
} else if (id.equals("3")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
} else if (id.equals("4")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y -= ReactionData.RECT_SIZE / 2;
+ x -= ReactionData.RECT_SIZE / 2;
} else if (id.equals("5")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- x += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y -= ReactionData.RECT_SIZE / 2;
+ x += ReactionData.RECT_SIZE / 2;
} else if (id.equals("6")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
+ x -= ReactionData.RECT_SIZE / 2;
} else if (id.equals("7")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- x += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
+ x += ReactionData.RECT_SIZE / 2;
} else if (id.equals("0")) {
// this is only workaround...
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
} else if (id.equals("1")) {
// this is only workaround...
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
} else {
throw new InvalidArgumentException("Unknown targetLineIndex: " + id);
}
} else {
logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction), "Invalid targetLineIndex: " + id);
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
}
Point2D p = new Point2D.Double(x, y);
PointTransformation pointTransformation = new PointTransformation();
@@ -249,9 +235,8 @@ public class ModifierTypeUtils {
/**
* Update line parameters to make it look like a proper modifier.
- *
- * @param modifier
- * modifier for which line will be modified
+ *
+ * @param modifier modifier for which line will be modified
*/
public void updateLineEndPoint(final Modifier modifier) {
ModifierType modType = getModifierTypeForClazz(modifier.getClass());
@@ -265,9 +250,8 @@ public class ModifierTypeUtils {
/**
* Updates line parameters of modifier operator to make it look like a proper
* modifier.
- *
- * @param operator
- * modifier operator for which line will be modified
+ *
+ * @param operator modifier operator for which line will be modified
*/
@SuppressWarnings("unchecked")
public void updateLineEndPoint(final NodeOperator operator) {
@@ -286,11 +270,9 @@ public class ModifierTypeUtils {
/**
* Updates line parameters to make it look like a proper modifier.
- *
- * @param modType
- * type of modifier
- * @param line
- * line to update
+ *
+ * @param modType type of modifier
+ * @param line line to update
*/
private void updateLineByType(final ModifierType modType, final PolylineData line) {
line.setEndAtd(modType.getAtd().copy());
@@ -300,9 +282,8 @@ public class ModifierTypeUtils {
/**
* Returns type of the modifier in modifier operator.
- *
- * @param modifierOperator
- * opertor for which type will be returned
+ *
+ * @param modifierOperator opertor for which type will be returned
* @return type of the modifier in modifier operator
*/
public ModifierType getModifierTypeForOperator(final NodeOperator modifierOperator) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
index 615388da0952036d46207f63def095e6c9c4fa9a..9140a5181ff06fca6499996af7b6cd119ee9042a 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java
@@ -1,11 +1,14 @@
package lcsb.mapviewer.converter.model.celldesigner;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.common.tests.TestUtils;
import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.Drawable;
@@ -13,16 +16,20 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.compartment.BottomSquareCompartment;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.LeftSquareCompartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.compartment.RightSquareCompartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.compartment.TopSquareCompartment;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerImage;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
@@ -34,9 +41,13 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.BindingRegion;
import lcsb.mapviewer.model.map.species.field.Residue;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import lcsb.mapviewer.model.overlay.GenericDataOverlayEntry;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Rule;
+import org.mockito.internal.util.collections.Sets;
import java.awt.Canvas;
import java.awt.Color;
@@ -44,9 +55,13 @@ import java.awt.Font;
import java.awt.FontMetrics;
import java.awt.geom.Point2D;
import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Paths;
import static org.junit.Assert.assertEquals;
@@ -90,19 +105,29 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
final InputStream is = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
final Model model2 = parser.createModel(new ConverterParams().inputStream(is, model.getName()).sizeAutoAdjust(false));
- for (final Drawable bioEntity : model2.getDrawables()) {
- bioEntity.setZ(null);
- }
+ clearModelFromZ(model2);
+ clearModelFromZ(model);
+ return model2;
+ }
+
+ protected void clearModelFromZ(final Model model) {
for (final Drawable bioEntity : model.getDrawables()) {
bioEntity.setZ(null);
+ if (bioEntity instanceof Element) {
+ ((Element) bioEntity).setVisibilityLevel(0);
+ }
}
- return model2;
+ }
+
+ protected void clearModelFromZ(final ModelData modelData) {
+ clearModelFromZ(modelData.getModel());
}
private static int idCounter = 0;
protected static GenericProtein createProtein() {
final GenericProtein protein = new GenericProtein("id" + (idCounter++));
+ protein.setName(faker.science().element());
protein.setActivity(true);
protein.setFontSize(4);
protein.setStateLabel("xxx");
@@ -145,6 +170,20 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
return compartment;
}
+ protected PathwayCompartment createPathway() {
+ final PathwayCompartment pathwayCompartment = new PathwayCompartment("art0");
+ pathwayCompartment.setName(faker.science().element());
+ assignCoordinates(13, 14, 100, 120, pathwayCompartment);
+ pathwayCompartment.setNameVerticalAlign(VerticalAlign.TOP);
+ pathwayCompartment.setNameHorizontalAlign(HorizontalAlign.LEFT);
+ pathwayCompartment.setNameX(pathwayCompartment.getX() + 10);
+ pathwayCompartment.setNameY(pathwayCompartment.getY() + 10);
+ pathwayCompartment.setNameWidth(pathwayCompartment.getWidth() - 20);
+ pathwayCompartment.setNameHeight(pathwayCompartment.getHeight() - 20);
+
+ return pathwayCompartment;
+ }
+
protected static LayerText createText() {
final LayerText layerText = new LayerText();
layerText.setX(256.0);
@@ -152,11 +191,22 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
layerText.setWidth(233.0);
layerText.setHeight(188.0);
layerText.setZ(0);
- layerText.setNotes("asd as");
- layerText.setColor(Color.BLACK);
+ layerText.setNotes(faker.lorem().paragraph());
+ layerText.setColor(new ColorParser().parse(faker.color().hex()));
return layerText;
}
+ protected LayerImage createImage() throws IOException {
+ final LayerImage image = new LayerImage();
+ image.setX(256.0);
+ image.setY(79.0);
+ image.setWidth(233.0);
+ image.setHeight(188.0);
+ image.setZ(0);
+ image.setGlyph(createGlyph());
+ return image;
+ }
+
protected static SbmlFunction createFunction() throws InvalidXmlSchemaException {
SbmlFunction fun = new SbmlFunction("fun_id" + (idCounter++));
fun.setDefinition("<math xmlns=\"http://www.w3.org/1998/Math/MathML\">\n"
@@ -245,6 +295,7 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
protected static Model createEmptyModel() {
final Model model = new ModelFullIndexed(null);
+ model.setName(faker.witcher().monster());
model.setIdModel("as");
model.setWidth(100);
model.setHeight(100);
@@ -283,4 +334,55 @@ public abstract class CellDesignerTestFunctions extends TestUtils {
result.setZ(faker.number().numberBetween(1, 100));
return result;
}
+
+ protected Project createProject() {
+ Project project = new Project();
+ project.setProjectId(faker.numerify("P########"));
+ return project;
+ }
+
+ protected Glyph createGlyph() throws IOException {
+ Glyph glyph = new Glyph();
+ glyph.setFile(createFile("testFiles/glyphs/uni.png"));
+
+ return glyph;
+ }
+
+ private UploadedFileEntry createFile(final String filePath) throws IOException {
+ UploadedFileEntry uploadedFileEntry = new UploadedFileEntry();
+ byte[] byteArray = Files.readAllBytes(Paths.get(filePath));
+ uploadedFileEntry.setFileContent(byteArray);
+ uploadedFileEntry.setOriginalFileName("glyphs/" + new File(filePath).getName());
+ uploadedFileEntry.setLength(byteArray.length);
+ uploadedFileEntry.setLocalPath(null);
+ return uploadedFileEntry;
+
+ }
+
+ protected DataOverlay createDataOverlay() {
+ DataOverlay dataOverlay = new DataOverlay();
+ dataOverlay.setPublic(faker.bool().bool());
+ dataOverlay.setName(faker.name().fullName());
+ dataOverlay.setDescription(faker.lorem().sentence());
+ return dataOverlay;
+ }
+
+ protected DataOverlayEntry createDataOverlayEntry() {
+ DataOverlayEntry entry = new GenericDataOverlayEntry();
+ entry.setName(faker.text().text(4).toUpperCase());
+ entry.setDescription(faker.lorem().sentence());
+ entry.setModelName(faker.witcher().monster());
+ entry.setCompartments(Sets.newSet(faker.witcher().potion(), faker.witcher().potion()));
+ entry.setElementId(faker.witcher().sign());
+ entry.setLineWidth(faker.number().randomDouble(2, 1, 3));
+ if (Math.random() < 0.5) {
+ entry.setColor(new ColorParser().parse(faker.color().hex()));
+ } else {
+ entry.setValue(faker.number().randomDouble(2, -1, 1));
+ }
+ entry.setReverseReaction(faker.bool().bool());
+ return entry;
+ }
+
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index 9b9e082d38390d3538fe8149f72d23c19b22d51d..b72982513fb120b7facdfaf6b87eb3f3f6372298 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -5,10 +5,11 @@ import lcsb.mapviewer.common.comparator.PointComparator;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
@@ -37,6 +38,7 @@ import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.SimpleMolecule;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.utils.RestAnnotationParser;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -1044,4 +1046,21 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
assertEquals("", model.getNotes());
}
+ @Test
+ public void testMoveAnnotationsFromNotes() throws Exception {
+ Model model = CellDesignerTestFunctions.getModelForFile("testFiles/copyingAnnotationModel.xml");
+
+ Set<Element> elements = model.getElements();
+ for (final Element element : elements) {
+ if (element.getName().equals("blabla")) {
+ assertEquals(2, element.getMiriamData().size());
+ element.getMiriamData()
+ .add(new MiriamData(MiriamType.PUBMED, "12345"));
+ element.getMiriamData()
+ .add(new MiriamData(MiriamType.PUBMED, "333666"));
+ assertEquals(2, element.getMiriamData().size());
+ }
+ assertFalse(element.getNotes().contains("rdf:RDF"));
+ }
+ }
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CopyCommandForCellDesignerFilesTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CopyCommandForCellDesignerFilesTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..3f106b59b0e0beda05c1f043d4c029418289fd0c
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CopyCommandForCellDesignerFilesTest.java
@@ -0,0 +1,116 @@
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertTrue;
+
+public class CopyCommandForCellDesignerFilesTest extends CellDesignerTestFunctions {
+
+ private final ModelComparator comparator = new ModelComparator();
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ private final int counter = 0;
+
+ @Test
+ public void testCopyModel() throws Exception {
+ Model model = getModelForFile("testFiles/sample.xml");
+ Model copy = new CopyCommand(model).execute();
+
+ assertEquals(0, comparator.compare(model, copy));
+ }
+
+ @Test
+ public void testCopyModelWithKinetics() throws Exception {
+ Model model = getModelForFile("testFiles/kinetics_with_compartment.xml");
+ Model copy = new CopyCommand(model).execute();
+
+ assertEquals(0, comparator.compare(model, copy));
+ for (final Reaction reaction : copy.getReactions()) {
+ if (reaction.getKinetics() != null) {
+ for (final Element element : reaction.getKinetics().getElements()) {
+ assertTrue("Element in the copy doesn't belong to copy", copy.getElements().contains(element));
+ }
+ for (final SbmlFunction function : reaction.getKinetics().getFunctions()) {
+ assertTrue("Function in the copy doesn't belong to copy", copy.getFunctions().contains(function));
+ }
+ for (final SbmlParameter parameter : reaction.getKinetics().getParameters()) {
+ if (parameter.getParameterId().equals("k2")) {
+ assertTrue("Global parameter in the function copy doesn't belong to copy",
+ copy.getParameters().contains(parameter));
+ }
+ }
+ }
+ }
+ }
+
+ @Test
+ public void testCopyModel3() throws Exception {
+ Model model = getModelForFile("testFiles/complex_with_state.xml");
+
+ Model copy = new CopyCommand(model).execute();
+
+ Model copy2 = serializeModel(copy);
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+ }
+
+ @Test
+ public void testCopyModel4() throws Exception {
+ Model model = getModelForFile("testFiles/problematic_description.xml");
+
+ Model copy = new CopyCommand(model).execute();
+
+ Model copy2 = serializeModel(copy);
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+ }
+
+ @Test
+ public void testCopyModelWithArtificialAliases() throws Exception {
+ Model model = getModelForFile("testFiles/artificial_compartments.xml");
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ Model copy = new CopyCommand(model).execute();
+
+ Model copy2 = serializeModel(copy);
+
+ new CreateHierarchyCommand(copy2, 2, 2).execute();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+ }
+
+ @Test
+ public void testCopyModelWithProject() throws Exception {
+ Model originalModel = getModelForFile("testFiles/sample.xml");
+ Project project = new Project();
+ project.addModel(originalModel);
+
+ Model colorModel = new CopyCommand(originalModel).execute();
+
+ assertNotEquals(originalModel.getProject(), colorModel.getProject());
+ }
+
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CreateHierarchyCommandForProblematicCDTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CreateHierarchyCommandForProblematicCDTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..386a67933e1623faf57bfdb0112e7e67f729e121
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CreateHierarchyCommandForProblematicCDTest.java
@@ -0,0 +1,304 @@
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
+
+public class CreateHierarchyCommandForProblematicCDTest extends CellDesignerTestFunctions {
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCyclicComplexes() throws Exception {
+ Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml");
+
+ new CreateHierarchyCommand(model, 8, 80).execute();
+
+ Species alias = model.getElementByElementId("sa5033");
+
+ Set<Element> parents = new HashSet<>();
+ while (alias.getComplex() != null) {
+ assertFalse("Cyclic nesting", parents.contains(alias.getComplex()));
+ alias = alias.getComplex();
+ parents.add(alias);
+ }
+
+ Set<String> levels = new HashSet<>();
+ for (final Element a : model.getElements()) {
+ levels.add(a.getVisibilityLevel());
+ }
+ assertTrue(levels.size() > 2);
+ }
+
+ @Test
+ public void testCreateHierarchy() throws Exception {
+ Model model = getModelForFile("testFiles/artificial_compartments.xml");
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+ // check if second call will throw an exception...
+ new CreateHierarchyCommand(model, 2, 2).execute();
+ }
+
+ @Test
+ public void testCreateHierarchy2() throws Exception {
+ Model model = getModelForFile("testFiles/artificial_compartments.xml");
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ boolean artificial = false;
+ for (final Compartment a : model.getCompartments()) {
+ if (a instanceof PathwayCompartment) {
+ artificial = true;
+ break;
+ }
+ }
+ assertTrue("No hierarchical structure element found", artificial);
+ }
+
+ @Test
+ public void testRecreateHierarchy() throws Exception {
+ Model model = getModelForFile("testFiles/artificial_compartments.xml");
+
+ int aliasSize0 = model.getCompartments().size();
+
+ logger.debug(aliasSize0);
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ int aliasSize = model.getCompartments().size();
+ logger.debug(aliasSize);
+
+ assertTrue(aliasSize0 != aliasSize);
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ int aliasSize2 = model.getCompartments().size();
+ logger.debug(aliasSize2);
+
+ assertEquals(aliasSize, aliasSize2);
+ }
+
+ @Test
+ public void testParenting() throws Exception {
+ Model model = getModelForFile("testFiles/artificial_compartments.xml");
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ assertFalse(model.getElementByElementId("sa1").getCompartment() instanceof PathwayCompartment);
+ }
+
+ @Test
+ public void testCreateComponentsMinVisibility() throws Exception {
+ double zoomFactor = 39.0625;
+ int levels = 6;
+
+ Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml");
+
+ new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+ for (final Compartment compartment : model.getCompartments()) {
+ if (compartment.getCompartment() == null) {
+ int visibilityLevel = Integer.parseInt(compartment.getVisibilityLevel());
+ assertTrue("Alias " + compartment.getElementId() + " is not visible at levels highers than "
+ + compartment.getVisibilityLevel(), visibilityLevel <= 1);
+ }
+ }
+
+ for (final Species species : model.getSpeciesList()) {
+ if (species.getCompartment() == null) {
+ int visibilityLevel = Integer.parseInt(species.getVisibilityLevel());
+ assertTrue("Alias " + species.getElementId() + " is not visible at levels highers than "
+ + species.getVisibilityLevel(), visibilityLevel <= 1);
+ }
+ }
+ }
+
+ @Test
+ public void testCreateComponentsMaxVisibility() throws Exception {
+ double zoomFactor = 39.0625;
+ int levels = 6;
+
+ Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml");
+
+ new CreateHierarchyCommand(model, levels, zoomFactor).execute();
+
+ for (final Element element : model.getElements()) {
+ int visibilityLevel = Integer.parseInt(element.getVisibilityLevel());
+ assertTrue("Alias " + element.getElementId() + " is not visible even at the bottom level (visibility: "
+ + element.getVisibilityLevel() + ") ", visibilityLevel <= levels);
+ }
+ }
+
+ @Test
+ public void testCompactComplexesInNestedView() throws Exception {
+ Model model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml");
+ Element alias = model.getElementByElementId("sa1");
+ Object parent1 = alias.getCompartment();
+ new CreateHierarchyCommand(model, 3, 16).execute();
+ Object parent2 = alias.getCompartment();
+ assertEquals(parent1, parent2);
+ }
+
+ @Test(expected = InvalidStateException.class)
+ public void testRecallHierarchyCreation() throws Exception {
+ Model model = getModelForFile("testFiles/artificial_compartments.xml");
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+ command.execute();
+ command.execute();
+ }
+
+ @Test
+ public void testClear() throws Exception {
+ Model model = getModelForFile("testFiles/artificial_compartments.xml");
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+ command.clean();
+ for (final Element alias : model.getElements()) {
+ assertNull(alias.getCompartment());
+ }
+ for (final Compartment alias : model.getCompartments()) {
+ assertNull(alias.getCompartment());
+ assertTrue(alias.getElements().isEmpty());
+ }
+ }
+
+ @Test
+ public void testNestedProblem() throws Exception {
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ Model model = parser
+ .createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
+
+ double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
+ int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
+ command.execute();
+
+ for (final Element alias : model.getElements()) {
+ Element parentAlias = alias.getCompartment();
+ if (parentAlias != null) {
+ int parentVisibilityLevel = Integer.parseInt(parentAlias.getVisibilityLevel());
+ int aliasVisibilityLevel = Integer.parseInt(alias.getVisibilityLevel());
+ assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
+ }
+ if (alias instanceof Species) {
+ parentAlias = ((Species) alias).getComplex();
+ if (parentAlias != null) {
+ int parentVisibilityLevel = Integer.parseInt(parentAlias.getVisibilityLevel());
+ int aliasVisibilityLevel = Integer.parseInt(alias.getVisibilityLevel());
+ assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
+ }
+ }
+ }
+ }
+
+ @Test
+ public void testDisconnectedChildInComplex() throws Exception {
+ Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml");
+
+ new CreateHierarchyCommand(model, 8, 80).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.model2String(model);
+
+ InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
+
+ parser.createModel(new ConverterParams().inputStream(stream));
+ }
+
+ @Test
+ public void testHierarchyWithCustomSemanticZooming() throws Exception {
+ Model model = getModelForFile("testFiles/custom_semantic_zooming.xml");
+
+ Map<Element, String> visibilityLevels = new HashMap<>();
+ for (final Element element : model.getElements()) {
+ if (element.getVisibilityLevel() != null && !element.getVisibilityLevel().isEmpty()) {
+ visibilityLevels.put(element, element.getVisibilityLevel());
+ }
+ }
+
+ new CreateHierarchyCommand(model, 4, 80).execute();
+
+ for (final Element element : model.getElements()) {
+ if (visibilityLevels.get(element) != null) {
+ assertEquals("Visibility level changed, but shouldn't", visibilityLevels.get(element),
+ element.getVisibilityLevel());
+ }
+ }
+ }
+
+ @Test
+ public void testHierarchyWithCustomSemanticZoomingPathwayLevels() throws Exception {
+ ElementUtils eu = new ElementUtils();
+ Model model = getModelForFile("testFiles/custom_semantic_zooming.xml");
+
+ Map<Element, String> visibilityLevels = new HashMap<>();
+ for (final Element element : model.getElements()) {
+ if (element.getVisibilityLevel() != null && !element.getVisibilityLevel().isEmpty()) {
+ visibilityLevels.put(element, element.getVisibilityLevel());
+ }
+ }
+
+ new CreateHierarchyCommand(model, 4, 80).execute();
+
+ for (final Element element : model.getElements()) {
+ if (visibilityLevels.get(element) == null) {
+ int visibilityLevel = Integer.parseInt(element.getVisibilityLevel());
+ if (element.getCompartment() != null) {
+ int parentTransparency = Integer.parseInt(element.getCompartment().getTransparencyLevel());
+ assertEquals(
+ eu.getElementTag(element) + eu.getElementTag(element.getCompartment())
+ + "Element should be directly visible when parent is transparent",
+ parentTransparency, visibilityLevel);
+ } else if (element instanceof Species) {
+ int parentTransparency = Integer.parseInt(((Species) element).getComplex().getTransparencyLevel());
+ assertEquals(
+ eu.getElementTag(element) + eu.getElementTag(((Species) element).getComplex())
+ + "Element should be directly visible when parent is transparent",
+ parentTransparency, visibilityLevel);
+ }
+ }
+ }
+ }
+
+ @Test
+ public void testLayerWithNotes() throws Exception {
+ Model model = getModelForFile("testFiles/layer_text_with_notes.xml");
+
+ new CreateHierarchyCommand(model, 4, 80).execute();
+
+ PathwayCompartment pathway = (PathwayCompartment) model.getCompartments().get(0);
+
+ assertEquals("test", pathway.getName());
+ assertEquals((Integer) 11, pathway.getZ());
+ assertEquals("5", pathway.getVisibilityLevel());
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
index e6fcbd17d99ec22b0142c65fd7b37b580fe951eb..ad1b8ef7b225d407017c4abdc245453cb35c6222 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java
@@ -25,6 +25,7 @@ import org.w3c.dom.Node;
import java.awt.Color;
import java.awt.geom.Rectangle2D;
import java.util.Collection;
+import java.util.HashSet;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
@@ -53,7 +54,7 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
assertNotNull(layers);
assertEquals(1, layers.size());
- xmlString = parser.layerCollectionToXml(layers);
+ xmlString = parser.layerCollectionToXml(layers, new HashSet<>());
node = getNodeFromXmlString(xmlString);
Collection<Layer> layers2 = parser.parseLayers(node);
assertNotNull(layers2);
@@ -119,7 +120,7 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
Layer layer = parser.getLayer(node);
assertNotNull(layer);
- xmlString = parser.layerToXml(layer);
+ xmlString = parser.layerToXml(layer, new HashSet<>());
node = getNodeFromXmlString(xmlString);
Layer layers2 = parser.getLayer(node);
assertNotNull(layers2);
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..adbeeabe2af42c1d37358a61b44d9936dac3637c
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ProjectExportTest.java
@@ -0,0 +1,257 @@
+package lcsb.mapviewer.converter.model.celldesigner;
+
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.converter.ComplexZipConverter;
+import lcsb.mapviewer.converter.ComplexZipConverterParams;
+import lcsb.mapviewer.converter.ProjectFactory;
+import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.ProjectComparator;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerImage;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import lcsb.mapviewer.model.overlay.GenericDataOverlayEntry;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+
+public class ProjectExportTest extends CellDesignerTestFunctions {
+
+ private final ProjectComparator projectComparator = new ProjectComparator();
+
+ private final ZipEntryFileFactory zefFactory = new ZipEntryFileFactory();
+
+ private ComplexZipConverter parser;
+ private ProjectFactory projectFactory;
+
+ @Before
+ public void setUp() throws Exception {
+ parser = new ComplexZipConverter(CellDesignerXmlParser.class);
+ projectFactory = new ProjectFactory(parser);
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testBasic() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ project.addModel(model);
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testWithManyModels() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ project.addModel(model);
+
+ Model model2 = createEmptyModel();
+ model2.setWidth(260);
+ model2.addElement(createProtein());
+ project.addModel(model2);
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, model2.getName()));
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testLinkToSubmodel() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ model.addElement(protein);
+ project.addModel(model);
+
+ Model model2 = createEmptyModel();
+ project.addModel(model2);
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, model2.getName()));
+ protein.setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, model2.getName()));
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testImmediateLink() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ protein.setImmediateLink("https://uni.lu/");
+ model.addElement(protein);
+ project.addModel(model);
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testGlyph() throws Exception {
+ Glyph glyph = createGlyph();
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ protein.setGlyph(glyph);
+ model.addElement(protein);
+ project.addModel(model);
+ project.addGlyph(glyph);
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testDataOverlay() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ model.addElement(protein);
+ project.addModel(model);
+
+ DataOverlay overlay = createDataOverlay();
+ overlay.setPublic(true);
+ overlay.addEntry(createDataOverlayEntry());
+ overlay.addEntry(createDataOverlayEntry());
+
+ project.addDataOverlay(overlay);
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testPrivateDataOverlay() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(260);
+ Protein protein = createProtein();
+ model.addElement(protein);
+ project.addModel(model);
+
+ DataOverlay overlay = createDataOverlay();
+ overlay.setPublic(false);
+ DataOverlayEntry entry = new GenericDataOverlayEntry();
+ entry.setName(protein.getName());
+ entry.setValue(faker.number().randomDouble(2, -1, 1));
+
+ project.addDataOverlay(overlay);
+
+ testSerializationOverZip(project, false);
+ }
+
+ private void testSerializationOverZip(final Project project) throws Exception {
+ testSerializationOverZip(project, true);
+ }
+
+ private void testSerializationOverZip(final Project project, final boolean shouldBeTheSame) throws Exception {
+ File tempFile = File.createTempFile("CD-", ".zip");
+ try (FileOutputStream outputStream = new FileOutputStream(tempFile)) {
+ byte[] data = projectFactory.project2zip(project);
+ outputStream.write(data);
+ }
+ final ComplexZipConverterParams complexParams = createDefaultParams(tempFile);
+ Project project2 = projectFactory.create(complexParams);
+
+ for (ModelData model : project.getModels()) {
+ clearModelFromZ(model);
+ }
+ for (ModelData model : project2.getModels()) {
+ new CreateHierarchyCommand(model.getModel(), 10, 1000).execute();
+ clearModelFromZ(model);
+ }
+
+ if (shouldBeTheSame) {
+ assertEquals(0, projectComparator.compare(project, project2));
+ } else {
+ assertNotEquals(0, projectComparator.compare(project, project2));
+ }
+ }
+
+ private ComplexZipConverterParams createDefaultParams(final File tempFile) throws IOException {
+ final ComplexZipConverterParams complexParams;
+ complexParams = new ComplexZipConverterParams().zipFile(new ZipFile(tempFile));
+ complexParams.visualizationDir(faker.name().username());
+
+ ZipFile zipFile = new ZipFile(tempFile.getAbsolutePath());
+ Enumeration<? extends ZipEntry> entries = zipFile.entries();
+ while (entries.hasMoreElements()) {
+ ZipEntry entry = entries.nextElement();
+ ZipEntryFile e = zefFactory.createZipEntryFile(entry, zipFile);
+ complexParams.entry(e);
+ }
+ zipFile.close();
+ return complexParams;
+ }
+
+ @Test
+ public void testLayerWithText() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(745);
+ model.setHeight(346);
+ Layer layer = createLayer();
+ LayerText layerText = createText();
+ layer.addLayerText(layerText);
+ model.addLayer(layer);
+
+ project.addModel(model);
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testLayerWithImage() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(745);
+ model.setHeight(346);
+ Layer layer = createLayer();
+ LayerImage image = createImage();
+ layer.addLayerImage(image);
+ model.addLayer(layer);
+
+ project.addModel(model);
+ project.addGlyph(image.getGlyph());
+
+ testSerializationOverZip(project);
+ }
+
+ @Test
+ public void testWithPathway() throws Exception {
+ Project project = createProject();
+ Model model = createEmptyModel();
+ model.setWidth(126);
+ model.setHeight(148);
+ PathwayCompartment pathway = createPathway();
+ model.addElement(pathway);
+
+ project.addModel(model);
+
+ testSerializationOverZip(project);
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SubModelCommandForCellDesignerFilesTest.java
similarity index 87%
rename from model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
rename to converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SubModelCommandForCellDesignerFilesTest.java
index 4086e83e143c69262d1f4046331d4c9aba6a3074..4fc38879370de39e73533cb3ca57194a2cc54faf 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/SubModelCommandTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/SubModelCommandForCellDesignerFilesTest.java
@@ -1,25 +1,26 @@
-package lcsb.mapviewer.commands;
+package lcsb.mapviewer.converter.model.celldesigner;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
+import lcsb.mapviewer.commands.MoveCommand;
+import lcsb.mapviewer.commands.SubModelCommand;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
import java.awt.geom.Path2D;
import java.awt.geom.Rectangle2D;
-import java.util.Arrays;
+import java.util.Collections;
import java.util.HashSet;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
-public class SubModelCommandTest extends CommandTestFunctions {
+public class SubModelCommandForCellDesignerFilesTest extends CellDesignerTestFunctions {
- private ModelComparator comparator = new ModelComparator();
+ private final ModelComparator comparator = new ModelComparator();
@Before
public void setUp() throws Exception {
@@ -31,7 +32,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodel1() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 0);
@@ -48,7 +49,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodel2() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(50, 50);
@@ -65,7 +66,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodelWithDisableStrictCutoof() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(50, 50);
@@ -82,7 +83,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodel3() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 200);
@@ -108,7 +109,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
assertEquals(model.getReactionByReactionId("re3").getLines().get(0).getY2(),
copy.getReactionByReactionId("re3").getLines().get(0).getY2() - dy, EPSILON);
- Model copy2 = serializeViaCellDesigner(copy);
+ Model copy2 = serializeModel(copy);
// check if after conversion to xml everything works
assertEquals(0, comparator.compare(copy, copy2));
@@ -116,7 +117,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodelWithoutCompartments() throws Exception {
- Model model = getModelForFile("testFiles/compartments.xml", true);
+ Model model = getModelForFile("testFiles/compartments.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 10);
@@ -128,13 +129,13 @@ public class SubModelCommandTest extends CommandTestFunctions {
Model copy = new SubModelCommand(model, polygon).execute();
// we should cut off some of compartments
- assertFalse(model.getLayers().iterator().next().getTexts().size() == copy.getLayers().iterator().next().getTexts()
+ assertNotEquals(model.getLayers().iterator().next().getTexts().size(), copy.getLayers().iterator().next().getTexts()
.size());
}
@Test
public void testGetSubmodelWithoutCompartments2() throws Exception {
- Model model = getModelForFile("testFiles/problematic/cutting_without_compartment.xml", true);
+ Model model = getModelForFile("testFiles/problematic/cutting_without_compartment.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 0);
@@ -145,14 +146,14 @@ public class SubModelCommandTest extends CommandTestFunctions {
Model copy = new SubModelCommand(model, polygon).execute();
- Model model2 = serializeViaCellDesigner(copy);
+ Model model2 = serializeModel(copy);
assertEquals(0, comparator.compare(copy, model2));
}
@Test
public void testGetSubmodelWithElementIds() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 0);
@@ -162,7 +163,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
polygon.closePath();
model.getElementByElementId("sa2").setId(-2);
- Model copy = new SubModelCommand(model, polygon, new HashSet<>(Arrays.asList(-2)), new HashSet<>()).execute();
+ Model copy = new SubModelCommand(model, polygon, new HashSet<>(Collections.singletonList(-2)), new HashSet<>()).execute();
assertEquals(1, copy.getElements().size());
assertEquals(0, copy.getReactions().size());
@@ -170,7 +171,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodelWithElementIdsAndTextArea() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 0);
@@ -185,7 +186,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
layer.addLayerText(text);
model.addLayer(layer);
- Model copy = new SubModelCommand(model, polygon, new HashSet<>(Arrays.asList(-2)), new HashSet<>()).execute();
+ Model copy = new SubModelCommand(model, polygon, new HashSet<>(Collections.singletonList(-2)), new HashSet<>()).execute();
assertEquals(1, copy.getElements().size());
assertEquals(0, copy.getReactions().size());
@@ -195,7 +196,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodelWithEmptyElementIds() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", true);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 0);
@@ -212,7 +213,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
@Test
public void testGetSubmodelWithReactionIds() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
+ Model model = getModelForFile("testFiles/spliting_test_Case.xml");
Path2D polygon = new Path2D.Double();
polygon.moveTo(0, 0);
@@ -222,7 +223,7 @@ public class SubModelCommandTest extends CommandTestFunctions {
polygon.closePath();
model.getReactions().iterator().next().setId(-2);
- Model copy = new SubModelCommand(model, polygon, new HashSet<>(), new HashSet<>(Arrays.asList(-2)), true).execute();
+ Model copy = new SubModelCommand(model, polygon, new HashSet<>(), new HashSet<>(Collections.singletonList(-2)), true).execute();
assertEquals(1, copy.getReactions().size());
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java
deleted file mode 100644
index 11cae750b81fcdec6a41d8ed846df7a0a284b9ef..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ReactionCellDesignerConverterTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- ReactionCellDesignerConverter onverter = new ReactionCellDesignerConverter();
- assertNotNull(onverter);
- }
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
index 2ba3323171ff82597c0bc5846d1babc63dbf264a..b4fae845cb49872b844fc677325bb95ad64fdbc5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
@@ -1,12 +1,13 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import static org.junit.Assert.assertNotNull;
-
+import lcsb.mapviewer.commands.layout.ModifierType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import static org.junit.Assert.assertNotNull;
+
public class ModifierTypeTest {
@AfterClass
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
index 618b51764663b91eade984b99c88bd1ffc63e916..5c3d102141a44a0ba848a101f22e7765bf88ae1c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
@@ -1,17 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -21,12 +10,23 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.awt.geom.Point2D;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
public class ModifierTypeUtilsTest extends CellDesignerTestFunctions {
- private ModifierTypeUtils utils = new ModifierTypeUtils();
+ private final ModifierTypeUtils utils = new ModifierTypeUtils();
- private Modifier invalidModifier = Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS);
+ private final Modifier invalidModifier = Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS);
@AfterClass
public static void tearDownAfterClass() throws Exception {
diff --git a/model-command/testFiles/artifitial_compartments.xml b/converter-CellDesigner/testFiles/artificial_compartments.xml
similarity index 99%
rename from model-command/testFiles/artifitial_compartments.xml
rename to converter-CellDesigner/testFiles/artificial_compartments.xml
index 069038f3620c28f7a4888409bdfc09b11b4fc302..d5901ee7b48882009c49a5803ef1b3e07f3c8959 100644
--- a/model-command/testFiles/artifitial_compartments.xml
+++ b/converter-CellDesigner/testFiles/artificial_compartments.xml
@@ -146,7 +146,7 @@
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers>
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:layer id="1" name="pathways" locked="false" visible="true">
<celldesigner:listOfTexts>
<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
<celldesigner:layerNotes>
diff --git a/model-command/testFiles/coloring_model.xml b/converter-CellDesigner/testFiles/coloring_model.xml
similarity index 100%
rename from model-command/testFiles/coloring_model.xml
rename to converter-CellDesigner/testFiles/coloring_model.xml
diff --git a/model-command/testFiles/compartments.xml b/converter-CellDesigner/testFiles/compartments.xml
similarity index 100%
rename from model-command/testFiles/compartments.xml
rename to converter-CellDesigner/testFiles/compartments.xml
diff --git a/model-command/testFiles/complex_with_state.xml b/converter-CellDesigner/testFiles/complex_with_state.xml
similarity index 100%
rename from model-command/testFiles/complex_with_state.xml
rename to converter-CellDesigner/testFiles/complex_with_state.xml
diff --git a/model-command/testFiles/custom_semantic_zooming.xml b/converter-CellDesigner/testFiles/custom_semantic_zooming.xml
similarity index 100%
rename from model-command/testFiles/custom_semantic_zooming.xml
rename to converter-CellDesigner/testFiles/custom_semantic_zooming.xml
diff --git a/model-command/testFiles/cyclic_hierarchy_problem.xml b/converter-CellDesigner/testFiles/cyclic_hierarchy_problem.xml
similarity index 100%
rename from model-command/testFiles/cyclic_hierarchy_problem.xml
rename to converter-CellDesigner/testFiles/cyclic_hierarchy_problem.xml
diff --git a/converter-CellDesigner/testFiles/glyphs/uni.png b/converter-CellDesigner/testFiles/glyphs/uni.png
new file mode 100644
index 0000000000000000000000000000000000000000..fd325269723c196ab52460e32a904db0e3bdc46f
Binary files /dev/null and b/converter-CellDesigner/testFiles/glyphs/uni.png differ
diff --git a/model-command/testFiles/kinetics_with_compartment.xml b/converter-CellDesigner/testFiles/kinetics_with_compartment.xml
similarity index 100%
rename from model-command/testFiles/kinetics_with_compartment.xml
rename to converter-CellDesigner/testFiles/kinetics_with_compartment.xml
diff --git a/model-command/testFiles/layer_text_with_notes.xml b/converter-CellDesigner/testFiles/layer_text_with_notes.xml
similarity index 97%
rename from model-command/testFiles/layer_text_with_notes.xml
rename to converter-CellDesigner/testFiles/layer_text_with_notes.xml
index 426b06f1c1bfce645530b256c8fc91b30ce355e8..8a2696938d2f49f8bf753791dcc11cc26cce8691 100644
--- a/model-command/testFiles/layer_text_with_notes.xml
+++ b/converter-CellDesigner/testFiles/layer_text_with_notes.xml
@@ -36,7 +36,7 @@
<celldesigner:listOfRNAs/>
<celldesigner:listOfAntisenseRNAs/>
<celldesigner:listOfLayers>
-<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:layer id="1" name="pathways" locked="false" visible="true">
<celldesigner:listOfTexts>
<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
<celldesigner:layerNotes>
diff --git a/model-command/testFiles/nested_test.xml b/converter-CellDesigner/testFiles/nested_test.xml
similarity index 100%
rename from model-command/testFiles/nested_test.xml
rename to converter-CellDesigner/testFiles/nested_test.xml
diff --git a/model-command/testFiles/problematic/cutting_without_compartment.xml b/converter-CellDesigner/testFiles/problematic/cutting_without_compartment.xml
similarity index 100%
rename from model-command/testFiles/problematic/cutting_without_compartment.xml
rename to converter-CellDesigner/testFiles/problematic/cutting_without_compartment.xml
diff --git a/model-command/testFiles/problematic/disconnected_child_in_complex.xml b/converter-CellDesigner/testFiles/problematic/disconnected_child_in_complex.xml
similarity index 100%
rename from model-command/testFiles/problematic/disconnected_child_in_complex.xml
rename to converter-CellDesigner/testFiles/problematic/disconnected_child_in_complex.xml
diff --git a/model-command/testFiles/problematic_description.xml b/converter-CellDesigner/testFiles/problematic_description.xml
similarity index 100%
rename from model-command/testFiles/problematic_description.xml
rename to converter-CellDesigner/testFiles/problematic_description.xml
diff --git a/model-command/testFiles/reactions_to_color.xml b/converter-CellDesigner/testFiles/reactions_to_color.xml
similarity index 100%
rename from model-command/testFiles/reactions_to_color.xml
rename to converter-CellDesigner/testFiles/reactions_to_color.xml
diff --git a/model-command/testFiles/spliting_test_Case.xml b/converter-CellDesigner/testFiles/spliting_test_Case.xml
similarity index 100%
rename from model-command/testFiles/spliting_test_Case.xml
rename to converter-CellDesigner/testFiles/spliting_test_Case.xml
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
index 7d132fdae47a1626351621690d24e79b0132510d..20445f8986f08fe24f8359289b0b8c49e9f607c5 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlConverter.java
@@ -1,11 +1,19 @@
package lcsb.mapviewer.converter.model.sbgnml;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.StringWriter;
-import java.util.Arrays;
-import java.util.List;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.common.MinervaLoggerAppender;
+import lcsb.mapviewer.converter.Converter;
+import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.modelutils.map.LogFormatter;
+import org.apache.commons.io.output.ByteArrayOutputStream;
+import org.sbgn.SbgnUtil;
+import org.sbgn.bindings.Sbgn;
+import org.springframework.stereotype.Component;
+import org.w3c.dom.Document;
import javax.xml.XMLConstants;
import javax.xml.parsers.DocumentBuilderFactory;
@@ -18,30 +26,17 @@ import javax.xml.transform.TransformerFactory;
import javax.xml.transform.dom.DOMSource;
import javax.xml.transform.stream.StreamResult;
import javax.xml.transform.stream.StreamSource;
-
-import org.apache.commons.io.output.ByteArrayOutputStream;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.sbgn.SbgnUtil;
-import org.sbgn.bindings.Sbgn;
-import org.springframework.stereotype.Component;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.modelutils.map.LogFormatter;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringWriter;
+import java.util.Collections;
+import java.util.List;
@Component
public class SbgnmlXmlConverter extends Converter {
- @SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger();
+ private final NotesConverter notesConverter = new NotesConverter();
@Override
public Model createModel(final ConverterParams params) throws InvalidInputDataExecption, ConverterException {
@@ -72,13 +67,13 @@ public class SbgnmlXmlConverter extends Converter {
Templates template = factory
.newTemplates(new StreamSource(classLoader.getResourceAsStream("rename_id_list_attribute.xsl")));
- Transformer xformer = template.newTransformer();
+ Transformer transformer = template.newTransformer();
ByteArrayOutputStream output = new ByteArrayOutputStream();
Source source = new StreamSource(inputStream);
Result result = new StreamResult(output);
- xformer.transform(source, result);
+ transformer.transform(source, result);
return inputStream2File(output.toInputStream());
} catch (final Exception e) {
@@ -96,13 +91,14 @@ public class SbgnmlXmlConverter extends Converter {
exportedData = exporter.toSbgnml(model);
if (!appender.getWarnings().isEmpty()) {
for (final String entry : new LogFormatter().createFormattedWarnings(appender.getWarnings())) {
- notes.append("\n" + entry);
+ notes.append("\n").append(entry);
}
}
} finally {
MinervaLoggerAppender.unregisterLogEventStorage(appender);
}
try {
+ exportedData.setNotes(notesConverter.createNotesNode(notes.toString()));
ByteArrayOutputStream baos = new ByteArrayOutputStream();
SbgnUtil.writeTo(exportedData, baos);
@@ -113,23 +109,12 @@ public class SbgnmlXmlConverter extends Converter {
.newDocumentBuilder()
.parse(baos.toInputStream());
- if (notes.length() > 0) {
- Element bodyNode = input.createElement("body");
- bodyNode.setAttribute("xmlns", "http://www.w3.org/1999/xhtml");
- bodyNode.setTextContent(notes.toString());
-
- Element notesNode = input.createElement("notes");
- notesNode.appendChild(bodyNode);
-
- input.getFirstChild().insertBefore(notesNode, input.getFirstChild().getFirstChild());
- }
-
TransformerFactory transformerFactory = TransformerFactory.newInstance();
transformerFactory.setFeature(XMLConstants.FEATURE_SECURE_PROCESSING, true);
- Transformer xformer = transformerFactory.newTransformer();
- xformer.setOutputProperty(OutputKeys.INDENT, "yes");
+ Transformer transformer = transformerFactory.newTransformer();
+ transformer.setOutputProperty(OutputKeys.INDENT, "yes");
StringWriter output = new StringWriter();
- xformer.transform(new DOMSource(input), new StreamResult(output));
+ transformer.transform(new DOMSource(input), new StreamResult(output));
return output.toString();
} catch (final Exception e) {
@@ -149,7 +134,7 @@ public class SbgnmlXmlConverter extends Converter {
@Override
public List<String> getFileExtensions() {
- return Arrays.asList("sbgn");
+ return Collections.singletonList("sbgn");
}
}
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index 62c8aadb932f260acf9db8c0c97e42e31856968f..4bd341bd1195569e94dc0afbc68455a9adcdddd7 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -4,7 +4,6 @@ import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.ColorParser;
import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.graphics.bioentity.reaction.ReactionConverter;
import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
import lcsb.mapviewer.model.LogMarker;
@@ -69,6 +68,7 @@ import lcsb.mapviewer.model.map.species.field.AbstractSiteModification;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.StructuralState;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.commons.lang3.RandomStringUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.LogManager;
@@ -178,7 +178,7 @@ public class SbgnmlXmlExporter {
* Transforms model into SBGN-ML xml.
*
* @param model model that should be transformed
- * @return SBGM-ML xml string for the model
+ * @return SBGN-ML xml string for the model
*/
public Sbgn toSbgnml(final Model model) throws ConverterException {
// Reset global variables
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
index c179bc2dccbf40b79f974328aabf46cbb3f89d09..5c0f2292db2e90505aaca29dde4d20a95c0ea82d 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java
@@ -3,8 +3,6 @@ package lcsb.mapviewer.converter.model.sbgnml;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ZIndexPopulator;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.sbgnml.parser.ElementParser;
import lcsb.mapviewer.converter.model.sbgnml.parser.NotesConverter;
import lcsb.mapviewer.converter.model.sbgnml.parser.ReactionParser;
@@ -22,6 +20,8 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
+import lcsb.mapviewer.utils.ZIndexPopulator;
import org.apache.commons.io.FilenameUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
index 012543645c8644136e7c49724a9a31a60094f604..4a21fe5899001806b22267c5dff7af64ea216833 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ElementParser.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.sbgnml.parser;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
import lcsb.mapviewer.converter.model.sbgnml.SbgnLogMarker;
import lcsb.mapviewer.converter.model.sbgnml.parser.newt.NewtExtension;
@@ -32,6 +31,7 @@ import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithStructuralState;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.sbgn.GlyphClazz;
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java
index 4db5742a0d245cab88137dbd7cc21491f6429335..199aafcf86903a27c025981e79f53becd1925b99 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/NotesConverter.java
@@ -2,7 +2,7 @@ package lcsb.mapviewer.converter.model.sbgnml.parser;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
+import lcsb.mapviewer.utils.RestAnnotationParser;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.sbgn.bindings.SBGNBase;
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java
index b5a6aa6121488755acb1ba45a78ea44bd4480ae2..03337681a024fddf737c4fea9ed9a6f686625e0b 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java
@@ -1,12 +1,12 @@
package lcsb.mapviewer.converter.model.sbgnml.parser;
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.sbgnml.SbgnLogMarker;
import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
import lcsb.mapviewer.model.LogMarker;
@@ -61,23 +61,23 @@ public class ReactionParser extends GlyphParser {
/**
* List of all logic operator glyphs parsed so far.
*/
- private List<Glyph> logicOperators = new ArrayList<>();
+ private final List<Glyph> logicOperators = new ArrayList<>();
/**
* List of all processes to be parsed.
*/
- private List<Process> processes = new ArrayList<>();
+ private final List<Process> processes = new ArrayList<>();
/**
* List of all logic arcs parsed so far.
*/
- private List<Arc> logicArcs = new ArrayList<>();
+ private final List<Arc> logicArcs = new ArrayList<>();
private final PointTransformation pt = new PointTransformation();
- private RenderParser renderParser;
+ private final RenderParser renderParser;
- private Model model;
+ private final Model model;
public ReactionParser(final RenderParser renderParser, final Model model) {
this.renderParser = renderParser;
@@ -160,7 +160,7 @@ public class ReactionParser extends GlyphParser {
public Reaction parseProcess(final Process p) throws Exception {
if (p.getProductArcs().isEmpty()) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, p, model),
- "The process must have at least one outgoing arc.");
+ "The process must have at least one outgoing arc.");
return null;
}
@@ -223,7 +223,7 @@ public class ReactionParser extends GlyphParser {
for (final Arc a : p.getProductArcs()) {
if (Objects.equals(getSourcePort(a), p.getProductsPort()) && ports.size() == 2
- || reaction.getProducts().size() == 0) {
+ || reaction.getProducts().size() == 0) {
Glyph target = getTargetGlyph(a);
Product product = new Product(model.getElementByElementId(target.getId()));
List<Point2D> pointList = getLinePoints(a);
@@ -255,13 +255,13 @@ public class ReactionParser extends GlyphParser {
boolean shouldReverse = reaction.getProducts().size() > 1;
for (final Product product : reaction.getProducts()) {
if (product.getLine().getStartPoint().distance(firstProduct.getLine().getStartPoint()) < Configuration.EPSILON
- && product.getLine().getEndPoint().distance(firstProduct.getLine().getEndPoint()) > Configuration.EPSILON) {
+ && product.getLine().getEndPoint().distance(firstProduct.getLine().getEndPoint()) > Configuration.EPSILON) {
shouldReverse = false;
}
}
if (shouldReverse) {
logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "process-arcs", p.getCentralPoint().getId(),
- model.getIdModel()), "Product lines should be reversed");
+ model.getIdModel()), "Product lines should be reversed");
for (final Product product : reaction.getProducts()) {
List<Line2D> lines = new ArrayList<>(product.getLine().getLines());
product.getLine().removeLines();
@@ -371,10 +371,10 @@ public class ReactionParser extends GlyphParser {
Point2D portPoint;
if (p.getReagentArcs().size() > 1) {
portPoint = new Point2D.Double(p.getReagentArcs().get(0).getEnd().getX(),
- p.getReagentArcs().get(0).getEnd().getY());
+ p.getReagentArcs().get(0).getEnd().getY());
} else {
portPoint = new Point2D.Double(p.getRevReagentArcs().get(0).getStart().getX(),
- p.getRevReagentArcs().get(0).getStart().getY());
+ p.getRevReagentArcs().get(0).getStart().getY());
}
PolylineData line = new PolylineData(portPoint, centerOfReactionPoint);
ArrowTypeData atd = new ArrowTypeData();
@@ -400,10 +400,10 @@ public class ReactionParser extends GlyphParser {
Point2D portPoint;
if (!p.isReversible()) {
portPoint = new Point2D.Double(p.getProductArcs().get(0).getStart().getX(),
- p.getProductArcs().get(0).getStart().getY());
+ p.getProductArcs().get(0).getStart().getY());
} else {
portPoint = new Point2D.Double(p.getRevProductArcs().get(0).getStart().getX(),
- p.getRevProductArcs().get(0).getStart().getY());
+ p.getRevProductArcs().get(0).getStart().getY());
}
PolylineData line = new PolylineData(portPoint, centerOfReactionPoint);
ArrowTypeData atd = new ArrowTypeData();
@@ -423,7 +423,7 @@ public class ReactionParser extends GlyphParser {
* @throws Exception thrown when parsed logic operator is invalid
*/
private void parseLogicOperator(final Arc arc, final Reaction reaction, final NodeOperator targetOperator)
- throws Exception {
+ throws Exception {
Port operatorPort = (Port) arc.getSource();
Glyph logicOperator = null;
for (final Glyph lo : getLogicOperators()) {
@@ -439,8 +439,8 @@ public class ReactionParser extends GlyphParser {
// inputs of Species
final Glyph tempLogicOperator = logicOperator;
boolean isCellDesignerValidLogicOperator = logicArcs.stream()
- .filter(a -> tempLogicOperator.getPort().contains(a.getTarget()) && !(a.getSource() instanceof Port))
- .count() == 2;
+ .filter(a -> tempLogicOperator.getPort().contains(a.getTarget()) && !(a.getSource() instanceof Port))
+ .count() == 2;
if (!isCellDesignerValidLogicOperator) {
throw new InvalidArgumentException("Parsed operator is not valid for CellDesigner: " + logicOperator.getId());
}
@@ -455,7 +455,7 @@ public class ReactionParser extends GlyphParser {
break;
case NOT:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, logicOperator, model),
- "NOT gates are not implemented in the platform.");
+ "NOT gates are not implemented in the platform.");
return;
default:
throw new InvalidArgumentException("Wrong logic operator class.");
@@ -463,8 +463,8 @@ public class ReactionParser extends GlyphParser {
// Parse line from arc and operator glyph
Point2D operatorCenterPoint = new Point2D.Double(
- logicOperator.getBbox().getX() + logicOperator.getBbox().getW() / 2,
- logicOperator.getBbox().getY() + logicOperator.getBbox().getH() / 2);
+ logicOperator.getBbox().getX() + logicOperator.getBbox().getW() / 2,
+ logicOperator.getBbox().getY() + logicOperator.getBbox().getH() / 2);
List<Point2D> linePoints = getLinePoints(arc);
new ArrayList<Point2D>();
@@ -507,7 +507,7 @@ public class ReactionParser extends GlyphParser {
if (logicArc.getSource() instanceof Port) {
// The arc has source in logic operator
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, logicArc, model),
- "Logic operators trees are not compatible with CellDesigner. Therefore they are not supported.");
+ "Logic operators trees are not compatible with CellDesigner. Therefore they are not supported.");
continue;
// parseLogicOperator(logicArc, reaction, modifierClass,
// operator, model);
@@ -541,11 +541,11 @@ public class ReactionParser extends GlyphParser {
switch (ac) {
case ABSOLUTE_INHIBITION:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model),
- ac + " modifier is not supported. Changing to " + Inhibition.class.getSimpleName());
+ ac + " modifier is not supported. Changing to " + Inhibition.class.getSimpleName());
return new Inhibition(element);
case ABSOLUTE_STIMULATION:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model),
- ac + " modifier is not supported. Changing to " + PhysicalStimulation.class.getSimpleName());
+ ac + " modifier is not supported. Changing to " + PhysicalStimulation.class.getSimpleName());
return new PhysicalStimulation(element);
case CATALYSIS:
return new Catalysis(element);
@@ -628,7 +628,7 @@ public class ReactionParser extends GlyphParser {
switch (ArcClazz.fromClazz(arc.getClazz())) {
case PRODUCTION:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model),
- "Activity flow arc type is invalid. Changing to " + StateTransitionReaction.class.getSimpleName());
+ "Activity flow arc type is invalid. Changing to " + StateTransitionReaction.class.getSimpleName());
result = new StateTransitionReaction(arc.getId());
break;
default:
@@ -797,7 +797,7 @@ public class ReactionParser extends GlyphParser {
if (productPointList.size() == 3) {
if (productPointList.get(0).distance(productPointList.get(1)) > productPointList.get(1)
- .distance(productPointList.get(2))) {
+ .distance(productPointList.get(2))) {
Point2D newPoint = pt.getPointOnLine(productPointList.get(0), productPointList.get(1), 0.5);
productPointList.add(1, newPoint);
} else {
@@ -816,12 +816,12 @@ public class ReactionParser extends GlyphParser {
reactant.setLine(reactantLine);
PolylineData centerLine = new PolylineData(productPointList.subList(reactantPointEnds, productPointStarts + 1))
- .copy();
+ .copy();
reaction.setLine(centerLine);
ArrowTypeData productAtd = extractArrowTypeDataFromArc(arc);
PolylineData productLine = new PolylineData(
- productPointList.subList(productPointStarts, productPointList.size())).copy();
+ productPointList.subList(productPointStarts, productPointList.size())).copy();
productLine.setEndAtd(productAtd);
product.setLine(productLine);
@@ -935,19 +935,19 @@ public class ReactionParser extends GlyphParser {
return parsePhenotypeArc(a);
} catch (Exception e) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model), "Probelm with importing arc",
- e);
+ e);
}
break;
}
if (a.getSource() instanceof Glyph) {
Glyph sourceGlyph = (Glyph) a.getSource();
if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)
- && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
+ && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
try {
return parsePhenotypeArc(a);
} catch (InvalidArgumentException ex) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "The arc is not a valid reduced notation arc.", ex);
+ "The arc is not a valid reduced notation arc.", ex);
}
break;
}
@@ -962,7 +962,7 @@ public class ReactionParser extends GlyphParser {
}
if (!found) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "Expected PHENOTYPE in reduced notation arc. Arc skipped.");
+ "Expected PHENOTYPE in reduced notation arc. Arc skipped.");
}
break;
} else {
@@ -984,13 +984,13 @@ public class ReactionParser extends GlyphParser {
}
if (!found) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "Cannot find a target for arc: " + a.getId() + ". Skipping");
+ "Cannot find a target for arc: " + a.getId() + ". Skipping");
}
}
break;
default:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "The arc has not been parsed, since it is invalid for SBGN PD map.");
+ "The arc has not been parsed, since it is invalid for SBGN PD map.");
}
return null;
}
diff --git a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
index df9a04f21c3860e441263d6a336af9fed10741a9..3a08e727ca55641d2a3194ac9a5cf32fecca530c 100644
--- a/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
+++ b/converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/AbstractImageGenerator.java
@@ -1,24 +1,6 @@
package lcsb.mapviewer.converter.graphics;
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.geom.Line2D;
-import java.awt.geom.Rectangle2D;
-import java.io.File;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.nio.file.FileStore;
-import java.nio.file.Files;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Objects;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.commands.ColorExtractor;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.commands.SemanticZoomLevelMatcher;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.MimeType;
@@ -35,7 +17,6 @@ import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.Drawable;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
@@ -46,6 +27,21 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.geom.Line2D;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.FileStore;
+import java.nio.file.Files;
+import java.util.ArrayList;
+import java.util.List;
/**
* This class is responsible for creation of the image from the model. It's an
@@ -78,9 +74,8 @@ import lcsb.mapviewer.model.overlay.DataOverlayEntry;
* from graphics2D and save it into separate files</li>
* </ul>
* </p>
- *
+ *
* @author Piotr Gawron
- *
*/
public abstract class AbstractImageGenerator {
@@ -99,13 +94,13 @@ public abstract class AbstractImageGenerator {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Class that allows to check if element is visible (or transparent) when
* drawing. It's used to filter out invisible elements when drawing
* semantic/hierarchy view.
*/
- private SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
+ private final SemanticZoomLevelMatcher zoomLevelMatcher = new SemanticZoomLevelMatcher();
/**
* On which level in hierarchical view we should visualize map.
*/
@@ -145,11 +140,8 @@ public abstract class AbstractImageGenerator {
* {@link lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params
* params}.
*
- * @param params
- * list of all params to create appropriate image
- * @throws DrawingException
- * thrown when there was a problem with drawing a map
- *
+ * @param params list of all params to create appropriate image
+ * @throws DrawingException thrown when there was a problem with drawing a map
*/
protected AbstractImageGenerator(final Params params) {
this.params = params;
@@ -167,18 +159,15 @@ public abstract class AbstractImageGenerator {
* This method creates a graphics object for different implementations of
* canvas with fixed width and height.
*
- * @param width
- * width of the canvas (graphics2d) to be created
- * @param height
- * height of the canvas (graphics2d) to be created
+ * @param width width of the canvas (graphics2d) to be created
+ * @param height height of the canvas (graphics2d) to be created
*/
protected abstract void createImageObject(final double width, final double height);
/**
* Draw a model into {@link #getGraphics()} object.
- *
- * @throws DrawingException
- * thrown when there is a problem with drawing
+ *
+ * @throws DrawingException thrown when there is a problem with drawing
*/
protected void draw() throws DrawingException {
if (isDrawn()) {
@@ -248,21 +237,8 @@ public abstract class AbstractImageGenerator {
}
private List<Drawable> getDrawables() {
- boolean isOriginallyVisible = false;
- for (Layer layer : params.getModel().getLayers()) {
- if (Objects.deepEquals(layer.getName(), CreateHierarchyCommand.TEXT_LAYER_NAME)) {
- isOriginallyVisible = layer.isVisible();
- layer.setVisible(true);
- }
- }
List<Drawable> drawables = new ArrayList<>(params.getModel().getDrawables(true));
drawables.sort(BioEntity.Z_INDEX_COMPARATOR);
- for (Layer layer : params.getModel().getLayers()) {
- if (Objects.deepEquals(layer.getName(), CreateHierarchyCommand.TEXT_LAYER_NAME)) {
- // revert change that was required to obtain drawables with text layer
- layer.setVisible(isOriginallyVisible);
- }
- }
return drawables;
}
@@ -300,10 +276,8 @@ public abstract class AbstractImageGenerator {
/**
* This method draw a {@link Compartment} on a graphics.
*
- * @param compartment
- * object that we want to draw
- * @throws DrawingException
- * thrown when there was a problem with drawing {@link Compartment}
+ * @param compartment object that we want to draw
+ * @throws DrawingException thrown when there was a problem with drawing {@link Compartment}
*/
protected void drawCompartment(final Compartment compartment) throws DrawingException {
// get a converter for this compartment
@@ -328,10 +302,8 @@ public abstract class AbstractImageGenerator {
/**
* This method draw a {@link Species} on a graphics.
*
- * @param species
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Species}
+ * @param species object to be drawn
+ * @throws DrawingException thrown when there was a problem with drawing a {@link Species}
*/
protected void drawSpecies(final Species species) throws DrawingException {
if (!cross(species.getBorder())) {
@@ -368,10 +340,8 @@ public abstract class AbstractImageGenerator {
/**
* This method draw a reaction on a graphics.
*
- * @param reaction
- * object to be drawn
- * @throws DrawingException
- * thrown when there was a problem with drawing a {@link Reaction}
+ * @param reaction object to be drawn
+ * @throws DrawingException thrown when there was a problem with drawing a {@link Reaction}
*/
protected void drawReaction(final Reaction reaction) throws DrawingException {
if (!cross(reaction.getLines())) {
@@ -385,8 +355,7 @@ public abstract class AbstractImageGenerator {
/**
* Checks if one of the lines in parameter cross the frame.
*
- * @param lines
- * list of lines to check
+ * @param lines list of lines to check
* @return true if the cross point exist, false otherwise
*/
private boolean cross(final List<Line2D> lines) {
@@ -402,8 +371,7 @@ public abstract class AbstractImageGenerator {
* Checks if the rectangle in the parameters cross the fram in which we are
* currently draw image.
*
- * @param rect
- * rectangle to check
+ * @param rect rectangle to check
* @return true if rectangle check the frame, false otherwise
*/
protected boolean cross(final Rectangle2D rect) {
@@ -418,8 +386,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param graphics
- * the graphics to set
+ * @param graphics the graphics to set
*/
protected void setGraphics(final Graphics2D graphics) {
this.graphics = graphics;
@@ -428,12 +395,9 @@ public abstract class AbstractImageGenerator {
/**
* Saves generated image into file.
*
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param fileName file where the images should be saved
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void saveToFile(final String fileName) throws IOException, DrawingException {
if (!isDrawn()) {
@@ -446,24 +410,18 @@ public abstract class AbstractImageGenerator {
/**
* Saves generated image from {@link #getGraphics()} into file.
*
- * @param fileName
- * file where the images should be saved
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param fileName file where the images should be saved
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
protected abstract void saveToFileImplementation(final String fileName) throws IOException;
/**
* Saves generated image into {@link OutputStream}.
*
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @throws IOException thrown when there is problem with output stream
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void saveToOutputStream(final OutputStream os) throws IOException, DrawingException {
if (!isDrawn()) {
@@ -476,32 +434,22 @@ public abstract class AbstractImageGenerator {
* Saves generated image from {@link #getGraphics()} into {@link OutputStream}
* .
*
- * @param os
- * stream where the images should be saved
- * @throws IOException
- * thrown when there is problem with output stream
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @throws IOException thrown when there is problem with output stream
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
protected abstract void saveToOutputStreamImplementation(final OutputStream os) throws IOException;
/**
* Saves part of the generated image file.
*
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param fileName file where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void savePartToFile(final int x, final int y, final int width, final int height, final String fileName)
throws IOException, DrawingException {
@@ -525,42 +473,29 @@ public abstract class AbstractImageGenerator {
/**
* Saves part of the generated image from {@link #getGraphics()} into file.
*
- * @param fileName
- * file where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
+ * @param fileName file where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
*/
protected abstract void savePartToFileImplementation(final int x, final int y, final int width, final int height,
- final String fileName) throws IOException;
+ final String fileName) throws IOException;
/**
* Saves part of the generated image into {@link OutputStream}.
*
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
public final void savePartToOutputStream(final int x, final int y, final int width, final int height,
- final OutputStream os) throws IOException, DrawingException {
+ final OutputStream os) throws IOException, DrawingException {
if (!isDrawn()) {
draw();
}
@@ -571,23 +506,16 @@ public abstract class AbstractImageGenerator {
* Saves part of the generated image from {@link #getGraphics()} into
* {@link OutputStream}.
*
- * @param os
- * stream where the images should be saved
- * @param x
- * x left margin of the image part
- * @param y
- * y top margin of the image part
- * @param width
- * width of the image part
- * @param height
- * height of the image part
- * @throws IOException
- * thrown when there is problem with output file
- * @throws DrawingException
- * thrown when there was a problem with drawing map
+ * @param os stream where the images should be saved
+ * @param x x left margin of the image part
+ * @param y y top margin of the image part
+ * @param width width of the image part
+ * @param height height of the image part
+ * @throws IOException thrown when there is problem with output file
+ * @throws DrawingException thrown when there was a problem with drawing map
*/
protected abstract void savePartToOutputStreamImplementation(final int x, final int y, final int width,
- final int height, final OutputStream os) throws IOException;
+ final int height, final OutputStream os) throws IOException;
/**
* Returns name of the format to which this graphic converter will transform.
@@ -600,8 +528,7 @@ public abstract class AbstractImageGenerator {
* Returns {@link MimeType} that should be used for files generated by this
* image generator.
*
- * @return {@link MimeType} that should be used for files generated by this
- * image generator
+ * @return {@link MimeType} that should be used for files generated by this image generator
*/
public abstract MimeType getMimeType();
@@ -620,8 +547,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param sbgnFormat
- * the sbgnFormat to set
+ * @param sbgnFormat the sbgnFormat to set
*/
protected void sbgnFormat(final boolean sbgnFormat) {
this.sbgnFormat = sbgnFormat;
@@ -636,8 +562,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param drawn
- * the drawn to set
+ * @param drawn the drawn to set
* @see #drawn
*/
private void setDrawn(final boolean drawn) {
@@ -653,8 +578,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param params
- * the params to set
+ * @param params the params to set
* @see #params
*/
protected void setParams(final Params params) {
@@ -665,7 +589,6 @@ public abstract class AbstractImageGenerator {
* This class contains a list of params that are used for drawing.
*
* @author Piotr Gawron
- *
*/
public static class Params {
@@ -740,9 +663,8 @@ public abstract class AbstractImageGenerator {
* single layout. In this map we have pairs between {@link Element}/
* {@link Reaction} and {@link DataOverlayEntry} used to visualize the
* element.
- *
*/
- private List<List<Pair<? extends BioEntity, DataOverlayEntry>>> visibleDataOverlays = new ArrayList<>();
+ private final List<List<Pair<? extends BioEntity, DataOverlayEntry>>> visibleDataOverlays = new ArrayList<>();
/**
* Color that should be used for drawing overlays with minimum value.
@@ -759,8 +681,7 @@ public abstract class AbstractImageGenerator {
private Color neutralColor = Color.WHITE;
/**
- * @param scale
- * scale to set
+ * @param scale scale to set
* @return object with all parameters
* @see #scale
*/
@@ -770,8 +691,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param scale
- * scale to set
+ * @param scale scale to set
* @return object with all parameters
* @see #scale
*/
@@ -781,9 +701,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param x
- * x coordinate to be set
+ * @param x x coordinate to be set
* @return object with all parameters
* @see #x
*/
@@ -793,8 +711,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param x
- * x coordinate to be set
+ * @param x x coordinate to be set
* @return object with all parameters
* @see #x
*/
@@ -804,8 +721,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param y
- * y coordinate to be set
+ * @param y y coordinate to be set
* @return object with all parameters
* @see #y
*/
@@ -815,8 +731,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param y
- * y coordinate to be set
+ * @param y y coordinate to be set
* @return object with all parameters
* @see #y
*/
@@ -826,8 +741,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param width
- * width to set
+ * @param width width to set
* @return object with all parameters
* @see #width
*/
@@ -837,8 +751,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param width
- * width to set
+ * @param width width to set
* @return object with all parameters
* @see #width
*/
@@ -848,9 +761,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param height
- * height to set
+ * @param height height to set
* @return object with all parameters
* @see #height
*/
@@ -860,8 +771,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param height
- * height to set
+ * @param height height to set
* @return object with all parameters
* @see #height
*/
@@ -871,9 +781,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param background
- * background flag to set
+ * @param background background flag to set
* @return object with all parameters
* @see #background
*/
@@ -883,9 +791,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param nested
- * nested flag to set
+ * @param nested nested flag to set
* @return object with all parameters
* @see #nested
*/
@@ -895,9 +801,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param model
- * model to set
+ * @param model model to set
* @return object with all parameters
* @see #model
*/
@@ -913,9 +817,7 @@ public abstract class AbstractImageGenerator {
}
/**
- *
- * @param level
- * level to set
+ * @param level level to set
* @return object with all parameters
* @see #level
*/
@@ -927,8 +829,7 @@ public abstract class AbstractImageGenerator {
/**
* Sets {@link #level} parameter from {@link String}.
*
- * @param zoomLevel
- * new {@link #level} value
+ * @param zoomLevel new {@link #level} value
* @return object with all parameters
*/
public Params level(final String zoomLevel) {
@@ -941,7 +842,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return scale value
* @see #scale
*/
@@ -950,7 +850,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return x coordinate value
* @see #x
*/
@@ -959,7 +858,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return y coordinate value
* @see #y
*/
@@ -968,7 +866,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return width value
* @see #width
*/
@@ -977,7 +874,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return height value
* @see #height
*/
@@ -986,7 +882,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return model object
* @see #model
*/
@@ -995,7 +890,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return background value
* @see #background
*/
@@ -1004,7 +898,6 @@ public abstract class AbstractImageGenerator {
}
/**
- *
* @return nested value
* @see #nested
*/
@@ -1033,10 +926,9 @@ public abstract class AbstractImageGenerator {
* contains mapping between {@link Element}/{@link Reaction} and
* {@link DataOverlayEntry} used for coloring specific element.
*
- * @param map
- * layout data containing mapping between {@link Element}/
- * {@link Reaction} and {@link DataOverlayEntry} used for coloring
- * specific element
+ * @param map layout data containing mapping between {@link Element}/
+ * {@link Reaction} and {@link DataOverlayEntry} used for coloring
+ * specific element
*/
public void addVisibleDataOverlay(final List<Pair<? extends BioEntity, DataOverlayEntry>> map) {
visibleDataOverlays.add(map);
@@ -1050,12 +942,9 @@ public abstract class AbstractImageGenerator {
* Returns list with {@link DataOverlayEntry} used to visualize the specific
* object in data overlays visualized in the JavaScript.
*
- * @param object
- * object ({@link Element} or {@link Reaction}) for which we return
- * list of {@link DataOverlayEntry} in different layouts
- * @return list with {@link DataOverlayEntry} used to visualize the specific
- * object in data overlays visualized in the JavaScript
- * @see #visibleDataOverlays
+ * @param object object ({@link Element} or {@link Reaction}) for which we return
+ * list of {@link DataOverlayEntry} in different layouts
+ * @return list with {@link DataOverlayEntry} used to visualize the specific object in data overlays visualized in the JavaScript
*/
public List<List<DataOverlayEntry>> getVisibleDataOverlaysForElement(final BioEntity object) {
List<List<DataOverlayEntry>> result = new ArrayList<>();
@@ -1075,8 +964,7 @@ public abstract class AbstractImageGenerator {
* Returns {@link Color} that should be used for drawing overlays with
* maximum value.
*
- * @return {@link Color} that should be used for drawing overlays with
- * maximum value
+ * @return {@link Color} that should be used for drawing overlays with maximum value
*/
public Color getMaxColor() {
return maxColor;
@@ -1090,16 +978,14 @@ public abstract class AbstractImageGenerator {
* Returns {@link Color} that should be used for drawing overlays with
* minimum value.
*
- * @return {@link Color} that should be used for drawing overlays with
- * minimum value
+ * @return {@link Color} that should be used for drawing overlays with minimum value
*/
public Color getMinColor() {
return minColor;
}
/**
- * @param minColor
- * minColor to set
+ * @param minColor minColor to set
* @return object with all parameters
* @see #minColor
*/
@@ -1109,8 +995,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param maxColor
- * maxColor to set
+ * @param maxColor maxColor to set
* @return object with all parameters
* @see #maxColor
*/
@@ -1120,8 +1005,7 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param simpleColor
- * simpleColor to set
+ * @param simpleColor simpleColor to set
* @return object with all parameters
* @see #simpleColor
*/
@@ -1139,10 +1023,9 @@ public abstract class AbstractImageGenerator {
}
/**
- * @param sbgn
- * the sbgn to set
- * @see #sbgn
+ * @param sbgn the sbgn to set
* @return object with all parameters
+ * @see #sbgn
*/
public Params sbgn(final boolean sbgn) {
this.sbgn = sbgn;
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
index d63c4b03e7e06cd9d3fc647b1f7147a9f3026fe6..88eb060e22f257bd5d0f2bc45c79ea4af067136c 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java
@@ -2,7 +2,6 @@ package lcsb.mapviewer.converter.graphics;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
@@ -32,6 +31,7 @@ public class NormalImageGeneratorTest extends GraphicsTestFunctions {
LayerText layerText = createText();
Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
layer.addLayerText(layerText);
layer.setVisible(true);
model.addLayer(layer);
@@ -45,13 +45,12 @@ public class NormalImageGeneratorTest extends GraphicsTestFunctions {
@Test
public void testArtificialInHierarchicalView() throws Exception {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
Model model = createCompartmentModel();
Layer layer = model.getLayers().iterator().next();
layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd xxx ret"));
new CreateHierarchyCommand(model, 1, 8).execute();
model.getCompartments().get(1).setTransparencyLevel("2");
diff --git a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
index d29c5f2166848dbdbe092196f3ea46fe990ceb9f..8b8911c6f22be13adc52a2e64ead37b0ec150d5a 100644
--- a/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
+++ b/converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/PdfImageGeneratorTest.java
@@ -1,23 +1,5 @@
package lcsb.mapviewer.converter.graphics;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import static org.mockito.ArgumentMatchers.any;
-import static org.mockito.Mockito.times;
-import static org.mockito.Mockito.verify;
-
-import java.awt.Color;
-import java.awt.Graphics2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.io.File;
-import java.io.IOException;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
@@ -28,6 +10,23 @@ import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.species.Complex;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.awt.Color;
+import java.awt.Graphics2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.io.IOException;
+
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.Mockito.times;
+import static org.mockito.Mockito.verify;
public class PdfImageGeneratorTest extends GraphicsTestFunctions {
@@ -45,17 +44,18 @@ public class PdfImageGeneratorTest extends GraphicsTestFunctions {
File f = new File(filename);
if (f.exists()) {
- f.delete();
+ assertTrue(f.delete());
}
assertFalse(f.exists());
Model model = createCompartmentModel();
Layer layer = model.getLayers().iterator().next();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
layer.addLayerText(new LayerText(new Rectangle2D.Double(10, 10, 500, 500), "X asd"));
layer.addLayerText(new LayerText(new Rectangle2D.Double(20, 20, 200, 200), "Y qwe ret"));
- layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd aaewq ret"));
+ layer.addLayerText(new LayerText(new Rectangle2D.Double(100, 100, 199, 220), "Z dgf fsd blah ret"));
for (final LayerText text : layer.getTexts()) {
text.setZ(0);
@@ -71,7 +71,7 @@ public class PdfImageGeneratorTest extends GraphicsTestFunctions {
pig.saveToFile("tmp.pdf");
assertTrue(f.exists());
- f.delete();
+ assertTrue(f.delete());
assertFalse(f.exists());
}
@@ -81,7 +81,7 @@ public class PdfImageGeneratorTest extends GraphicsTestFunctions {
File f = new File(filename);
if (f.exists()) {
- f.delete();
+ assertTrue(f.delete());
}
assertFalse(f.exists());
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
index d1a5d04b3ce0b6acd387176d8676582334a054ee..5940cbddd495f8264f467de9473a5d76d8d3b683 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/NotesUtility.java
@@ -1,8 +1,8 @@
package lcsb.mapviewer.converter.model.sbml;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.commons.text.StringEscapeUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index e59598fdee22e8e4ee224eadfd9be65048f47b3b..c43d706b5f0480ebd8852435baa09efb3214d125 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.sbml;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.sbml.species.ElementColorEnum;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
@@ -13,6 +12,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Author;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.sbml.jsbml.AbstractNamedSBase;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 62f06b1aac1e5492ccea3556ebdf342f97c28ce3..da0478b878bb02535413b087aa7aa6aace8ee77e 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -2,13 +2,13 @@ package lcsb.mapviewer.converter.model.sbml;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.apache.commons.io.output.ByteArrayOutputStream;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java
index 82e31e6801feb52bf13e68d1c08440cff4832169..894be0c3f46e1b298f898324db05319a5da98f17 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlLayerParser.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.converter.model.sbml;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
@@ -22,7 +21,7 @@ public class SbmlLayerParser extends SbmlBioEntityParser {
Layer layer = new Layer();
layer.setLayerId(1);
layer.setZ(1);
- layer.setName(CreateHierarchyCommand.TEXT_LAYER_NAME);
+ layer.setName("text");
SbmlModelUtils sbmlModelUtils = new SbmlModelUtils(sbmlModel);
Layout layout = sbmlModelUtils.getLayout();
if (layout != null) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 5258d5f7eda95eb44b0843a4f481ed4e7d9c0ad5..6e22fcf4078a0d4ce5779e5a1b703be7d799ed70 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -1,24 +1,5 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.xml.stream.XMLStreamException;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.sbml.jsbml.SBMLDocument;
-import org.sbml.jsbml.SBMLReader;
-import org.sbml.jsbml.ext.SBasePlugin;
-import org.sbml.jsbml.ext.layout.Layout;
-import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
-import org.sbml.jsbml.ext.multi.MultiModelPlugin;
-import org.springframework.stereotype.Component;
-
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
import lcsb.mapviewer.common.Configuration;
@@ -27,7 +8,6 @@ import lcsb.mapviewer.converter.Converter;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ZIndexPopulator;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
@@ -45,6 +25,24 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+import lcsb.mapviewer.utils.ZIndexPopulator;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLReader;
+import org.sbml.jsbml.ext.SBasePlugin;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
+import org.sbml.jsbml.ext.multi.MultiModelPlugin;
+import org.springframework.stereotype.Component;
+
+import javax.xml.stream.XMLStreamException;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
@Component
public class SbmlParser extends Converter {
@@ -52,7 +50,7 @@ public class SbmlParser extends Converter {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
private boolean provideDefaults = true;
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index cf6e21fcd562237486f7c03f1f3fb93d82d8efac..5f28eaeace3356ed1a6bca4fd3a575c942db5ad8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
+import lcsb.mapviewer.commands.layout.ModifierType;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
@@ -9,8 +11,6 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
import lcsb.mapviewer.converter.model.sbml.SbmlModelUtils;
import lcsb.mapviewer.converter.model.sbml.SbmlParameterParser;
@@ -72,14 +72,14 @@ import java.util.Map;
import java.util.Set;
public class SbmlReactionParser extends SbmlBioEntityParser {
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
- private ElementUtils eu = new ElementUtils();
+ private final ElementUtils eu = new ElementUtils();
- private SbmlSpeciesParser speciesParser;
- private SbmlCompartmentParser compartmentParser;
+ private final SbmlSpeciesParser speciesParser;
+ private final SbmlCompartmentParser compartmentParser;
- private PointTransformation pt = new PointTransformation();
+ private final PointTransformation pt = new PointTransformation();
public SbmlReactionParser(final Model sbmlModel, final lcsb.mapviewer.model.map.model.Model minervaModel,
final SbmlSpeciesParser speciesParser, final SbmlCompartmentParser compartmentParser) {
@@ -325,8 +325,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
// if there is no layout don't create center line
if (startNode.getLine() != null && startNode.getLine().length() > Configuration.EPSILON
&& endNode.getLine() != null && endNode.getLine().length() > Configuration.EPSILON) {
- startNode.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE);
- endNode.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE);
+ startNode.getLine().trimEnd(ReactionData.RECT_SIZE);
+ endNode.getLine().trimBegin(ReactionData.RECT_SIZE);
line.addLine(pt.copyPoint(startNode.getLine().getEndPoint()), pt.copyPoint(endNode.getLine().getStartPoint()));
line.setType(startNode.getLine().getType());
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GeneratedSbmlValidationTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GeneratedSbmlValidationTests.java
index d265f40ca65438ac638c76781db8c98a4062b97e..ab64ae9b16d676846018ca1c38d9191a5ed2c66d 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GeneratedSbmlValidationTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GeneratedSbmlValidationTests.java
@@ -1,28 +1,27 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-
-import org.junit.Ignore;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
-import lcsb.mapviewer.converter.ZIndexPopulator;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.utils.ZIndexPopulator;
+import org.junit.Ignore;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
@RunWith(Parameterized.class)
public class GeneratedSbmlValidationTests extends SbmlTestFunctions {
- private Model model;
+ private final Model model;
public GeneratedSbmlValidationTests(final Model model, final String name) {
this.model = model;
@@ -57,7 +56,7 @@ public class GeneratedSbmlValidationTests extends SbmlTestFunctions {
private static Object[] createRow(final Model model) {
new ZIndexPopulator().populateZIndex(model);
- return new Object[] { model, model.getName() };
+ return new Object[]{model, model.getName()};
}
private static Model createModelWithSingleSpecies() throws Exception {
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index bb2acde6f338b0ac3b09436348e999fd8f803ebe..b43073d0c40be477b8b65fac284631dcdc588a80 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.sbml;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import org.junit.Test;
@@ -58,8 +57,7 @@ public class GenericSbmlToXmlParserTest extends SbmlTestFunctions {
testSbmlSerialization(model);
}
- private void testSbmlSerialization(final Model model) throws InconsistentModelException,
- IOException, ConverterException, InvalidInputDataExecption {
+ private void testSbmlSerialization(final Model model) throws ConverterException, InvalidInputDataExecption {
final SbmlParser converter = new SbmlParser();
converter.setProvideDefaults(false);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
index f9578be9aa77b284f941b057b83bbe3e3cc49870..ab1037f51e3da0184f35922e050803aa310f0969 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -1,6 +1,5 @@
package lcsb.mapviewer.converter.model.sbml;
-import lcsb.mapviewer.commands.CreateHierarchyCommand;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.ListComparator;
import lcsb.mapviewer.converter.ConverterParams;
@@ -742,7 +741,7 @@ public class SbmlExporterTest extends SbmlTestFunctions {
final Layer layer = new Layer();
layer.setLayerId(1);
- layer.setName(CreateHierarchyCommand.TEXT_LAYER_NAME);
+ layer.setName("text");
final LayerText text = new LayerText(new Rectangle2D.Double(10, 20, 30, 40), "str a");
text.setZ(0);
layer.addLayerText(text);
diff --git a/converter/pom.xml b/converter/pom.xml
index 79f569c12236f1cfc16b3209e2b661e975d91f81..942e233f0ee9e1f3fc44e3495f35e386ec1455db 100644
--- a/converter/pom.xml
+++ b/converter/pom.xml
@@ -1,41 +1,46 @@
<?xml version="1.0"?>
<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
- xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>19.0.0~alpha.0</version>
- </parent>
-
- <artifactId>converter</artifactId>
- <name>converter</name>
-
- <dependencies>
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>19.0.0~alpha.0</version>
- </dependency>
- <dependency>
- <groupId>xerces</groupId>
- <artifactId>xercesImpl</artifactId>
- <version>${xercesImp.version}</version>
- </dependency>
- <!-- mockito used for testing -->
- <dependency>
- <groupId>org.mockito</groupId>
- <artifactId>mockito-core</artifactId>
- <version>${mockito.version}</version>
- <scope>test</scope>
- </dependency>
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </parent>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
-
- </dependencies>
+ <artifactId>converter</artifactId>
+ <name>converter</name>
+
+ <dependencies>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </dependency>
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model-command</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </dependency>
+ <dependency>
+ <groupId>xerces</groupId>
+ <artifactId>xercesImpl</artifactId>
+ <version>${xercesImp.version}</version>
+ </dependency>
+ <!-- mockito used for testing -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-core</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
</project>
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaWriter.java b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaWriter.java
new file mode 100644
index 0000000000000000000000000000000000000000..543cf68ed10f2a4dd7ca8ccffd5d403323bf02e6
--- /dev/null
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ColorSchemaWriter.java
@@ -0,0 +1,167 @@
+package lcsb.mapviewer.converter;
+
+import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.species.AntisenseRna;
+import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
+import lcsb.mapviewer.model.map.species.Drug;
+import lcsb.mapviewer.model.map.species.Gene;
+import lcsb.mapviewer.model.map.species.Ion;
+import lcsb.mapviewer.model.map.species.Phenotype;
+import lcsb.mapviewer.model.map.species.Protein;
+import lcsb.mapviewer.model.map.species.Rna;
+import lcsb.mapviewer.model.map.species.SimpleMolecule;
+import lcsb.mapviewer.model.map.species.Unknown;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayEntry;
+import lcsb.mapviewer.model.overlay.DataOverlayType;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+public class ColorSchemaWriter {
+
+ private static final Map<String, Class<? extends BioEntity>> speciesMapping;
+
+ static {
+ speciesMapping = new HashMap<>();
+ speciesMapping.put("protein", Protein.class);
+ speciesMapping.put("gene", Gene.class);
+ speciesMapping.put("complex", Complex.class);
+ speciesMapping.put("simple_molecule", SimpleMolecule.class);
+ speciesMapping.put("ion", Ion.class);
+ speciesMapping.put("phenotype", Phenotype.class);
+ speciesMapping.put("drug", Drug.class);
+ speciesMapping.put("rna", Rna.class);
+ speciesMapping.put("antisense_rna", AntisenseRna.class);
+ speciesMapping.put("unknown", Unknown.class);
+ speciesMapping.put("degraded", Degraded.class);
+ }
+
+ /**
+ * Object that parses colors from string.
+ */
+ private final ColorParser colorParser = new ColorParser();
+
+ /**
+ * Default class logger.
+ */
+ private final Logger logger = LogManager.getLogger();
+
+ public String entriesToStringTable(final Set<DataOverlayEntry> entries) {
+ List<ColorSchemaColumn> columns = new ArrayList<>();
+ for (ColorSchemaColumn column : ColorSchemaColumn.values()) {
+ if (column.getTypes().contains(DataOverlayType.GENERIC)) {
+ columns.add(column);
+ }
+ }
+
+ StringBuilder builder = new StringBuilder();
+ builder.append(getHeader(columns));
+ for (DataOverlayEntry entry : entries) {
+ builder.append("\n").append(getRow(entry, columns));
+ }
+
+ return builder.toString();
+ }
+
+ private String getRow(final DataOverlayEntry entry, final List<ColorSchemaColumn> columns) {
+ StringBuilder row = new StringBuilder();
+ int counter = 0;
+ for (ColorSchemaColumn column : columns) {
+ if (counter > 0) {
+ row.append("\t");
+ }
+ counter++;
+ String data = "";
+ switch (column) {
+ case COLOR:
+ if (entry.getColor() != null) {
+ data = new ColorParser().colorToHtml(entry.getColor());
+ }
+ break;
+ case NAME:
+ if (entry.getName() != null) {
+ data = entry.getName();
+ }
+ break;
+ case ELEMENT_IDENTIFIER:
+ if (entry.getElementId() != null) {
+ data = entry.getElementId();
+ }
+ break;
+ case MAP_NAME:
+ if (entry.getModelName() != null) {
+ data = entry.getModelName();
+ }
+ break;
+ case LINE_WIDTH:
+ if (entry.getLineWidth() != null) {
+ data = entry.getLineWidth().toString();
+ }
+ break;
+ case VALUE:
+ if (entry.getValue() != null) {
+ data = entry.getValue().toString();
+ }
+ break;
+ case REVERSE_REACTION:
+ if (entry.getReverseReaction() != null) {
+ data = entry.getReverseReaction().toString();
+ }
+ break;
+ case COMPARTMENT:
+ data = StringUtils.join(entry.getCompartments(), ",");
+ break;
+ case DESCRIPTION:
+ if (entry.getDescription() != null) {
+ data = entry.getDescription().replace("\t", " ").replace("\n", " ");
+ }
+ break;
+ default:
+ data = "";
+ break;
+ }
+ row.append(data);
+ }
+ return row.toString();
+ }
+
+ private String getHeader(final List<ColorSchemaColumn> columns) {
+ StringBuilder header = new StringBuilder();
+ for (ColorSchemaColumn column : columns) {
+ if (header.length() > 0) {
+ header.append("\t");
+ }
+ header.append(column.toString());
+ }
+ return header.toString();
+ }
+
+ public String overlayToString(final DataOverlay overlay) {
+ String metaData = overlayMetaData(overlay);
+
+ String content = metaData + entriesToStringTable(overlay.getEntries());
+ return content;
+ }
+
+ private String overlayMetaData(final DataOverlay overlay) {
+ StringBuilder metaData = new StringBuilder();
+ if (overlay.getName() != null) {
+ metaData.append("#" + ZipEntryFileFactory.LAYOUT_HEADER_PARAM_NAME + "=" + overlay.getName() + "\n");
+ }
+ if (overlay.getDescription() != null) {
+ metaData.append("#" + ZipEntryFileFactory.LAYOUT_HEADER_PARAM_DESCRIPTION + "=" + overlay.getDescription().replace("\n", " ") + "\n");
+ }
+
+ return metaData.toString();
+ }
+}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
index 3c320b72e1dc3aba3ba6ee53c0605dd595d237a1..cf641959f46da1474be42bb3c9da763077078201 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ComplexZipConverter.java
@@ -10,9 +10,11 @@ import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.layout.ReferenceGenomeType;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -40,6 +42,7 @@ import java.lang.reflect.Modifier;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.HashSet;
+import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
@@ -64,7 +67,8 @@ public class ComplexZipConverter {
* Default class logger.
*/
private static final Logger logger = LogManager.getLogger();
- private static final String IMMEDIATE_LINK_PREFIX = "IMMEDIATE_LINK:";
+ protected static final String IMMEDIATE_LINK_PREFIX = "IMMEDIATE_LINK:";
+ public static final String GLYPH_PREFIX = "Glyph:";
/**
* Class used to create single submap from a file.
@@ -97,7 +101,7 @@ public class ComplexZipConverter {
* @return complex {@link Model} created from input data
* @throws InvalidInputDataExecption thrown when there is a problem with accessing input data
*/
- public Model createModel(final ComplexZipConverterParams params) throws InvalidInputDataExecption, ConverterException {
+ public Model createModel(final ComplexZipConverterParams params, final Project project) throws InvalidInputDataExecption, ConverterException {
try {
ZipFile zipFile = params.getZipFile();
Enumeration<? extends ZipEntry> entries;
@@ -154,16 +158,22 @@ public class ComplexZipConverter {
processReaction(mapping, nameModelMap, result, reaction);
}
for (final Species species : mappingModel.getSpeciesList()) {
- processSpecies(species, nameModelMap);
+ processSpecies(species, nameModelMap, project.getGlyphs());
}
}
+
+ project.addModel(result);
+ for (final Model model : result.getSubmodels()) {
+ project.addModel(model);
+ }
+
return result;
} catch (final IOException e) {
throw new InvalidArgumentException(e);
}
}
- private void processSpecies(final Species species, final Map<String, Model> nameModelMap) {
+ private void processSpecies(final Species species, final Map<String, Model> nameModelMap, final List<Glyph> glyphs) {
String notes = species.getNotes();
if (notes != null) {
String[] lines = notes.split("\n");
@@ -172,28 +182,49 @@ public class ComplexZipConverter {
if (line.startsWith(IMMEDIATE_LINK_PREFIX)) {
String link = line.replace(IMMEDIATE_LINK_PREFIX, "").trim();
- Compartment compartment = species.getCompartment();
- if (compartment == null) {
- logger.warn("[SUBMODEL MAPPING] Species {} in mapping file doesn't start inside compartment. Skipped. Link skipped",
- species.getElementId());
- } else {
- String modelName = compartment.getName().toLowerCase();
- Model model = nameModelMap.get(modelName);
- if (model == null) {
- throw new InvalidArgumentException("Mapping file references to " + modelName + " submodel. But such model doesn't exist");
- }
- Element elementToChange = model.getElementByElementId(species.getName());
- if (elementToChange == null) {
- throw new InvalidArgumentException("Mapping file references to element with alias: " + species.getName()
- + ". But such element doesn't exist");
- }
+ Element elementToChange = getElementToChange(species, nameModelMap);
+ if (elementToChange != null) {
elementToChange.setImmediateLink(link);
}
+ } else if (line.startsWith(GLYPH_PREFIX)) {
+ String filename = line.replace(GLYPH_PREFIX, "").trim();
+
+ Element elementToChange = getElementToChange(species, nameModelMap);
+ if (elementToChange != null) {
+ for (Glyph glyph : glyphs) {
+ if (glyph.getFile().getOriginalFileName().equalsIgnoreCase(filename)) {
+ elementToChange.setGlyph(glyph);
+ }
+ }
+ }
}
}
}
}
+ private static Element getElementToChange(
+ final Species species,
+ final Map<String, Model> nameModelMap) {
+ Compartment compartment = species.getCompartment();
+ if (compartment == null) {
+ logger.warn("[SUBMODEL MAPPING] Species {} in mapping file doesn't start inside compartment. Skipped. Link skipped",
+ species.getElementId());
+ } else {
+ String modelName = compartment.getName().toLowerCase();
+ Model model = nameModelMap.get(modelName);
+ if (model == null) {
+ throw new InvalidArgumentException("Mapping file references to " + modelName + " submodel. But such model doesn't exist");
+ }
+ Element result = model.getElementByElementId(species.getName());
+ if (result == null) {
+ throw new InvalidArgumentException("Mapping file references to element with alias: " + species.getName()
+ + ". But such element doesn't exist");
+ }
+ return result;
+ }
+ return null;
+ }
+
protected boolean isIgnoredFile(final String name) {
if (name == null) {
return true;
@@ -427,4 +458,5 @@ public class ComplexZipConverter {
}
return converter;
}
+
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/Converter.java b/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
index b7a35755296babc5ef6c05135162a7ffe9ef757f..a3a40b1fdf0b24d7368c01aa9ea68669928777f1 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/Converter.java
@@ -1,5 +1,12 @@
package lcsb.mapviewer.converter;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+import org.apache.commons.io.FileUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import java.io.ByteArrayInputStream;
import java.io.File;
import java.io.IOException;
@@ -9,29 +16,22 @@ import java.nio.charset.StandardCharsets;
import java.util.List;
import java.util.UUID;
-import org.apache.commons.io.FileUtils;
-
-import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.model.Model;
-
/**
* Interface used for reading data from file and putting it into {@link Model}
* object.
- *
+ *
* @author Piotr Gawron
- *
*/
public abstract class Converter {
+ protected static final Logger logger = LogManager.getLogger();
+
/**
* Parse input source and transforms it into a model object.
- *
- * @param params
- * input params used for reading data
+ *
+ * @param params input params used for reading data
* @return model obtained from input source
- * @throws InvalidInputDataExecption
- * thrown when input parameters are invalid
+ * @throws InvalidInputDataExecption thrown when input parameters are invalid
*/
public abstract Model createModel(final ConverterParams params) throws InvalidInputDataExecption, ConverterException;
@@ -39,8 +39,7 @@ public abstract class Converter {
* Generate String representation of the model. Traditionally often XML but can
* be any other format as well.
*
- * @param model
- * The MINERVA ${@link Model} to be serialized
+ * @param model The MINERVA ${@link Model} to be serialized
* @return The translated Model
*/
public abstract String model2String(final Model model) throws InconsistentModelException, ConverterException;
@@ -68,12 +67,10 @@ public abstract class Converter {
/**
* Export model to {@link InputStream}.
- *
- * @param model
- * model to be exported
+ *
+ * @param model model to be exported
* @return {@link InputStream} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
+ * @throws InconsistentModelException thrown when given model is inconsistent and unable to be exported
*/
public InputStream model2InputStream(final Model model)
throws InconsistentModelException, ConverterException {
@@ -83,14 +80,11 @@ public abstract class Converter {
/**
* Export model to {@link File}.
- *
- * @param model
- * model to be exported
- * @param filePath
- * exported file path
+ *
+ * @param model model to be exported
+ * @param filePath exported file path
* @return {@link File} with exported data
- * @throws InconsistentModelException
- * thrown when given model is inconsistent and unable to be exported
+ * @throws InconsistentModelException thrown when given model is inconsistent and unable to be exported
*/
public File model2File(final Model model, final String filePath)
throws InconsistentModelException, IOException, ConverterException {
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
index 6be2c0667115a0e7bf148fd87bd26656a9bb4d01..00f51f01df6db6f3144fdfd0f4b9191b7fc1bec4 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/OverviewParser.java
@@ -1,5 +1,23 @@
package lcsb.mapviewer.converter;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.module.SimpleModule;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.converter.zip.OverviewLinkDeserializer;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewImageLink;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.OverviewSearchLink;
+import lcsb.mapviewer.model.map.model.ModelData;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import javax.imageio.ImageIO;
import java.awt.Polygon;
import java.awt.geom.Area;
import java.awt.geom.Point2D;
@@ -20,33 +38,11 @@ import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import javax.imageio.ImageIO;
-
-import org.apache.commons.io.FilenameUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-import com.fasterxml.jackson.core.type.TypeReference;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.databind.module.SimpleModule;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.converter.zip.OverviewLinkDeserializer;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewImageLink;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.OverviewSearchLink;
-import lcsb.mapviewer.model.map.model.Model;
-
/**
* Parser used to extract data about {@link OverviewImage overview images} from
* zip file.
- *
+ *
* @author Piotr Gawron
- *
*/
public class OverviewParser {
/**
@@ -58,37 +54,17 @@ public class OverviewParser {
private static final String JSON_COORDINATES_FILENAME = "coords.json";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#zoomLevel} is stored.
- */
private static final String ZOOM_LEVEL_COORDINATES_COLUMN = "MODEL_ZOOM_LEVEL";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#xCoord},{@link OverviewModelLink#yCoord} is stored.
- */
+
private static final String REDIRECTION_COORDINATES_COORDINATE_COLUMN = "MODEL_COORDINATES";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewModelLink#linkedModel} or
- * {@link OverviewImageLink#linkedOverviewImage} is stored.
- */
+
private static final String TARGET_FILENAME_COORDINATE_COLUMN = "LINK_TARGET";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewLink#polygon} is stored.
- */
+
private static final String POLYGON_COORDINATE_COLUMN = "POLYGON";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * {@link OverviewLink#overviewImage source of the image} is stored.
- */
+
private static final String FILENAME_COORDINATE_COLUMN = "FILE";
- /**
- * Name of the column in {@link #COORDINATES_FILENAME} where information about
- * type of the link (implementation of {@link OverviewLink} class) is stored.
- */
+
private static final String TARGET_TYPE_COORDINATE_COLUMN = "LINK_TYPE";
/**
@@ -126,20 +102,16 @@ public class OverviewParser {
* Method that parse zip file and creates list of {@link OverviewImage images}
* from it.
*
- * @param models
- * map with models where the key is name of the file and value is model
- * that was parsed from the file
- * @param files
- * list with files to parse
- * @param outputDirectory
- * directory where images should be stored, directory path should be
- * absolute
+ * @param models map with models where the key is name of the file and value is model
+ * that was parsed from the file
+ * @param files list with files to parse
+ * @param outputDirectory directory where images should be stored, directory path should be
+ * absolute
* @return list of {@link OverviewImage images}
- * @throws InvalidOverviewFile
- * thrown when the zip file contains invalid data
+ * @throws InvalidOverviewFile thrown when the zip file contains invalid data
*/
- public List<OverviewImage> parseOverviewLinks(final Set<Model> models, final List<ImageZipEntryFile> files,
- final String outputDirectory, final ZipFile zipFile) throws InvalidOverviewFile {
+ public List<OverviewImage> parseOverviewLinks(final Set<ModelData> models, final List<ImageZipEntryFile> files,
+ final String outputDirectory, final ZipFile zipFile) throws InvalidOverviewFile {
if (outputDirectory != null) {
File f = new File(outputDirectory);
if (!f.exists()) {
@@ -220,9 +192,9 @@ public class OverviewParser {
}
}
- private Map<String, Model> createMapping(final Set<Model> models) {
- Map<String, Model> result = new HashMap<>();
- for (final Model model : models) {
+ private Map<String, ModelData> createMapping(final Set<ModelData> models) {
+ Map<String, ModelData> result = new HashMap<>();
+ for (final ModelData model : models) {
result.put(model.getName().toLowerCase(), model);
}
return result;
@@ -232,20 +204,16 @@ public class OverviewParser {
* This method process data from {@link #COORDINATES_FILENAME} in zip archive.
* This method adds connections between images and between images and models.
*
- * @param models
- * map with models where the key is name of the file and value is model
- * that was parsed from the file
- * @param images
- * list of {@link OverviewImage images} that should be connected
- * @param coordinatesData
- * {@link String} with the data taken from
- * {@link #COORDINATES_FILENAME} file
- * @throws InvalidOverviewFile
- * thrown when the data are invalid
+ * @param models map with models where the key is name of the file and value is model
+ * that was parsed from the file
+ * @param images list of {@link OverviewImage images} that should be connected
+ * @param coordinatesData {@link String} with the data taken from
+ * {@link #COORDINATES_FILENAME} file
+ * @throws InvalidOverviewFile thrown when the data are invalid
*/
- protected List<OverviewImage> processCoordinates(final Set<Model> models, final List<OverviewImage> images, final String coordinatesData)
+ protected List<OverviewImage> processCoordinates(final Set<ModelData> models, final List<OverviewImage> images, final String coordinatesData)
throws InvalidOverviewFile {
- Map<String, Model> modelMapping = createMapping(models);
+ Map<String, ModelData> modelMapping = createMapping(models);
String[] rows = coordinatesData.replaceAll("\r", "\n").split("\n");
Integer filenameColumn = null;
Integer polygonColumn = null;
@@ -399,9 +367,9 @@ public class OverviewParser {
return images;
}
- protected List<OverviewImage> processJsonCoordinates(final Set<Model> models, final List<OverviewImage> images, final String json)
+ protected List<OverviewImage> processJsonCoordinates(final Set<ModelData> models, final List<OverviewImage> images, final String json)
throws InvalidOverviewFile {
- Map<String, Model> modelMapping = createMapping(models);
+ Map<String, ModelData> modelMapping = createMapping(models);
ObjectMapper mapper = new ObjectMapper();
final SimpleModule module = new SimpleModule();
module.addDeserializer(OverviewLink.class, new OverviewLinkDeserializer());
@@ -429,7 +397,7 @@ public class OverviewParser {
((OverviewImageLink) link).setLinkedOverviewImage(linkImage);
}
if (link instanceof OverviewModelLink) {
- Model model = modelMapping.get(((OverviewModelLink) link).getLinkedModel().getName().toLowerCase());
+ ModelData model = modelMapping.get(((OverviewModelLink) link).getLinkedModel().getName().toLowerCase());
if (model == null) {
throw new InvalidOverviewFile(((OverviewModelLink) link).getLinkedModel().getName() + " is missing");
@@ -454,35 +422,32 @@ public class OverviewParser {
* Creates a link from parameters and place it in appropriate
* {@link OverviewImage}.
*
- * @param filename
- * {@link OverviewImage#filename name of the image}
- * @param polygon
- * {@link OverviewImage#polygon polygon} describing link
- * @param linkTarget
- * defines target that should be invoked when the link is activated.
- * This target is either a file name (in case of
- * {@link #MODEL_LINK_TYPE} or {@link #IMAGE_LINK_TYPE}) or a search
- * string (in case of {@link #SEARCH_LINK_TYPE}).
- * @param coord
- * coordinates on the model where redirection should be placed in case
- * of {@link #MODEL_LINK_TYPE} connection
- * @param zoomLevel
- * zoom level on the model where redirection should be placed in case
- * of {@link #MODEL_LINK_TYPE} connection
- * @param linkType
- * type of the connection. This will define implementation of
- * {@link OverviewImage} that will be used. For now three values are
- * acceptable: {@link #MODEL_LINK_TYPE}, {@link #IMAGE_LINK_TYPE},
- * {@link #SEARCH_LINK_TYPE}.
- * @param images
- * list of images that are available
- * @param models
- * list of models that are available
- * @throws InvalidCoordinatesFile
- * thrown when one of the input parameters is invalid
+ * @param filename filename name of the image
+ * @param polygon polygon polygon describing link
+ * @param linkTarget defines target that should be invoked when the link is activated.
+ * This target is either a file name (in case of
+ * {@link #MODEL_LINK_TYPE} or {@link #IMAGE_LINK_TYPE}) or a search
+ * string (in case of {@link #SEARCH_LINK_TYPE}).
+ * @param coord coordinates on the model where redirection should be placed in case
+ * of {@link #MODEL_LINK_TYPE} connection
+ * @param zoomLevel zoom level on the model where redirection should be placed in case
+ * of {@link #MODEL_LINK_TYPE} connection
+ * @param linkType type of the connection. This will define implementation of
+ * {@link OverviewImage} that will be used. For now three values are
+ * acceptable: {@link #MODEL_LINK_TYPE}, {@link #IMAGE_LINK_TYPE},
+ * {@link #SEARCH_LINK_TYPE}.
+ * @param images list of images that are available
+ * @param models list of models that are available
+ * @throws InvalidCoordinatesFile thrown when one of the input parameters is invalid
*/
- private void createOverviewLink(final String filename, final String polygon, final String linkTarget, final String coord, final String zoomLevel,
- final String linkType, final List<OverviewImage> images, final Map<String, Model> models) throws InvalidCoordinatesFile {
+ private void createOverviewLink(final String filename,
+ final String polygon,
+ final String linkTarget,
+ final String coord,
+ final String zoomLevel,
+ final String linkType,
+ final List<OverviewImage> images,
+ final Map<String, ModelData> models) throws InvalidCoordinatesFile {
OverviewImage image = null;
for (final OverviewImage oi : images) {
if (oi.getFilename().equalsIgnoreCase(filename)) {
@@ -494,7 +459,7 @@ public class OverviewParser {
}
OverviewLink ol = null;
if (linkType.equals(MODEL_LINK_TYPE)) {
- Model model = models.get(linkTarget.toLowerCase());
+ ModelData model = models.get(linkTarget.toLowerCase());
if (model == null) {
throw new InvalidCoordinatesFile("Unknown model in \"" + COORDINATES_FILENAME + "\" file: " + linkTarget);
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index e8af1d4bac741185e0e7f8cd943cef003f1d6d9b..fd05cbb417d35b14bc8e022e9d1027726b867cc5 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -1,30 +1,49 @@
package lcsb.mapviewer.converter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipFile;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
+import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.zip.GlyphZipEntryFile;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ZipEntryFile;
+import lcsb.mapviewer.converter.zip.ZipEntryFileFactory;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerImage;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
+import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+import java.util.zip.ZipOutputStream;
public class ProjectFactory {
@@ -32,16 +51,25 @@ public class ProjectFactory {
* Default class logger.
*/
@SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
- private ComplexZipConverter converter;
+ private final ComplexZipConverter converter;
- private GlyphParser glyphParser = new GlyphParser();
+ private final GlyphParser glyphParser = new GlyphParser();
public ProjectFactory(final ComplexZipConverter converter) {
this.converter = converter;
}
+ private static void addModelFileToZip(final Model model, final String filename, final Converter converter, final ZipOutputStream zos)
+ throws IOException, InconsistentModelException, ConverterException {
+ ZipEntry entry = new ZipEntry(filename);
+ zos.putNextEntry(entry);
+ String topModelContent = converter.model2String(model);
+ zos.write(topModelContent.getBytes());
+ zos.closeEntry();
+ }
+
public Project create(final ComplexZipConverterParams params) throws InvalidInputDataExecption, ConverterException {
return create(params, new Project());
}
@@ -49,17 +77,6 @@ public class ProjectFactory {
public Project create(final ComplexZipConverterParams params, final Project project)
throws InvalidInputDataExecption, ConverterException {
try {
- Model model = converter.createModel(params);
-
- Set<Model> models = new HashSet<>();
- models.add(model);
- models.addAll(model.getSubmodels());
-
- project.addModel(model);
- for (final Model m : model.getSubmodels()) {
- project.addModel(m);
- }
-
ZipFile zipFile = params.getZipFile();
Enumeration<? extends ZipEntry> entries;
@@ -80,12 +97,14 @@ public class ProjectFactory {
}
}
}
- if (imageEntries.size() > 0) {
+ converter.createModel(params, project);
+
+
+ if (!imageEntries.isEmpty()) {
OverviewParser parser = new OverviewParser();
- project
- .addOverviewImages(parser.parseOverviewLinks(models, imageEntries, params.getVisualizationDir(), zipFile));
+ project.addOverviewImages(parser.parseOverviewLinks(project.getModels(), imageEntries, params.getVisualizationDir(), zipFile));
}
- if (project.getGlyphs().size() > 0) {
+ if (!project.getGlyphs().isEmpty()) {
assignGlyphsToElements(project);
}
return project;
@@ -97,8 +116,7 @@ public class ProjectFactory {
}
private void assignGlyphsToElements(final Project project) throws InvalidGlyphFile {
- Set<ModelData> models = new HashSet<>();
- models.addAll(project.getModels());
+ Set<ModelData> models = new HashSet<>(project.getModels());
for (final ModelData model : project.getModels()) {
for (final ModelSubmodelConnection connection : model.getSubmodels()) {
@@ -127,10 +145,10 @@ public class ProjectFactory {
String removeGlyph(final String notes) {
String[] lines = notes.split("[\n\r]+");
- StringBuilder result = new StringBuilder("");
+ StringBuilder result = new StringBuilder();
for (final String line : lines) {
- if (!line.startsWith("Glyph:")) {
- result.append(line + "\n");
+ if (!line.startsWith(ComplexZipConverter.GLYPH_PREFIX)) {
+ result.append(line).append("\n");
}
}
return result.toString();
@@ -139,8 +157,8 @@ public class ProjectFactory {
Glyph extractGlyph(final Project project, final String notes) throws InvalidGlyphFile {
String[] lines = notes.split("[\n\r]+");
for (final String line : lines) {
- if (line.startsWith("Glyph:")) {
- String glyphString = line.replace("Glyph:", "").trim().toLowerCase();
+ if (line.startsWith(ComplexZipConverter.GLYPH_PREFIX)) {
+ String glyphString = line.replace(ComplexZipConverter.GLYPH_PREFIX, "").trim().toLowerCase();
for (final Glyph glyph : project.getGlyphs()) {
if (glyph.getFile().getOriginalFileName().toLowerCase().equalsIgnoreCase(glyphString)) {
return glyph;
@@ -152,4 +170,190 @@ public class ProjectFactory {
return null;
}
+ public byte[] project2zip(final Project project) throws ConverterException, InconsistentModelException {
+ Converter converter = this.converter.createConverterInstance();
+
+ ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
+ try (ZipOutputStream zos = new ZipOutputStream(byteArrayOutputStream)) {
+ addModelFileToZip(project.getTopModel(), project.getTopModel().getName() + "." + converter.getFileExtensions().get(0), converter, zos);
+ for (ModelData model : project.getModels()) {
+ if (model != project.getTopModelData()) {
+ addModelFileToZip(model.getModel(),
+ ZipEntryFileFactory.SUBMODEL_DIRECTORY + model.getName() + "." + converter.getFileExtensions().get(0), converter,
+ zos);
+ }
+ }
+ Model mapping = createMappingModel(project.getModels());
+
+ addModelFileToZip(mapping, ZipEntryFileFactory.SUBMODEL_DIRECTORY + "mapping." + converter.getFileExtensions().get(0), converter, zos);
+
+ for (ModelData model : project.getModels()) {
+ addGlyphsToZip(model.getModel(), zos);
+ }
+
+ for (DataOverlay overlay : project.getDataOverlays()) {
+ if (overlay.isPublic()) {
+ addDataOverlayToZip(overlay, zos);
+ }
+ }
+
+ } catch (IOException ioe) {
+ throw new ConverterException(ioe);
+ }
+ return byteArrayOutputStream.toByteArray();
+ }
+
+ private void addDataOverlayToZip(final DataOverlay overlay, final ZipOutputStream zos) throws IOException {
+ ColorSchemaWriter writer = new ColorSchemaWriter();
+ ZipEntry entry = new ZipEntry(ZipEntryFileFactory.LAYOUT_DIRECTORY + overlay.getId() + "_" + overlay.getName());
+ zos.putNextEntry(entry);
+ zos.write(writer.overlayToString(overlay).getBytes());
+ zos.closeEntry();
+ }
+
+ private void addGlyphsToZip(final Model model, final ZipOutputStream zos) throws IOException {
+ for (Element element : model.getElements()) {
+ if (element.getGlyph() != null) {
+ UploadedFileEntry uploadedFileEntry = element.getGlyph().getFile();
+ ZipEntry entry = new ZipEntry(ZipEntryFileFactory.GLYPHS_DIRECTORY + new File(uploadedFileEntry.getOriginalFileName()).getName());
+ zos.putNextEntry(entry);
+ zos.write(uploadedFileEntry.getFileContent());
+ zos.closeEntry();
+ }
+ }
+ for (Layer layer : model.getLayers()) {
+ for (LayerImage image : layer.getImages()) {
+ if (image.getGlyph() != null) {
+ UploadedFileEntry uploadedFileEntry = image.getGlyph().getFile();
+ ZipEntry entry = new ZipEntry(ZipEntryFileFactory.GLYPHS_DIRECTORY + new File(uploadedFileEntry.getOriginalFileName()).getName());
+ zos.putNextEntry(entry);
+ zos.write(uploadedFileEntry.getFileContent());
+ zos.closeEntry();
+ }
+ }
+ }
+ }
+
+ private int idCounter = 0;
+
+ private Model createMappingModel(final Set<ModelData> models) {
+ Model mapping = new ModelFullIndexed(null);
+ for (ModelData parentModel : models) {
+ for (Element parentElement : parentModel.getElements()) {
+ ElementSubmodelConnection connection = parentElement.getSubmodel();
+ if (connection != null) {
+ ModelData childModel = connection.getSubmodel();
+
+ Complex mappingParentElement = getComplexForConnection(parentModel.getName(), mapping);
+
+ Species sourceElement = getComplexChildForConnection(parentElement.getElementId(), mappingParentElement);
+
+ Complex mappingChildElement = getComplexForConnection(childModel.getName(), mapping);
+
+ Species targetElement;
+ if (connection.getToElement() != null) {
+ targetElement = getComplexChildForConnection(connection.getToElement().getElementId(), mappingChildElement);
+ } else {
+ targetElement = mappingChildElement;
+ }
+
+ Reaction reaction = new TransportReaction("re" + idCounter++);
+ reaction.addReactant(new Reactant(sourceElement));
+ reaction.addProduct(new Product(targetElement));
+ mapping.addReaction(reaction);
+ }
+ if (parentElement.getImmediateLink() != null) {
+ Compartment mappingParentCompartment = getCompartmentForConnection(parentModel.getName(), mapping);
+
+ Species sourceElement = getCompartmentChildForConnection(parentElement.getElementId(), mappingParentCompartment);
+ String notes = sourceElement.getNotes();
+ notes += "\n" + ComplexZipConverter.IMMEDIATE_LINK_PREFIX + parentElement.getImmediateLink();
+ sourceElement.setNotes(notes);
+ }
+ if (parentElement.getGlyph() != null) {
+ UploadedFileEntry uploadedFileEntry = parentElement.getGlyph().getFile();
+ Compartment mappingParentCompartment = getCompartmentForConnection(parentModel.getName(), mapping);
+
+ Species sourceElement = getCompartmentChildForConnection(parentElement.getElementId(), mappingParentCompartment);
+ String notes = sourceElement.getNotes();
+ notes += "\n" + ComplexZipConverter.GLYPH_PREFIX + "glyphs/" + new File(uploadedFileEntry.getOriginalFileName()).getName();
+ sourceElement.setNotes(notes);
+ }
+ }
+ }
+ try {
+ new ApplySimpleLayoutModelCommand(mapping).execute();
+ } catch (Exception e) {
+ logger.error("Problem with preparing mapping file", e);
+ }
+ return mapping;
+ }
+
+ private Species getComplexChildForConnection(final String elementId, final Complex mappingParentElement) {
+ Species sourceElement = null;
+ for (Species child : mappingParentElement.getAllChildren()) {
+ if (child.getName().equals(elementId)) {
+ sourceElement = child;
+ }
+ }
+
+ if (sourceElement == null) {
+ sourceElement = new GenericProtein("sa" + idCounter++);
+ sourceElement.setName(elementId);
+ mappingParentElement.addSpecies(sourceElement);
+ mappingParentElement.getModel().addElement(sourceElement);
+ }
+ return sourceElement;
+ }
+
+ private Species getCompartmentChildForConnection(final String elementId, final Compartment mappingParentElement) {
+ Species sourceElement = null;
+ for (Element child : mappingParentElement.getElements()) {
+ if (child instanceof Species && child.getName().equals(elementId)) {
+ sourceElement = (Species) child;
+ }
+ }
+
+ if (sourceElement == null) {
+ sourceElement = new GenericProtein("sa" + idCounter++);
+ sourceElement.setName(elementId);
+ mappingParentElement.addElement(sourceElement);
+ mappingParentElement.getModel().addElement(sourceElement);
+ }
+ return sourceElement;
+ }
+
+ private Complex getComplexForConnection(final String modelName, final Model mapping) {
+ List<Element> mappingParentElements = mapping.getElementsByName(modelName);
+
+ Complex mappingParentElement = null;
+ for (Element mappingElement : mappingParentElements) {
+ if (mappingElement instanceof Complex) {
+ mappingParentElement = (Complex) mappingElement;
+ }
+ }
+ if (mappingParentElement == null) {
+ mappingParentElement = new Complex("ca" + idCounter++);
+ mappingParentElement.setName(modelName);
+ mapping.addElement(mappingParentElement);
+ }
+ return mappingParentElement;
+ }
+
+ private Compartment getCompartmentForConnection(final String modelName, final Model mapping) {
+ List<Element> mappingParentElements = mapping.getElementsByName(modelName);
+
+ Compartment mappingParentElement = null;
+ for (Element mappingElement : mappingParentElements) {
+ if (mappingElement instanceof Compartment) {
+ mappingParentElement = (Compartment) mappingElement;
+ }
+ }
+ if (mappingParentElement == null) {
+ mappingParentElement = new SquareCompartment("ca" + idCounter++);
+ mappingParentElement.setName(modelName);
+ mapping.addElement(mappingParentElement);
+ }
+ return mappingParentElement;
+ }
}
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
index 317842d7637aa49750ab95b12430bddded8cdb0b..8bc71e00b22f0b86c15142f679a7e9adea5d60ef 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/zip/ZipEntryFileFactory.java
@@ -1,23 +1,21 @@
package lcsb.mapviewer.converter.zip;
+import lcsb.mapviewer.common.TextFileUtils;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import org.apache.commons.io.FilenameUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
import java.io.IOException;
import java.io.InputStream;
import java.util.Map;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import org.apache.commons.io.FilenameUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-import lcsb.mapviewer.common.TextFileUtils;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-
/**
* Factory class used to create {@link ZipEntryFile} objects.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ZipEntryFileFactory {
/**
@@ -39,7 +37,7 @@ public class ZipEntryFileFactory {
* Directory in a zip file where information about submodels is stored. These
* entries should be by default transformed into {@link ModelZipEntryFile}.
*/
- private static final String SUBMODEL_DIRECTORY = "submaps/";
+ public static final String SUBMODEL_DIRECTORY = "submaps/";
/**
* Directory in a zip file where information about
* {@link lcsb.mapviewer.model.map.OverviewImage OverviewImage} is stored. These
@@ -51,24 +49,24 @@ public class ZipEntryFileFactory {
* {@link lcsb.mapviewer.model.map.layout.graphics.Glyph} is stored. These
* entries should be by default transformed into {@link GlyphZipEntryFile}.
*/
- private static final String GLYPHS_DIRECTORY = "glyphs/";
+ public static final String GLYPHS_DIRECTORY = "glyphs/";
/**
* Directory in a zip file where information about
* {@link lcsb.mapviewer.model.map.layout.Layout Layout} is stored. These
* entries should be by default transformed into {@link LayoutZipEntryFile}.
*/
- private static final String LAYOUT_DIRECTORY = "layouts/";
+ public static final String LAYOUT_DIRECTORY = "layouts/";
/**
* Name of the parameter in {@link LayoutZipEntryFile file describing layout}
* corresponding to the {@link LayoutZipEntryFile#name layout name}.
*/
- private static final String LAYOUT_HEADER_PARAM_NAME = "NAME";
+ public static final String LAYOUT_HEADER_PARAM_NAME = "NAME";
/**
* Name of the parameter in {@link LayoutZipEntryFile file describing layout}
* corresponding to the {@link LayoutZipEntryFile#description layout
* description}.
*/
- private static final String LAYOUT_HEADER_PARAM_DESCRIPTION = "DESCRIPTION";
+ public static final String LAYOUT_HEADER_PARAM_DESCRIPTION = "DESCRIPTION";
/**
* Default class logger.
*/
@@ -78,14 +76,11 @@ public class ZipEntryFileFactory {
/**
* Generates instance of {@link ZipEntryFile} representing entry in the zip file
* with pre-parsed structural data (like: type, name, description, etc).
- *
- * @param entry
- * {@link ZipEntry entry} in the {@link ZipFile}
- * @param zipFile
- * original {@link ZipFile}
+ *
+ * @param entry {@link ZipEntry entry} in the {@link ZipFile}
+ * @param zipFile original {@link ZipFile}
* @return {@link ZipEntryFile} for the given {@link ZipEntry}
- * @throws IOException
- * thrown when there is a problem with accessing zip file
+ * @throws IOException thrown when there is a problem with accessing zip file
*/
public ZipEntryFile createZipEntryFile(final ZipEntry entry, final ZipFile zipFile) throws IOException {
if (entry.isDirectory()) {
@@ -142,14 +137,11 @@ public class ZipEntryFileFactory {
/**
* Creates {@link LayoutZipEntryFile layout entry} from input stream and given
* name of the layout.
- *
- * @param name
- * name of the layout
- * @param inputStream
- * stream where data is stored
+ *
+ * @param name name of the layout
+ * @param inputStream stream where data is stored
* @return {@link LayoutZipEntryFile} processed from input data
- * @throws IOException
- * thrown when there is problem with accessing input data
+ * @throws IOException thrown when there is problem with accessing input data
*/
public LayoutZipEntryFile createLayoutZipEntryFile(final String name, final InputStream inputStream) throws IOException {
LayoutZipEntryFile result = new LayoutZipEntryFile();
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
index 5850f0dad1bc7462da0d3249e7b4de1a83f6f784..bea7c1a8885b1d67c9bc966c546ece254a9cb132 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ComplexZipConverterTest.java
@@ -4,6 +4,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidClassException;
import lcsb.mapviewer.converter.zip.LayoutZipEntryFile;
import lcsb.mapviewer.converter.zip.ModelZipEntryFile;
+import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
@@ -40,7 +41,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
}
@Test
- public void testConstructor3() throws Exception {
+ public void testConstructor3() {
new ComplexZipConverter(MockConverter.class);
}
@@ -54,7 +55,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
+ Model model = converter.createModel(params, new Project());
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(3, model.getSubmodelConnections().size());
@@ -108,7 +109,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- Model model = converter.createModel(params);
+ Model model = converter.createModel(params, new Project());
assertNotNull(model);
assertEquals("main", model.getName());
assertEquals(3, model.getSubmodelConnections().size());
@@ -160,7 +161,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s1.xml", "s1", false, false, SubmodelType.DOWNSTREAM_TARGETS));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -174,7 +175,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -188,7 +189,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -202,7 +203,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test
@@ -216,7 +217,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s2.xml", "s2", false, false, SubmodelType.PATHWAY));
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
- Model model = converter.createModel(params);
+ Model model = converter.createModel(params, new Project());
assertNotNull(model);
@@ -247,7 +248,7 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.entry(new ModelZipEntryFile("s3.xml", "s3", false, false, SubmodelType.UNKNOWN));
params.entry(new ModelZipEntryFile("mapping.xml", "", false, false, null));
params.entry(new ModelZipEntryFile("blabla.xml", "s3", false, false, SubmodelType.UNKNOWN));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test(expected = InvalidArgumentException.class)
@@ -258,11 +259,11 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
params.zipFile(new ZipFile("testFiles/invalid_mapping.zip"));
params.entry(new ModelZipEntryFile("main.xml", "main", true, false, null));
params.entry(new ModelZipEntryFile("mapping.xml", null, false, true, null));
- converter.createModel(params);
+ converter.createModel(params, new Project());
}
@Test
- public void testIsIgnoredFileForMac() throws Exception {
+ public void testIsIgnoredFileForMac() {
ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
assertTrue(converter.isIgnoredFile("__MACOSX/.desc"));
assertTrue(converter.isIgnoredFile(".DS_Store"));
@@ -272,13 +273,13 @@ public class ComplexZipConverterTest extends ConverterTestFunctions {
}
@Test
- public void testIsIgnoredFileForOldMacEntries() throws Exception {
+ public void testIsIgnoredFileForOldMacEntries() {
ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
assertTrue(converter.isIgnoredFile(".DS_Store/.desc"));
}
@Test
- public void testIsIgnoredFileForValidFiles() throws Exception {
+ public void testIsIgnoredFileForValidFiles() {
ComplexZipConverter converter = new ComplexZipConverter(MockConverter.class);
assertFalse(converter.isIgnoredFile("mapping.xml"));
}
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
index 02ddc58b20808b342eaa3c85d701483c48e696fe..1485ed962095df0b1426cb10c0d77fa66a1479c4 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/OverviewParserTest.java
@@ -1,8 +1,16 @@
package lcsb.mapviewer.converter;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
+import lcsb.mapviewer.model.map.OverviewImage;
+import lcsb.mapviewer.model.map.OverviewLink;
+import lcsb.mapviewer.model.map.OverviewModelLink;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import org.apache.commons.io.FileUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
import java.awt.geom.Point2D;
import java.io.File;
@@ -16,23 +24,15 @@ import java.util.Set;
import java.util.zip.ZipEntry;
import java.util.zip.ZipFile;
-import org.apache.commons.io.FileUtils;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
-import lcsb.mapviewer.model.map.OverviewImage;
-import lcsb.mapviewer.model.map.OverviewLink;
-import lcsb.mapviewer.model.map.OverviewModelLink;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
public class OverviewParserTest extends ConverterTestFunctions {
private static final String TEST_FILES_VALID_OVERVIEW_ZIP = "testFiles/valid_overview.zip";
private static final String TEST_FILES_VALID_OVERVIEW_CASE_SENSITIVE_ZIP = "testFiles/valid_overview_case_sensitive.zip";
- private OverviewParser parser = new OverviewParser();
+ private final OverviewParser parser = new OverviewParser();
@Before
public void setUp() throws Exception {
@@ -44,7 +44,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParsingValidFile() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<ImageZipEntryFile> imageEntries = createImageEntries(TEST_FILES_VALID_OVERVIEW_ZIP);
List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, null,
new ZipFile(TEST_FILES_VALID_OVERVIEW_ZIP));
@@ -66,8 +66,8 @@ public class OverviewParserTest extends ConverterTestFunctions {
assertTrue(link instanceof OverviewModelLink);
OverviewModelLink modelLink = (OverviewModelLink) link;
- Model mainModel = models.iterator().next();
- assertEquals(mainModel.getModelData(), modelLink.getLinkedModel());
+ ModelData mainModel = models.iterator().next();
+ assertEquals(mainModel, modelLink.getLinkedModel());
assertEquals((Integer) 10, modelLink.getxCoord());
assertEquals((Integer) 10, modelLink.getyCoord());
assertEquals((Integer) 3, modelLink.getZoomLevel());
@@ -75,7 +75,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParsingValidCaseSensitiveFile() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<ImageZipEntryFile> imageEntries = createImageEntries(TEST_FILES_VALID_OVERVIEW_CASE_SENSITIVE_ZIP);
for (final ImageZipEntryFile imageZipEntryFile : imageEntries) {
imageZipEntryFile.setFilename(imageZipEntryFile.getFilename().toLowerCase());
@@ -99,8 +99,8 @@ public class OverviewParserTest extends ConverterTestFunctions {
assertTrue(link instanceof OverviewModelLink);
OverviewModelLink modelLink = (OverviewModelLink) link;
- Model mainModel = models.iterator().next();
- assertEquals(mainModel.getModelData(), modelLink.getLinkedModel());
+ ModelData mainModel = models.iterator().next();
+ assertEquals(mainModel, modelLink.getLinkedModel());
assertEquals((Integer) 10, modelLink.getxCoord());
assertEquals((Integer) 10, modelLink.getyCoord());
assertEquals((Integer) 3, modelLink.getZoomLevel());
@@ -109,8 +109,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
private List<ImageZipEntryFile> createImageEntries(final String string) throws IOException {
List<ImageZipEntryFile> result = new ArrayList<>();
- ZipFile zipFile = new ZipFile(string);
- try {
+ try (ZipFile zipFile = new ZipFile(string)) {
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = entries.nextElement();
@@ -119,14 +118,12 @@ public class OverviewParserTest extends ConverterTestFunctions {
}
}
return result;
- } finally {
- zipFile.close();
}
}
@Test
public void testParsingValidFile2() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
String tmpDir = Files.createTempDirectory("tmp").toFile().getAbsolutePath();
@@ -145,7 +142,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test(expected = InvalidOverviewFile.class)
public void testParsingInvalidFile1() throws Exception {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_1.zip");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_1.zip"));
}
@@ -153,7 +150,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test(expected = InvalidOverviewFile.class)
public void testParsingInvalidFile2() throws Exception {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_2.zip");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_2.zip"));
}
@@ -161,16 +158,16 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test(expected = InvalidOverviewFile.class)
public void testParsingInvalidFile3() throws Exception {
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/invalid_overview_3.zip");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/invalid_overview_3.zip"));
}
- private Set<Model> createValidTestMapModel() {
- Set<Model> result = new HashSet<>();
+ private Set<ModelData> createValidTestMapModel() {
+ Set<ModelData> result = new HashSet<>();
Model model = new ModelFullIndexed(null);
model.setName("main");
- result.add(model);
+ result.add(model.getModelData());
return result;
}
@@ -181,9 +178,9 @@ public class OverviewParserTest extends ConverterTestFunctions {
public void testParseInvalidCoordinates() throws Exception {
String invalidCoordinates = "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\n"
+ "test.png\t10,10 10,400 400,400 400,10\tmain.xml\t10,10\t4";
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
- List<OverviewImage> images = new ArrayList<OverviewImage>();
+ List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
oi.setFilename("test.png");
oi.setWidth(1000);
@@ -198,9 +195,9 @@ public class OverviewParserTest extends ConverterTestFunctions {
String invalidCoordinates = "FILE\tPOLYGON\tLINK_TARGET\tMODEL_COORDINATES\tMODEL_ZOOM_LEVEL\tLINK_TYPE\n"
+ "test.png\t10,10 100,10 100,100 10,10\tmain.xml\t10,10\t3\tMODEL\n"
+ "test.png\t200,200 200,400 400,400 400,200\tmain.xml\t10,10\t4\tMODEL";
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
- List<OverviewImage> images = new ArrayList<OverviewImage>();
+ List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
oi.setFilename("test.png");
oi.setWidth(1000);
@@ -215,7 +212,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParseValidComplexCoordinates() throws Exception {
String invalidCoordinates = FileUtils.readFileToString(new File("testFiles/coordinates.txt"), "UTF-8");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
@@ -239,7 +236,7 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testParseValidComplexCoordinatesWithExtraImages() throws Exception {
String invalidCoordinates = FileUtils.readFileToString(new File("testFiles/coordinates.txt"), "UTF-8");
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
List<OverviewImage> images = new ArrayList<>();
OverviewImage oi = new OverviewImage();
@@ -267,10 +264,10 @@ public class OverviewParserTest extends ConverterTestFunctions {
@Test
public void testJsonCoordinates() throws Exception {
- Set<Model> models = createValidTestMapModel();
+ Set<ModelData> models = createValidTestMapModel();
Model child = new ModelFullIndexed(null);
child.setName("child");
- models.add(child);
+ models.add(child.getModelData());
List<ImageZipEntryFile> imageEntries = createImageEntries("testFiles/valid_overview_with_json.zip");
List<OverviewImage> result = parser.parseOverviewLinks(models, imageEntries, null, new ZipFile("testFiles/valid_overview_with_json.zip"));
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
index 327f984bdc2ab4ec4d4574fdf6c1e679b6800550..ea88c764532c884c45bd397a0572489ff5e9fe9c 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ProjectFactoryTest.java
@@ -149,7 +149,7 @@ public class ProjectFactoryTest extends ConverterTestFunctions {
public void testParseGlyphsAndPutThemAsElementGlyphs() throws Exception {
Model model = new ModelFullIndexed(null);
final GenericProtein protein = createProtein();
- protein.setNotes("Glyph: glyphs/g1.png");
+ protein.setNotes(ComplexZipConverter.GLYPH_PREFIX + "glyphs/g1.png");
model.addElement(protein);
MockConverter.modelToBeReturned = model;
@@ -188,7 +188,7 @@ public class ProjectFactoryTest extends ConverterTestFunctions {
final Layer layer = new Layer();
final LayerText text = new LayerText();
- text.setNotes("Glyph: glyphs/g1.png");
+ text.setNotes(ComplexZipConverter.GLYPH_PREFIX + " glyphs/g1.png");
layer.addLayerText(text);
model.addLayer(layer);
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java b/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java
index d64ce0e7a4cb69a5065c44b097ecf7f67432b9e3..2691ea372301777002d69ae4d757c8557c8ef935 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/ZIndexPopulatorTest.java
@@ -10,6 +10,7 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import lcsb.mapviewer.utils.ZIndexPopulator;
import org.junit.Test;
import static org.junit.Assert.assertNotNull;
diff --git a/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java b/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java
index 5c03c95b12acf2e6ff624496d7eea126ccce9543..89ccd70f0022c1add05c9d0d2db0f54e2985be5e 100644
--- a/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java
+++ b/converter/src/test/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParserTest.java
@@ -5,6 +5,7 @@ import lcsb.mapviewer.converter.ConverterTestFunctions;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamRelationType;
import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.utils.XmlAnnotationParser;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index 8965fe3a575b33146f5be0df4bea5ae4b33aa85b..2f02a80b2feeb3b98638ed2596b0fece426fbd9a 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -1173,6 +1173,12 @@ ServerConnector.getProjectSourceUrl = function (queryParams, filterParams) {
});
};
+ServerConnector.getDownloadProjectZipUrl = function (queryParams, filterParams) {
+ return this.getNewApiUrl({
+ type: "projects/" + queryParams.projectId + ":downloadGeneratedZip",
+ params: filterParams
+ });
+};
ServerConnector.getFilesUrl = function () {
return this.getApiUrl({
@@ -2744,6 +2750,20 @@ ServerConnector.getProjectSourceDownloadUrl = function (params) {
});
};
+ServerConnector.getProjectGenerateZipUrl = function (params) {
+ if (params === undefined) {
+ params = {};
+ }
+ var queryParams = {};
+ var filterParams = {};
+ var self = this;
+ return self.getProjectId(params.projectId).then(function (result) {
+ queryParams.projectId = result;
+ return self.getDownloadProjectZipUrl(queryParams, filterParams);
+ });
+};
+
+
ServerConnector.getDrugNamesByTarget = function (params) {
var self = this;
var queryParams = {};
diff --git a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
index 520d4b0760a7bea85e6c44237f2c852662028c4a..70d94fa46f1dbf046ebd745d1b4fd0aca9e052ef 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
@@ -158,6 +158,22 @@ ProjectInfoPanel.prototype._createInfoPanelGui = function () {
liElement.appendChild(projectOriginalFileButton);
dataTab.appendChild(liElement);
+ var projectGenerateZipFileButton = Functions.createElement({
+ type: "a",
+ name: "projectGenerateZipFileButton",
+ href: "#",
+ content: "<i class='fa fa-files-o'></i> get generated zip",
+ xss: false,
+ onclick: function () {
+ return self.downloadGeneratedZipFile();
+ }
+ });
+ liElement = Functions.createElement({
+ type: "li"
+ });
+ liElement.appendChild(projectGenerateZipFileButton);
+ dataTab.appendChild(liElement);
+
var projectLicenseButton = Functions.createElement({
type: "a",
name: "projectLicenseButton",
@@ -286,6 +302,17 @@ ProjectInfoPanel.prototype.downloadSourceFile = function () {
}).then(null, GuiConnector.alert);
};
+/**
+ *
+ * @returns {Promise}
+ */
+ProjectInfoPanel.prototype.downloadGeneratedZipFile = function () {
+ var self = this;
+ return ServerConnector.getProjectGenerateZipUrl().then(function (url) {
+ return self.downloadFile(url);
+ }).then(null, GuiConnector.alert);
+};
+
/**
*
* @returns {Promise}
@@ -334,7 +361,7 @@ ProjectInfoPanel.prototype.refresh = function () {
$("[name='projectLicenseButton']", self.getElement()).off('click');
if (project.getLicense() !== null) {
projectLicenseText.innerHTML = project.getLicense().getName();
- $("[name='projectLicenseButton']", self.getElement()).on('click', function(){
+ $("[name='projectLicenseButton']", self.getElement()).on('click', function () {
GuiConnector.info(project.getLicense().getContent());
});
} else {
diff --git a/model-command/pom.xml b/model-command/pom.xml
index 0dd05cf739543e86a3b0c488f2d7b990e6fac5c8..419bcff8842b889bf1b22664af24f5709586741c 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -1,60 +1,54 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>19.0.0~alpha.0</version>
- </parent>
- <artifactId>model-command</artifactId>
- <name>Model commands</name>
- <description>Tool with (undoable) commands that can be performed on model</description>
-
-
- <dependencies>
-
- <!-- the MapViewer model -->
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>model</artifactId>
- <version>19.0.0~alpha.0</version>
- </dependency>
-
-
- <!-- the MapViewer CellDEsigner converter -->
- <dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>converter-CellDesigner</artifactId>
- <version>19.0.0~alpha.0</version>
- </dependency>
-
- <!-- Log4J2-->
- <dependency>
- <groupId>org.apache.logging.log4j</groupId>
- <artifactId>log4j-api</artifactId>
- <version>${log4j2.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.logging.log4j</groupId>
- <artifactId>log4j-core</artifactId>
- <version>${log4j2.version}</version>
- </dependency>
-
- <!-- mockito used for testing -->
- <dependency>
- <groupId>org.mockito</groupId>
- <artifactId>mockito-core</artifactId>
- <version>${mockito.version}</version>
- <scope>test</scope>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
-
-
- </dependencies>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </parent>
+ <artifactId>model-command</artifactId>
+ <name>Model commands</name>
+ <description>Tool with (undoable) commands that can be performed on model</description>
+
+
+ <dependencies>
+
+ <!-- the MapViewer model -->
+ <dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>model</artifactId>
+ <version>19.0.0~alpha.0</version>
+ </dependency>
+
+
+ <!-- Log4J2-->
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-api</artifactId>
+ <version>${log4j2.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.logging.log4j</groupId>
+ <artifactId>log4j-core</artifactId>
+ <version>${log4j2.version}</version>
+ </dependency>
+
+ <!-- mockito used for testing -->
+ <dependency>
+ <groupId>org.mockito</groupId>
+ <artifactId>mockito-core</artifactId>
+ <version>${mockito.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+
+ </dependencies>
</project>
\ No newline at end of file
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index 9f43ffdc9d6ebc9ea170f5a7384caf2bf8c80ec8..56278534534733f14cd829988410ef5650b393c6 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -3,18 +3,19 @@ package lcsb.mapviewer.commands;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.layout.graphics.LayerImage;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.utils.RestAnnotationParser;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -33,7 +34,7 @@ import java.util.Set;
*/
public class CreateHierarchyCommand extends ModelCommand {
- public static final String TEXT_LAYER_NAME = "text";
+ public static final String PATHWAY_LAYER_NAME = "pathways";
/**
* Natural logarithm of four.
@@ -127,7 +128,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Cleans hierarchical information from the model.
*/
- protected void clean() {
+ public void clean() {
for (final Element alias : getModel().getElements()) {
alias.setCompartment(null);
alias.setPathway(null);
@@ -135,15 +136,6 @@ public class CreateHierarchyCommand extends ModelCommand {
alias.setTransparencyLevel("");
}
}
- Set<Compartment> toRemove = new HashSet<>();
- for (final Compartment alias : getModel().getCompartments()) {
- if (alias instanceof PathwayCompartment) {
- toRemove.add(alias);
- }
- }
- for (final Compartment alias : toRemove) {
- getModel().removeElement(alias);
- }
}
/**
@@ -154,8 +146,10 @@ public class CreateHierarchyCommand extends ModelCommand {
RestAnnotationParser rap = new RestAnnotationParser();
Model model = getModel();
int id = 0;
+ Layer pathwayLayer = null;
for (final Layer layer : model.getLayers()) {
- if (!Objects.equals(layer.getName(), TEXT_LAYER_NAME)) {
+ if (Objects.equals(layer.getName(), PATHWAY_LAYER_NAME)) {
+ pathwayLayer = layer;
for (final LayerRect rect : layer.getRectangles()) {
int nextId = getNextArtId(model, id);
id = nextId + 1;
@@ -207,8 +201,33 @@ public class CreateHierarchyCommand extends ModelCommand {
model.addElement(compartment);
}
+ } else {
+ Set<LayerText> objectsToRemove = new HashSet<>();
+ for (final LayerText text : layer.getTexts()) {
+ int nextId = getNextArtId(model, id);
+ id = nextId + 1;
+
+ if (text.getGlyph() != null) {
+ objectsToRemove.add(text);
+
+ LayerImage image = new LayerImage();
+ image.setX(text.getX());
+ image.setY(text.getY());
+ image.setZ(text.getZ());
+ image.setWidth(text.getWidth());
+ image.setHeight(text.getHeight());
+ image.setGlyph(text.getGlyph());
+ layer.addLayerImage(image);
+ }
+ }
+ for (LayerText image : objectsToRemove) {
+ layer.removeLayerText(image);
+ }
}
}
+ if (pathwayLayer != null) {
+ model.removeLayer(pathwayLayer);
+ }
}
private int getNextArtId(final Model model, final int id) {
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
deleted file mode 100644
index 65f76495848c5153d175a73ef7daa84a2a2f7167..0000000000000000000000000000000000000000
--- a/model-command/src/main/java/lcsb/mapviewer/commands/MoveElementsCommand.java
+++ /dev/null
@@ -1,192 +0,0 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
-
-/**
- * Command which moves elements in model by dx, dy coordinates.
- *
- * @author Piotr Gawron
- *
- */
-public class MoveElementsCommand extends ModelCommand {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private final Logger logger = LogManager.getLogger();
-
- /**
- * Delta x.
- */
- private double dx;
-
- /**
- * Delta y.
- */
- private double dy;
-
- /**
- * List of objects to move.
- */
- private List<Object> objectsToMove = new ArrayList<>();
-
- /**
- * Default constructor.
- *
- * @param model
- * model to move
- * @param elements
- * elements that should be moved
- * @param dx
- * delta x
- * @param dy
- * delta y
- */
- public MoveElementsCommand(final Model model, final Collection<? extends BioEntity> elements, final double dx, final double dy) {
- super(model);
- this.dx = dx;
- this.dy = dy;
- for (final Object object : elements) {
- if (object instanceof Element) {
- if (((Element) object).getModel() != model) {
- throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
- }
- } else if (object instanceof Reaction) {
- if (((Reaction) object).getModel() != model) {
- throw new InvalidArgumentException("Object doesnt belong to specified model: " + object);
- }
- } else {
- throw new InvalidArgumentException("Cannot move element: " + object);
- }
- }
- objectsToMove.addAll(elements);
- }
-
- @Override
- protected void undoImplementation() {
- dx = -dx;
- dy = -dy;
- executeImplementation();
- dx = -dx;
- dy = -dy;
- setStatus(ModelCommandStatus.UNDONE);
- }
-
- @Override
- protected void redoImplementation() {
- executeImplementation();
- setStatus(ModelCommandStatus.EXECUTED);
- }
-
- @Override
- protected void executeImplementation() {
- Set<Element> aliases = new HashSet<>();
-
- for (final Object object : objectsToMove) {
- if (object instanceof Element) {
- Element alias = (Element) object;
-
- includeInAffectedRegion(alias);
-
- alias.setX(alias.getX() + dx);
- alias.setY(alias.getY() + dy);
- alias.setNameX(alias.getNameX() + dx);
- alias.setNameY(alias.getNameY() + dy);
-
- if (alias instanceof SpeciesWithModificationResidue) {
- for (final ModificationResidue mr : ((SpeciesWithModificationResidue) alias).getModificationResidues()) {
- mr.setX(mr.getX() + dx);
- mr.setY(mr.getY() + dy);
- }
- }
- includeInAffectedRegion(alias);
-
- aliases.add(alias);
- } else if (object instanceof Reaction) {
- Reaction reaction = (Reaction) object;
- for (final Reactant node : reaction.getReactants()) {
- Point2D startPoint = node.getLine().getStartPoint();
- moveNode(node);
- node.getLine().setStartPoint(startPoint);
- }
- for (final Product node : reaction.getProducts()) {
- Point2D endPoint = node.getLine().getEndPoint();
- moveNode(node);
- node.getLine().setEndPoint(endPoint);
- }
- for (final Modifier node : reaction.getModifiers()) {
- Point2D startPoint = node.getLine().getStartPoint();
- moveNode(node);
- node.getLine().setStartPoint(startPoint);
- }
- for (final NodeOperator node : reaction.getOperators()) {
- moveNode(node);
- }
- includeInAffectedRegion(reaction);
- } else {
- throw new InvalidStateException("Unknown class type: " + object);
- }
- }
- if (aliases.size() > 0) {
- // TODO this must be improved, we cannot do full search on every move
- for (final Reaction reaction : getModel().getReactions()) {
- for (final ReactionNode node : reaction.getReactionNodes()) {
- if (aliases.contains(node.getElement())) {
- if (node instanceof Reactant) {
- Point2D point = node.getLine().getStartPoint();
- node.getLine().setStartPoint(point.getX() + dx, point.getY() + dy);
-
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getLines().get(0).getP2());
- } else if (node instanceof Modifier) {
- Point2D point = node.getLine().getStartPoint();
- node.getLine().setStartPoint(point.getX() + dx, point.getY() + dy);
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getLines().get(0).getP2());
- } else if (node instanceof Product) {
- Point2D point = node.getLine().getEndPoint();
- node.getLine().setEndPoint(point.getX() + dx, point.getY() + dy);
- // we don't have to include point that we change as it's already
- // on the border of the element
- includeInAffectedRegion(node.getLine().getEndPoint());
- }
- }
- }
- }
- }
- }
-
- private void moveNode(final AbstractNode node) {
- for (int i = 0; i < node.getLine().getLines().size(); i++) {
- Line2D line = node.getLine().getLines().get(i);
- node.getLine().setLine(i, line.getX1() + dx, line.getY1() + dy, line.getX2() + dx, line.getY2() + dy);
- }
- }
-}
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index 46a9798be3662e9af447bfb93a203e9da10573f7..dc27092f8fb434681a7d9f91a68209899576a035 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -7,8 +7,6 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.DoubleDimension;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.ZIndexPopulator;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.graphics.ArrowType;
@@ -31,6 +29,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+import lcsb.mapviewer.utils.ZIndexPopulator;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -347,8 +346,14 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
if (startPoint != null) {
line.setStartPoint(startPoint);
}
+ for (final ModifierType mt : ModifierType.values()) {
+ if (mt.getClazz().equals(modifier.getClass())) {
+ line.setEndAtd(mt.getAtd());
+ line.setType(mt.getLineType());
+ }
+ }
+
modifier.setLine(line);
- new ModifierTypeUtils().updateLineEndPoint(modifier);
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ModifierType.java
similarity index 72%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
rename to model-command/src/main/java/lcsb/mapviewer/commands/layout/ModifierType.java
index 24696c519e645025d4519d25c1a2f5f07573e0bc..49e8cf069db513c92b218abc7cc776244d1c260f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ModifierType.java
@@ -1,6 +1,5 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
+package lcsb.mapviewer.commands.layout;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.LineType;
@@ -16,9 +15,8 @@ import lcsb.mapviewer.model.map.reaction.Modifier;
/**
* This enum defines how different types of CellDesigner modifiers should be
* translated into the reaction {@link Modifier} class.
- *
+ *
* @author Piotr Gawron
- *
*/
public enum ModifierType {
@@ -30,7 +28,7 @@ public enum ModifierType {
/**
* Inhibition.
*/
- INHIBITION("INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0, ReactionCellDesignerConverter.RECT_SIZE / 2 - 1),
+ INHIBITION("INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0, ReactionData.RECT_SIZE / 2 - 1),
/**
* Unknown catalysis.
@@ -41,7 +39,7 @@ public enum ModifierType {
* Unknown inhibition.
*/
UNKNOWN_INHIBITION("UNKNOWN_INHIBITION", UnknownInhibition.class, ArrowType.CROSSBAR, 8.0,
- ReactionCellDesignerConverter.RECT_SIZE / 2 - 1, LineType.DASHED),
+ ReactionData.RECT_SIZE / 2 - 1, LineType.DASHED),
/**
* Physical stimulation.
@@ -57,32 +55,32 @@ public enum ModifierType {
* Trigger.
*/
TRIGGER_STRING("TRIGGER", Trigger.class, ArrowType.BLANK_CROSSBAR),
-
+
/**
* CellDesigner 2.5 modification type.
*/
TRANSCRIPTIONAL_ACTIVATION("TRANSCRIPTIONAL_ACTIVATION", Trigger.class, ArrowType.BLANK_CROSSBAR),
-
+
/**
* CellDesigner 2.5 modification type.
*/
- TRANSCRIPTIONAL_INHIBITION("TRANSCRIPTIONAL_INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0,
- ReactionCellDesignerConverter.RECT_SIZE / 2 - 1),
-
+ TRANSCRIPTIONAL_INHIBITION("TRANSCRIPTIONAL_INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0,
+ ReactionData.RECT_SIZE / 2 - 1),
+
;
/**
* CellDesigner string describing this type.
*/
- private String stringName;
+ private final String stringName;
/**
* Which class should be used for this type.
*/
- private Class<? extends Modifier> clazz;
+ private final Class<? extends Modifier> clazz;
/**
* How the arrow head of the line should look like.
*/
- private ArrowTypeData atd = new ArrowTypeData();
+ private final ArrowTypeData atd = new ArrowTypeData();
/**
* How much should be the arrow line trimmed.
*/
@@ -94,13 +92,10 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at) {
this(string, clazz, at, null, null, null);
@@ -108,15 +103,11 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
+ * @param arrowLength length of the arrow
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at, final Double arrowLength) {
this(string, clazz, at, arrowLength, null, null);
@@ -124,17 +115,12 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
- * @param trimLength
- * {@link #trimLength}
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
+ * @param arrowLength length of the arrow
+ * @param trimLength {@link #trimLength}
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at, final Double arrowLength, final Double trimLength) {
this(string, clazz, at, arrowLength, trimLength, null);
@@ -142,22 +128,16 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
- * @param trimLength
- * {@link #trimLength}
- * @param lt
- * {@link #lineType}
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
+ * @param arrowLength length of the arrow
+ * @param trimLength {@link #trimLength}
+ * @param lt {@link #lineType}
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at, final Double arrowLength, final Double trimLength,
- final LineType lt) {
+ final LineType lt) {
stringName = string;
this.clazz = clazz;
if (at != null) {
@@ -176,7 +156,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #stringName}
*/
public String getStringName() {
@@ -184,7 +163,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #clazz}
*/
public Class<? extends Modifier> getClazz() {
@@ -192,7 +170,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #atd}
*/
public ArrowTypeData getAtd() {
@@ -200,7 +177,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #trimLength}
*/
public double getTrimLength() {
@@ -208,7 +184,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #lineType}
*/
public LineType getLineType() {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ReactionData.java
similarity index 70%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java
rename to model-command/src/main/java/lcsb/mapviewer/commands/layout/ReactionData.java
index 3c412c80daf0d34ea354342ad66954ac8f0a014b..4b4781f5404160dcef8687fd47ddc2eb418e1586 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ReactionData.java
@@ -1,13 +1,12 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
+package lcsb.mapviewer.commands.layout;
/**
* Class that provides CellDesigner specific graphical information for Reaction.
* It's used for conversion from xml to normal x,y coordinates.
- *
+ *
* @author Piotr Gawron
- *
*/
-public final class ReactionCellDesignerConverter {
+public final class ReactionData {
/**
* What is the size of rectangle that is drawn in center point of the reaction.
*/
@@ -16,7 +15,7 @@ public final class ReactionCellDesignerConverter {
/**
* Default constructor that prevents instantiation.
*/
- protected ReactionCellDesignerConverter() {
+ ReactionData() {
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java b/model-command/src/main/java/lcsb/mapviewer/utils/ImportOnly.java
similarity index 80%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java
rename to model-command/src/main/java/lcsb/mapviewer/utils/ImportOnly.java
index 3f62862dcf85fb80346ec3911cbf9b9d26ef2284..98d3aa6713e53bc7eb453197de174636537f56fd 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java
+++ b/model-command/src/main/java/lcsb/mapviewer/utils/ImportOnly.java
@@ -1,11 +1,11 @@
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
-
-import static java.lang.annotation.ElementType.FIELD;
-import static java.lang.annotation.RetentionPolicy.RUNTIME;
+package lcsb.mapviewer.utils;
import java.lang.annotation.Retention;
import java.lang.annotation.Target;
+import static java.lang.annotation.ElementType.FIELD;
+import static java.lang.annotation.RetentionPolicy.RUNTIME;
+
@Retention(RUNTIME)
@Target(FIELD)
public @interface ImportOnly {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java b/model-command/src/main/java/lcsb/mapviewer/utils/NoteField.java
similarity index 91%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
rename to model-command/src/main/java/lcsb/mapviewer/utils/NoteField.java
index d24ff4c4be2dd90ac4d86fdecc90981b69275755..fc7127415614451261222ee5c9193e5a806db625 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java
+++ b/model-command/src/main/java/lcsb/mapviewer/utils/NoteField.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
+package lcsb.mapviewer.utils;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.Drawable;
@@ -10,9 +10,8 @@ import lcsb.mapviewer.model.map.species.Species;
/**
* Describes structural information that appears in the cell designer notes.
- *
+ *
* @author Piotr Gawron
- *
*/
public enum NoteField {
/**
@@ -151,12 +150,12 @@ public enum NoteField {
/**
* Name used in the notes to distinguish fields.
*/
- private String commonName;
+ private final String commonName;
/**
* What object class can have this field.
*/
- private Class<? extends Drawable> clazz;
+ private final Class<? extends Drawable> clazz;
/**
* What {@link MiriamType} is associated with the field.
@@ -165,11 +164,9 @@ public enum NoteField {
/**
* Default constructor.
- *
- * @param name
- * {@link #commonName}
- * @param clazz
- * {@link #clazz}
+ *
+ * @param name {@link #commonName}
+ * @param clazz {@link #clazz}
*/
NoteField(final String name, final Class<? extends Drawable> clazz) {
this.commonName = name;
@@ -178,13 +175,10 @@ public enum NoteField {
/**
* Default constructor.
- *
- * @param name
- * {@link #commonName}
- * @param clazz
- * {@link #clazz}
- * @param type
- * {@link #miriamType}
+ *
+ * @param name {@link #commonName}
+ * @param clazz {@link #clazz}
+ * @param type {@link #miriamType}
*/
NoteField(final String name, final Class<? extends Drawable> clazz, final MiriamType type) {
this(name, clazz);
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java b/model-command/src/main/java/lcsb/mapviewer/utils/RestAnnotationParser.java
similarity index 88%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
rename to model-command/src/main/java/lcsb/mapviewer/utils/RestAnnotationParser.java
index 9c0db8c9f418f77247a321a39be7d61666b26f1a..675807a38ac458adb7cee2d62f0d342d507a82d1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java
+++ b/model-command/src/main/java/lcsb/mapviewer/utils/RestAnnotationParser.java
@@ -1,20 +1,4 @@
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
-
-import java.awt.Color;
-import java.lang.annotation.Annotation;
-import java.lang.reflect.Field;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.apache.commons.text.StringEscapeUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.w3c.dom.Node;
+package lcsb.mapviewer.utils;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.comparator.DoubleComparator;
@@ -26,8 +10,6 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.ColorParser;
-import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.map.BioEntity;
@@ -40,38 +22,68 @@ import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import org.apache.commons.text.StringEscapeUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.w3c.dom.Node;
+
+import java.awt.Color;
+import java.lang.annotation.Annotation;
+import java.lang.reflect.Field;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
/**
* This class is a converter of annotation provided by lcsb in raw text format
* into set of MiriamData that can be used later on.
- *
+ *
* @author Piotr Gawron
- *
*/
public class RestAnnotationParser {
+ public static final Set<MiriamRelationType> RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER;
+
+ static {
+ Set<MiriamRelationType> types = new HashSet<>();
+ types.addAll(Arrays.asList(MiriamRelationType.values()));
+ types.remove(MiriamRelationType.BQ_MODEL_IS_DERIVED_FROM);
+ types.remove(MiriamRelationType.BQ_BIOL_HAS_PROPERTY);
+ types.remove(MiriamRelationType.BQ_BIOL_IS_PROPERTY_OF);
+ types.remove(MiriamRelationType.BQ_MODEL_IS_INSTANCE_OF);
+ types.remove(MiriamRelationType.BQ_MODEL_HAS_INSTANCE);
+ types.remove(MiriamRelationType.BQ_BIOL_HAS_TAXON);
+ RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER = Collections.unmodifiableSet(types);
+ }
+
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Pattern used to find rdf node in string xml.
*/
- private Pattern rdfNodePattern = Pattern.compile("(?<=<rdf:RDF)([\\s\\S]*?)(?=</rdf:RDF>)");
+ private final Pattern rdfNodePattern = Pattern.compile("(?<=<rdf:RDF)([\\s\\S]*?)(?=</rdf:RDF>)");
/**
* Parser used for parsing annotations in rdf format.
*/
- private XmlAnnotationParser xmlAnnotationParser;
+ private final XmlAnnotationParser xmlAnnotationParser;
/**
* Class used for some simple operations on {@link BioEntity} elements.
*/
- private ElementUtils elementUtils = new ElementUtils();
+ private final ElementUtils elementUtils = new ElementUtils();
public RestAnnotationParser() {
- xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+ xmlAnnotationParser = new XmlAnnotationParser(RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
}
/**
@@ -79,8 +91,7 @@ public class RestAnnotationParser {
* Parsing has been prepared based on the information provided by Kazuhiro
* Fujita, kaf@sbi.jp.
*
- * @param annotationString
- * - string with data to parse
+ * @param annotationString - string with data to parse
* @return list of {@link MiriamData annotations}
*/
public Set<MiriamData> getMiriamData(final String annotationString) {
@@ -110,8 +121,7 @@ public class RestAnnotationParser {
/**
* Creates note string with structural information about element.
*
- * @param element
- * element for which notes are created
+ * @param element element for which notes are created
* @return note string with structural information about element
*/
public String createAnnotationString(final Element element) {
@@ -121,11 +131,9 @@ public class RestAnnotationParser {
/**
* Creates note string with structural information about element.
*
- * @param element
- * element for which notes are created
- * @param forceFullInfo
- * when true annotation string will contain information about empty
- * fields
+ * @param element element for which notes are created
+ * @param forceFullInfo when true annotation string will contain information about empty
+ * fields
* @return note string with structural information about element
*/
public String createAnnotationString(final Element element, final boolean forceFullInfo) {
@@ -219,10 +227,8 @@ public class RestAnnotationParser {
* ...
* </pre>
*
- * @param annotationString
- * whole annotation string
- * @param prefix
- * prefix used for identifying line
+ * @param annotationString whole annotation string
+ * @param prefix prefix used for identifying line
* @return value for the given type in structured annotation
*/
private String getParamByPrefix(final String annotationString, final String prefix) {
@@ -248,8 +254,7 @@ public class RestAnnotationParser {
/**
* Returns list of symbols from the annotation string.
*
- * @param annotationString
- * annotation string
+ * @param annotationString annotation string
* @return list of symbol
*/
public List<String> getSynonyms(final String annotationString) {
@@ -268,8 +273,7 @@ public class RestAnnotationParser {
/**
* Returns list of former symbols from the annotation string.
*
- * @param annotationString
- * annotation string
+ * @param annotationString annotation string
* @return list of former symbol
*/
public List<String> getFormerSymbols(final String annotationString) {
@@ -290,10 +294,8 @@ public class RestAnnotationParser {
* database_ID: idfield1, idfield2, ..., idfieldn<br>
* into a vector of string ids.
*
- * @param line
- * - a line to be parsed
- * @param baseId
- * - database string id
+ * @param line - a line to be parsed
+ * @param baseId - database string id
* @return vector of string ids
*/
protected ArrayList<String> getIds(final String line, final String baseId) {
@@ -316,12 +318,9 @@ public class RestAnnotationParser {
/**
* This method transform the vector of ids into a set of MiriamData.
*
- * @param type
- * - relationtype of the annotaion ids
- * @param miriamType
- * {@link MiriamType type} of the reference resource
- * @param ids
- * - list of ids
+ * @param type - relationtype of the annotaion ids
+ * @param miriamType {@link MiriamType type} of the reference resource
+ * @param ids - list of ids
* @return set of miriam data
*/
private Set<MiriamData> idsToData(final MiriamRelationType type, final MiriamType miriamType, final ArrayList<String> ids) {
@@ -336,10 +335,8 @@ public class RestAnnotationParser {
/**
* Process element notes and assign structural information from it.
*
- * @param node
- * node with notes about element
- * @param element
- * where the structural data should be put
+ * @param node node with notes about element
+ * @param element where the structural data should be put
*/
public void processNotes(final Node node, final BioEntity element) {
String notes = getNotes(node);
@@ -349,8 +346,7 @@ public class RestAnnotationParser {
/**
* Process notes and assign structural information from it.
*
- * @param element
- * object with notes to be processed
+ * @param element object with notes to be processed
*/
public void processNotes(final Element element) {
processNotes(element.getNotes(), element);
@@ -359,16 +355,14 @@ public class RestAnnotationParser {
/**
* Process notes and assign structural information from it.
*
- * @param notes
- * notes about element
- * @param object
- * where the structural data should be put
+ * @param notes notes about element
+ * @param object where the structural data should be put
*/
public void processNotes(final String notes, final Drawable object) {
StringBuilder annotations = new StringBuilder();
String[] string = notes.split("\n");
- StringBuilder newNotes = new StringBuilder("");
+ StringBuilder newNotes = new StringBuilder();
for (final String string2 : string) {
boolean remove = false;
for (final NoteField field : NoteField.values()) {
@@ -434,8 +428,7 @@ public class RestAnnotationParser {
/**
* Transforms xml node into notes.
*
- * @param node
- * xml node with notes
+ * @param node xml node with notes
* @return string with notes
*/
public String getNotes(final Node node) {
@@ -465,10 +458,8 @@ public class RestAnnotationParser {
/**
* Assigns synonyms to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setSynonyms(final BioEntity element, final String annotationString) {
List<String> synonyms = getSynonyms(annotationString);
@@ -493,10 +484,8 @@ public class RestAnnotationParser {
/**
* Assigns list of symbols to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setFormerSymbolsToSpecies(final Element element, final String annotationString) {
List<String> formerSymbols = getFormerSymbols(annotationString);
@@ -517,10 +506,8 @@ public class RestAnnotationParser {
/**
* Assigns full name to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setFullNameToSpecies(final Element element, final String annotationString) {
StringComparator stringComparator = new StringComparator();
@@ -543,10 +530,8 @@ public class RestAnnotationParser {
/**
* Assigns abbreviation to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setAbbreviation(final BioEntity element, final String annotationString) {
StringComparator stringComparator = new StringComparator();
@@ -569,10 +554,8 @@ public class RestAnnotationParser {
/**
* Assigns subsystem to the reaction from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setSubsystemToReaction(final Reaction element, final String annotationString) {
StringComparator stringComparator = new StringComparator();
@@ -591,10 +574,8 @@ public class RestAnnotationParser {
/**
* Assigns gene protein reaction to the reaction from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setGeneProteinReactionToReaction(final Reaction element, final String annotationString) {
StringComparator stringComparator = new StringComparator();
@@ -613,10 +594,8 @@ public class RestAnnotationParser {
/**
* Assigns formula to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setFormula(final BioEntity element, final String annotationString) {
StringComparator stringComparator = new StringComparator();
@@ -642,10 +621,8 @@ public class RestAnnotationParser {
/**
* Assigns mechanical confidence score to the reaction from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setMechanicalConfidenceScoreToReaction(final Reaction element, final String annotationString) {
IntegerComparator integerComparator = new IntegerComparator();
@@ -666,10 +643,8 @@ public class RestAnnotationParser {
/**
* Assigns charge to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setCharge(final Species element, final String annotationString) {
IntegerComparator integerComparator = new IntegerComparator();
@@ -693,10 +668,8 @@ public class RestAnnotationParser {
/**
* Assigns lower bound to the reaction from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setLowerBoundToReaction(final Reaction element, final String annotationString) {
DoubleComparator doubleComparator = new DoubleComparator();
@@ -716,10 +689,8 @@ public class RestAnnotationParser {
/**
* Assigns upper bound to the reaction from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setUpperBoundToReaction(final Reaction element, final String annotationString) {
DoubleComparator doubleComparator = new DoubleComparator();
@@ -739,10 +710,8 @@ public class RestAnnotationParser {
/**
* Assigns symbol to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setSymbol(final BioEntity element, final String annotationString) {
String symbol = getSymbol(annotationString);
@@ -764,10 +733,8 @@ public class RestAnnotationParser {
/**
* Assigns semanticZoomingLevel to the element from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setSemanticZoomLevelVisibility(final BioEntity element, final String annotationString) {
String zoomLevelVisibility = getParamByPrefix(annotationString,
@@ -819,10 +786,8 @@ public class RestAnnotationParser {
* data from these sources should be merged. So, this method in fact merges
* notes in the element and description extracted from notes string.
*
- * @param element
- * element to which data should be put to
- * @param annotationString
- * notes string
+ * @param element element to which data should be put to
+ * @param annotationString notes string
*/
private void setNotes(final BioEntity element, final String annotationString) {
String description = getDescription(annotationString);
@@ -832,7 +797,7 @@ public class RestAnnotationParser {
if (element.getNotes().trim().equals("")) {
element.setNotes(description);
} else if (element.getNotes().contains(description)) {
- return;
+ //
} else {
element.setNotes(element.getNotes().trim() + "\n" + description + "\n");
}
@@ -887,10 +852,8 @@ public class RestAnnotationParser {
* Process RDF description from notes, removes it from the description and
* adds appropriate information to miriam data set.
*
- * @param element
- * notes of this element will be processed
- * @throws InvalidXmlSchemaException
- * thrown when there is a problem with xml
+ * @param element notes of this element will be processed
+ * @throws InvalidXmlSchemaException thrown when there is a problem with xml
*/
void processRdfDescription(final BioEntity element) throws InvalidXmlSchemaException {
String notes = element.getNotes();
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java b/model-command/src/main/java/lcsb/mapviewer/utils/XmlAnnotationParser.java
similarity index 99%
rename from converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
rename to model-command/src/main/java/lcsb/mapviewer/utils/XmlAnnotationParser.java
index 8f4b496202c077d9a998731d6dd02d0997d95be5..421b161d5c05fc8105146c925c294d2f0db68d7d 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/annotation/XmlAnnotationParser.java
+++ b/model-command/src/main/java/lcsb/mapviewer/utils/XmlAnnotationParser.java
@@ -1,4 +1,4 @@
-package lcsb.mapviewer.converter.annotation;
+package lcsb.mapviewer.utils;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
diff --git a/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java b/model-command/src/main/java/lcsb/mapviewer/utils/ZIndexPopulator.java
similarity index 91%
rename from converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
rename to model-command/src/main/java/lcsb/mapviewer/utils/ZIndexPopulator.java
index bad89a1306168d5a32f5bbc3e0fad3578449cba4..3be218d856d5ca16d2d021543980bca5f83141fe 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ZIndexPopulator.java
+++ b/model-command/src/main/java/lcsb/mapviewer/utils/ZIndexPopulator.java
@@ -1,13 +1,4 @@
-package lcsb.mapviewer.converter;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
+package lcsb.mapviewer.utils;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
@@ -22,22 +13,29 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
/**
* This util class populate with z-index data if necessary.
- *
- * @author Piotr Gawron
*
+ * @author Piotr Gawron
*/
public class ZIndexPopulator {
@SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
- private static DoubleComparator DOUBLE_COMPARATOR = new DoubleComparator(Configuration.EPSILON);
- private static StringComparator STRING_COMPARATOR = new StringComparator();
+ private static final DoubleComparator DOUBLE_COMPARATOR = new DoubleComparator(Configuration.EPSILON);
+ private static final StringComparator STRING_COMPARATOR = new StringComparator();
- private static Comparator<Drawable> COMPARATOR = new Comparator<Drawable>() {
+ private static final Comparator<Drawable> COMPARATOR = new Comparator<Drawable>() {
@Override
public int compare(final Drawable o1, final Drawable o2) {
if (o1 instanceof StructuralState) {
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index fac16a48f95c717876ccba665c8ce70e2c7e9e8f..2a3b2cebfcfe2ca83126c712023003ee6afd0418 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -1,20 +1,5 @@
package lcsb.mapviewer.commands;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
@@ -31,10 +16,25 @@ import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.field.TranscriptionSite;
import lcsb.mapviewer.model.overlay.DataOverlayEntry;
import lcsb.mapviewer.model.overlay.GenericDataOverlayEntry;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
public class ColorModelCommandTest extends CommandTestFunctions {
- private ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
+ private final ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE, Color.WHITE);
@Before
public void setUp() throws Exception {
@@ -45,10 +45,185 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColorFullModel() throws Exception {
+ public void testAliasMatchWithInvalidElementId() {
+ GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
+ colorSchema.setName(null);
+ colorSchema.setElementId("1");
+
+ BioEntity protein = new GenericProtein("id");
+ protein.setName("test");
+
+ List<DataOverlayEntry> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertFalse(factory.match(protein, colorSchema));
+
+ colorSchema.setElementId(null);
+ assertTrue(factory.match(protein, colorSchema));
+ }
+
+ @Test
+ public void testSpeciesMatchWithProteinType() {
+ GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
+ colorSchema.setName("s1");
+ colorSchema.addType(Protein.class);
+
+ GenericProtein species = new GenericProtein("id");
+ species.setName("s1");
+
+ List<DataOverlayEntry> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(species, colorSchema));
+ }
+
+ @Test
+ public void testSpeciesMatchWithMiriamData() {
+ GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
+ colorSchema.setName("s1");
+ colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ GenericDataOverlayEntry colorSchema2 = new GenericDataOverlayEntry();
+ colorSchema2.setName("s1");
+ colorSchema2.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7"));
+
+ GenericProtein species = new GenericProtein("id");
+ species.setName("s1");
+ species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ List<DataOverlayEntry> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(species, colorSchema));
+ assertFalse(factory.match(species, colorSchema2));
+ }
+
+ @Test
+ public void testSpeciesMatchWithMiriamDataDifferentAnnotator() {
+ GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
+ colorSchema.setName("s1");
+ colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ GenericProtein species = new GenericProtein("id");
+ species.setName("s1");
+ species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA", Object.class));
+
+ List<DataOverlayEntry> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(species, colorSchema));
+ }
+
+ @Test
+ public void testReactionMatchWithProteinMiriamData() {
+ GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
+ colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
+
+ Reaction reaction = new Reaction("re");
+
+ List<DataOverlayEntry> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertFalse(factory.match(reaction, colorSchema));
+ }
+
+ @Test
+ public void testReactionMatchWithMiriamData() {
+ GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
+ colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+
+ Reaction reaction = new Reaction("re");
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+
+ List<DataOverlayEntry> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(reaction, colorSchema));
+ }
+
+
+ @Test
+ public void testGetModifiedElements() {
+ Reaction reaction = new Reaction("re");
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+
+ Model model = new ModelFullIndexed(null);
+ model.addReaction(reaction);
+
+ GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
+ colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
+
+ List<DataOverlayEntry> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+
+ assertNotNull(factory.getModifiedElements().get(reaction));
+ }
+
+ @Test
+ public void testApplyColorToReaction() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ reaction.setIdReaction("re1");
+ model.addReaction(reaction);
+
+ DataOverlayEntry schema = new GenericDataOverlayEntry();
+ schema.setElementId("re1");
+ schema.setColor(Color.YELLOW);
+ schema.setName(null);
+
+ ColorModelCommand factory = new ColorModelCommand(model, new ArrayList<>(), colorExtractor);
+
+ factory.applyColor(reaction, schema);
+
+ assertEquals(Color.YELLOW, reaction.getLine().getColor());
+ }
+
+ @Test
+ public void testColorTranscriptionFactor() {
+ Model model = new ModelFullIndexed(null);
+
+ Gene gene = createGene();
+ TranscriptionSite site = new TranscriptionSite();
+ site.setBorderColor(Color.YELLOW);
+ gene.addTranscriptionSite(site);
+ model.addElement(gene);
+
+ ColorModelCommand factory = new ColorModelCommand(model, new ArrayList<>(), colorExtractor);
+ factory.execute();
+
+ assertEquals(Color.BLACK, site.getBorderColor());
+ }
+
+
+ @Test
+ public void testColorFullModel() {
ModelComparator comparator = new ModelComparator();
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model model2 = getModelForFile("testFiles/sample.xml", false);
+ Model model = createSimpleModel();
+ GenericProtein protein = createProteinWithLayout();
+ protein.setElementId("sa14");
+ protein.setName("CNC");
+ model.addElement(protein);
+
+ Model model2 = copyModel(model);
+
Model coloredModel = new CopyCommand(model).execute();
List<DataOverlayEntry> schemas = new ArrayList<>();
@@ -58,20 +233,32 @@ public class ColorModelCommandTest extends CommandTestFunctions {
schemas.add(schema);
ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas, colorExtractor);
- assertFalse(Color.RED.equals(coloredModel.getElementByElementId("sa14").getFillColor()));
+ assertNotEquals(Color.RED, coloredModel.getElementByElementId("sa14").getFillColor());
factory.execute();
assertEquals(0, comparator.compare(model, model2));
- assertFalse(comparator.compare(model, coloredModel) == 0);
+ assertNotEquals(0, comparator.compare(model, coloredModel));
assertEquals(Color.RED, coloredModel.getElementByElementId("sa14").getFillColor());
}
+ private Model copyModel(final Model model) {
+ return new CopyCommand(model).execute();
+ }
+
@Test
- public void testColoring2() throws Exception {
- Model model = getModelForFile("testFiles/coloring_model.xml", true);
+ public void testColoring2() {
+ Model model = createSimpleModel();
+ GenericProtein protein = createProteinWithLayout();
+ protein.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
+ model.addElement(protein);
+
+ Gene gene = createGene();
+ gene.addMiriamData(new MiriamData(MiriamType.CHEBI, "CHEBI:15377"));
+ model.addElement(gene);
+
Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
@@ -93,8 +280,13 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColorTheSameElementTwiceUsingDifferentSelector() throws Exception {
- Model model = getModelForFile("testFiles/coloring_model.xml", true);
+ public void testColorTheSameElementTwiceUsingDifferentSelector() {
+ Model model = createSimpleModel();
+ GenericProtein protein = createProteinWithLayout();
+ protein.setName("SNCA");
+ protein.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
+ model.addElement(protein);
+
Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.addMiriamData(new MiriamData(MiriamType.HGNC, "11138"));
@@ -108,67 +300,93 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<BioEntity, DataOverlayEntry> modifiedElements = factory.getModifiedElements();
- assertEquals(1, modifiedElements.keySet().size());
+ assertEquals(1, modifiedElements.size());
}
@Test
- public void testReactionColoring1() throws Exception {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re4 = model.getReactionByReactionId("re4");
- Collection<DataOverlayEntry> schemas = new ArrayList<DataOverlayEntry>();
+ public void testReactionColoring1() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ reaction.getNodes().get(0).getLine().setColor(Color.RED);
+ model.addReaction(reaction);
+
+ Collection<DataOverlayEntry> schemas = new ArrayList<>();
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
+ assertNotEquals(Color.BLACK, reaction.getNodes().get(0).getLine().getColor());
factory.execute();
- re4 = model.getReactionByReactionId("re4");
+ reaction = model.getReactionByReactionId(reaction.getIdReaction());
- assertEquals(Color.BLACK, re4.getNodes().get(0).getLine().getColor());
+ assertEquals(Color.BLACK, reaction.getNodes().get(0).getLine().getColor());
}
@Test
- public void testReactionColoring2() throws Exception {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re1 = model.getReactionByReactionId("re1");
- Collection<DataOverlayEntry> schemas = new ArrayList<DataOverlayEntry>();
+ public void testReactionColoring2() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ model.addReaction(reaction);
+
+ Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
- schema.setElementId("re1");
+ schema.setElementId(reaction.getIdReaction());
schema.setColor(Color.RED);
schemas.add(schema);
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
+ assertEquals(Color.BLACK, reaction.getNodes().get(0).getLine().getColor());
factory.execute();
- re1 = model.getReactionByReactionId("re1");
+ reaction = model.getReactionByReactionId(reaction.getIdReaction());
- assertEquals(Color.RED, re1.getNodes().get(0).getLine().getColor());
+ assertEquals(Color.RED, reaction.getNodes().get(0).getLine().getColor());
}
@Test
- public void testReactionColoring3() throws Exception {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re2 = model.getReactionByReactionId("re2");
- Collection<DataOverlayEntry> schemas = new ArrayList<DataOverlayEntry>();
+ public void testReactionColoring3() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ model.addReaction(reaction);
+
+ Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
- schema.setElementId("re2");
+ schema.setElementId(reaction.getIdReaction());
schema.setValue(-1.0);
schemas.add(schema);
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
+ assertEquals(Color.BLACK, reaction.getNodes().get(0).getLine().getColor());
factory.execute();
- re2 = model.getReactionByReactionId("re2");
+ reaction = model.getReactionByReactionId(reaction.getIdReaction());
- assertEquals(Color.RED, re2.getNodes().get(0).getLine().getColor());
+ assertEquals(Color.RED, reaction.getNodes().get(0).getLine().getColor());
}
@Test
- public void testReactionColoring4() throws Exception {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re3 = model.getReactionByReactionId("re3");
- Collection<DataOverlayEntry> schemas = new ArrayList<DataOverlayEntry>();
+ public void testReactionColoring4() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
+ model.addReaction(reaction);
+
+ Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
schema.setValue(-1.0);
@@ -176,18 +394,22 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
+ assertEquals(Color.BLACK, reaction.getNodes().get(0).getLine().getColor());
factory.execute();
- re3 = model.getReactionByReactionId("re3");
+ reaction = model.getReactionByReactionId(reaction.getIdReaction());
- assertEquals(Color.RED, re3.getNodes().get(0).getLine().getColor());
+ assertEquals(Color.RED, reaction.getNodes().get(0).getLine().getColor());
}
@Test
- public void testColoringComplexModel() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model model2 = getModelForFile("testFiles/sample.xml", false);
+ public void testColoringComplexModel() {
+ Model model = createSimpleModel();
+ Model model2 = createSimpleModel();
+
+ Protein protein1 = createProteinWithLayout();
+ protein1.setFillColor(Color.PINK);
+ model2.addElement(protein1);
model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "BLA"));
@@ -198,15 +420,22 @@ public class ColorModelCommandTest extends CommandTestFunctions {
Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
- assertFalse(
- coloredModel2.getElementByElementId("sa2").getFillColor().equals(model2.getElementByElementId("sa2").getFillColor()));
- assertFalse(
- coloredModel3.getElementByElementId("sa2").getFillColor().equals(model2.getElementByElementId("sa2").getFillColor()));
+ assertNotEquals(coloredModel2.getElementByElementId(protein1.getElementId()).getFillColor(),
+ model2.getElementByElementId(protein1.getElementId()).getFillColor());
+ assertNotEquals(coloredModel3.getElementByElementId(protein1.getElementId()).getFillColor(),
+ model2.getElementByElementId(protein1.getElementId()).getFillColor());
}
@Test
- public void testColoredAliases() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ public void testColoredAliases() {
+ Model model = createSimpleModel();
+ Protein p1 = createProtein();
+ p1.setName("CNC");
+ model.addElement(p1);
+ Protein protein = createProtein();
+ protein.setName("BDH1");
+ model.addElement(protein);
+
Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setName("CNC");
@@ -226,11 +455,18 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColoredReactions() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ public void testColoredReactions() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ model.addReaction(reaction);
+
Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
- schema.setElementId("re1");
+ schema.setElementId(reaction.getIdReaction());
schema.setLineWidth(3.0);
schema.setColor(Color.BLUE);
schema.setName("not matching name");
@@ -243,11 +479,18 @@ public class ColorModelCommandTest extends CommandTestFunctions {
}
@Test
- public void testColoredReactions2() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ public void testColoredReactions2() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ model.addReaction(reaction);
+
Collection<DataOverlayEntry> schemas = new ArrayList<>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
- schema.setElementId("re1");
+ schema.setElementId(reaction.getIdReaction());
schema.setLineWidth(3.0);
schema.setColor(Color.BLUE);
schema.setName(null);
@@ -259,126 +502,23 @@ public class ColorModelCommandTest extends CommandTestFunctions {
assertEquals(1, map.size());
for (Map.Entry<BioEntity, DataOverlayEntry> entry : map.entrySet()) {
assertTrue(entry.getKey() instanceof Reaction);
- assertEquals("re1", ((Reaction) entry.getKey()).getIdReaction());
+ assertEquals(reaction.getIdReaction(), ((Reaction) entry.getKey()).getIdReaction());
assertEquals(entry.getValue(), schema);
}
}
@Test
- public void testAliasMatchWithInvalidElementId() throws Exception {
- GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
- colorSchema.setName(null);
- colorSchema.setElementId("1");
-
- BioEntity protein = new GenericProtein("id");
- protein.setName("test");
-
- List<DataOverlayEntry> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
-
- assertFalse(factory.match(protein, colorSchema));
-
- colorSchema.setElementId(null);
- assertTrue(factory.match(protein, colorSchema));
- }
-
- @Test
- public void testSpeciesMatchWithProteinType() throws Exception {
- GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
- colorSchema.setName("s1");
- colorSchema.addType(Protein.class);
-
- GenericProtein species = new GenericProtein("id");
- species.setName("s1");
-
- List<DataOverlayEntry> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
-
- assertTrue(factory.match(species, colorSchema));
- }
-
- @Test
- public void testSpeciesMatchWithMiriamData() throws Exception {
- GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
- colorSchema.setName("s1");
- colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-
- GenericDataOverlayEntry colorSchema2 = new GenericDataOverlayEntry();
- colorSchema2.setName("s1");
- colorSchema2.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "PARK7"));
-
- GenericProtein species = new GenericProtein("id");
- species.setName("s1");
- species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-
- List<DataOverlayEntry> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
-
- assertTrue(factory.match(species, colorSchema));
- assertFalse(factory.match(species, colorSchema2));
- }
-
- @Test
- public void testSpeciesMatchWithMiriamDataDifferentAnnotator() throws Exception {
- GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
- colorSchema.setName("s1");
- colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-
- GenericProtein species = new GenericProtein("id");
- species.setName("s1");
- species.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA", Object.class));
-
- List<DataOverlayEntry> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
-
- assertTrue(factory.match(species, colorSchema));
- }
-
- @Test
- public void testReactionMatchWithProteinMiriamData() throws Exception {
- GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
- colorSchema.addMiriamData(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA"));
-
- Reaction reaction = new Reaction("re");
-
- List<DataOverlayEntry> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
-
- assertFalse(factory.match(reaction, colorSchema));
- }
-
- @Test
- public void testReactionMatchWithMiriamData() throws Exception {
- GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
- colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
-
- Reaction reaction = new Reaction("re");
- reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
-
- List<DataOverlayEntry> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
-
- assertTrue(factory.match(reaction, colorSchema));
- }
-
- @Test
- public void testReactionColoringWithModelNotMatching() throws Exception {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ public void testReactionColoringWithModelNotMatching() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ model.addReaction(reaction);
DataOverlayEntry schema = new GenericDataOverlayEntry();
- schema.setElementId("re4");
+ schema.setElementId(reaction.getIdReaction());
schema.setName(null);
schema.setModelName(model.getName() + "XXX");
@@ -387,15 +527,21 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<BioEntity, DataOverlayEntry> map = factory.getModifiedElements();
- assertEquals(0, map.values().size());
+ assertEquals(0, map.size());
}
@Test
- public void testReactionColoringWithModelMatch() throws Exception {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ public void testReactionColoringWithModelMatch() {
+ Model model = createSimpleModel();
+ Protein protein1 = createProteinWithLayout();
+ Protein protein2 = createProteinWithLayout();
+ model.addElement(protein1);
+ model.addElement(protein2);
+ Reaction reaction = createReactionWithLayout(protein1, protein1);
+ model.addReaction(reaction);
DataOverlayEntry schema = new GenericDataOverlayEntry();
- schema.setElementId("re4");
+ schema.setElementId(reaction.getIdReaction());
schema.setName(null);
schema.setModelName(model.getName());
@@ -404,12 +550,15 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<BioEntity, DataOverlayEntry> map = factory.getModifiedElements();
- assertEquals(1, map.values().size());
+ assertEquals(1, map.size());
}
@Test
- public void testAliasColoringWithModelNotMatching() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ public void testAliasColoringWithModelNotMatching() {
+ Model model = createSimpleModel();
+ Protein p1 = createProtein();
+ p1.setName("CNC");
+ model.addElement(p1);
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setName("CNC");
@@ -420,12 +569,15 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<BioEntity, DataOverlayEntry> map = factory.getModifiedElements();
- assertEquals(0, map.values().size());
+ assertEquals(0, map.size());
}
@Test
- public void testAliasColoringWithModelMatch() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ public void testAliasColoringWithModelMatch() {
+ Model model = createSimpleModel();
+ Protein p1 = createProtein();
+ p1.setName("CNC");
+ model.addElement(p1);
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setName("CNC");
@@ -436,11 +588,13 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<BioEntity, DataOverlayEntry> map = factory.getModifiedElements();
- assertEquals(1, map.values().size());
+ assertEquals(1, map.size());
}
- public void testAliasColoringWithUnknownElementSourceId() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ @Test
+ public void testAliasColoringWithUnknownElementSourceId() {
+ Model model = createSimpleModel();
+ model.addElement(createProtein());
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setElementId("xxx");
@@ -450,12 +604,13 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<BioEntity, DataOverlayEntry> map = factory.getModifiedElements();
- assertEquals(0, map.values().size());
+ assertEquals(0, map.size());
}
@Test
- public void testAliasColoringWithElementIdMatch() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ public void testAliasColoringWithElementIdMatch() {
+ Model model = createSimpleModel();
+ model.addElement(createProtein());
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setElementId(model.getElements().iterator().next().getElementId());
@@ -465,59 +620,7 @@ public class ColorModelCommandTest extends CommandTestFunctions {
ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
Map<BioEntity, DataOverlayEntry> map = factory.getModifiedElements();
- assertEquals(1, map.values().size());
- }
-
- @Test
- public void testGetModifiedElements() throws Exception {
- Reaction reaction = new Reaction("re");
- reaction.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
-
- Model model = new ModelFullIndexed(null);
- model.addReaction(reaction);
-
- GenericDataOverlayEntry colorSchema = new GenericDataOverlayEntry();
- colorSchema.addMiriamData(new MiriamData(MiriamType.PUBMED, "1234"));
-
- List<DataOverlayEntry> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
-
- assertNotNull(factory.getModifiedElements().get(reaction));
- }
-
- @Test
- public void testApplyColorToReaction() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Reaction re4 = model.getReactionByReactionId("re1");
-
- DataOverlayEntry schema = new GenericDataOverlayEntry();
- schema.setElementId("re1");
- schema.setColor(Color.YELLOW);
- schema.setName(null);
-
- ColorModelCommand factory = new ColorModelCommand(model, new ArrayList<>(), colorExtractor);
-
- factory.applyColor(re4, schema);
-
- assertEquals(Color.YELLOW, re4.getLine().getColor());
- }
-
- @Test
- public void testColorTranscriptionFactor() {
- Model model = new ModelFullIndexed(null);
-
- Gene gene = createGene();
- TranscriptionSite site = new TranscriptionSite();
- site.setBorderColor(Color.YELLOW);
- gene.addTranscriptionSite(site);
- model.addElement(gene);
-
- ColorModelCommand factory = new ColorModelCommand(model, new ArrayList<>(), colorExtractor);
- factory.execute();
-
- assertEquals(Color.BLACK, site.getBorderColor());
+ assertEquals(1, map.size());
}
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
index e02274c2ff8704a181ea3814f057b4f69873442d..a9f361fbdfb3148e2b25be8737f7a7f1d8d3fcb4 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CommandTestFunctions.java
@@ -1,14 +1,16 @@
package lcsb.mapviewer.commands;
import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.tests.TestUtils;
import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
import lcsb.mapviewer.model.graphics.HorizontalAlign;
+import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.graphics.VerticalAlign;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
+import lcsb.mapviewer.model.map.layout.graphics.LayerImage;
+import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -24,15 +26,14 @@ import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Rule;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
+import java.awt.Color;
+import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
-public abstract class CommandTestFunctions {
+public abstract class CommandTestFunctions extends TestUtils {
private static final Map<String, Model> models = new HashMap<>();
protected static final double EPSILON = Configuration.EPSILON;
@@ -43,27 +44,9 @@ public abstract class CommandTestFunctions {
private int counter;
- protected Model getModelForFile(final String fileName, final boolean fromCache) throws Exception {
- if (!fromCache) {
- logger.debug("File without cache: " + fileName);
- final Model result = new CellDesignerXmlParser().createModel(new ConverterParams().filename(fileName));
- result.setName("Unknown");
- return result;
- }
- Model result = models.get(fileName);
- if (result == null) {
- logger.debug("File to cache: " + fileName);
-
- final CellDesignerXmlParser parser = new CellDesignerXmlParser();
- result = parser.createModel(new ConverterParams().filename(fileName).sizeAutoAdjust(false));
- result.setName("Unknown");
- models.put(fileName, result);
- }
- return result;
- }
-
protected Model createSimpleModel() {
final Model model = new ModelFullIndexed(null);
+ model.setName(faker.name().fullName());
final GenericProtein alias = new GenericProtein("alias_id");
assignCoordinates(alias);
@@ -89,22 +72,6 @@ public abstract class CommandTestFunctions {
return model;
}
- protected Model serializeViaCellDesigner(final Model original)
- throws InconsistentModelException, InvalidInputDataExecption {
- final CellDesignerXmlParser parser = new CellDesignerXmlParser();
- final String xmlString = parser.model2String(original);
- final InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
- final Model result = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
-
- for (final Drawable bioEntity : original.getDrawables()) {
- bioEntity.setZ(null);
- }
- for (final Drawable bioEntity : result.getDrawables()) {
- bioEntity.setZ(null);
- }
- return result;
- }
-
protected Reaction createReaction(final Protein protein, final Protein protein2) {
final Reaction reaction = new TransportReaction("" + counter++);
reaction.addReactant(new Reactant(protein));
@@ -112,6 +79,18 @@ public abstract class CommandTestFunctions {
return reaction;
}
+ protected Reaction createReactionWithLayout(final Protein protein, final Protein protein2) {
+ final Reaction reaction = new TransportReaction("" + counter++);
+ Reactant reactant = new Reactant(protein);
+ reactant.setLine(new PolylineData(new Point2D.Double(protein.getX(), protein.getY()), protein.getCenter()));
+ Product product = new Product(protein2);
+ product.setLine(new PolylineData(new Point2D.Double(protein2.getX(), protein2.getY()), protein2.getCenter()));
+ reaction.addReactant(reactant);
+ reaction.addProduct(product);
+ reaction.setLine(new PolylineData(protein.getCenter(), protein2.getCenter()));
+ return reaction;
+ }
+
protected GenericProtein createProtein() {
final GenericProtein result = new GenericProtein("" + counter++);
result.setWidth((Double) null);
@@ -121,6 +100,15 @@ public abstract class CommandTestFunctions {
return result;
}
+ protected GenericProtein createProteinWithLayout() {
+ final GenericProtein result = createProtein();
+ result.setWidth(faker.number().numberBetween(100, 200));
+ result.setHeight(faker.number().numberBetween(100, 200));
+ result.setX(faker.number().numberBetween(100, 200));
+ result.setY(faker.number().numberBetween(100, 200));
+ return result;
+ }
+
protected Gene createGene() {
final Gene result = new Gene("" + counter++);
return result;
@@ -155,4 +143,38 @@ public abstract class CommandTestFunctions {
element.setNameHorizontalAlign(HorizontalAlign.CENTER);
}
+ protected LayerRect createLayerRect() {
+ LayerRect layerRect = new LayerRect();
+ layerRect.setBorderColor(Color.BLUE);
+ layerRect.setFillColor(Color.YELLOW);
+ return layerRect;
+ }
+
+ protected LayerImage createLayerImage() {
+ LayerImage layerImage = new LayerImage();
+ layerImage.setGlyph(createGlyph());
+ return layerImage;
+ }
+
+ protected LayerText createLayerText() {
+ LayerText layerText = new LayerText();
+ layerText.setGlyph(createGlyph());
+ layerText.setFillColor(Color.YELLOW);
+ layerText.setNotes(faker.lorem().sentence());
+ return layerText;
+ }
+
+ protected Glyph createGlyph() {
+ Glyph glyph = new Glyph();
+ glyph.setFile(createFile());
+ return glyph;
+ }
+
+ private UploadedFileEntry createFile() {
+ UploadedFileEntry file = new UploadedFileEntry();
+ file.setOriginalFileName(faker.file().fileName());
+ return file;
+ }
+
+
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index c9d4eeb036f26bd1da4cddec937eb61797703b1d..a75ff5b35a5e8fd6374800a16ec68864f0ed636e 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -5,8 +5,6 @@ import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.Author;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
@@ -38,7 +36,6 @@ import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
public class CopyCommandTest extends CommandTestFunctions {
@@ -54,38 +51,6 @@ public class CopyCommandTest extends CommandTestFunctions {
private int counter = 0;
- @Test
- public void testCopyModel() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model copy = new CopyCommand(model).execute();
-
- assertEquals(0, comparator.compare(model, copy));
- }
-
- @Test
- public void testCopyModelWithKinetics() throws Exception {
- Model model = getModelForFile("testFiles/kinetics_with_compartment.xml", false);
- Model copy = new CopyCommand(model).execute();
-
- assertEquals(0, comparator.compare(model, copy));
- for (final Reaction reaction : copy.getReactions()) {
- if (reaction.getKinetics() != null) {
- for (final Element element : reaction.getKinetics().getElements()) {
- assertTrue("Element in the copy doesn't belong to copy", copy.getElements().contains(element));
- }
- for (final SbmlFunction function : reaction.getKinetics().getFunctions()) {
- assertTrue("Function in the copy doesn't belong to copy", copy.getFunctions().contains(function));
- }
- for (final SbmlParameter parameter : reaction.getKinetics().getParameters()) {
- if (parameter.getParameterId().equals("k2")) {
- assertTrue("Global parameter in the function copy doesn't belong to copy",
- copy.getParameters().contains(parameter));
- }
- }
- }
- }
- }
-
@Test
public void testCopyCustomModel() {
Model model = new ModelFullIndexed(null);
@@ -122,45 +87,6 @@ public class CopyCommandTest extends CommandTestFunctions {
assertEquals(0, comparator.compare(model, copy));
}
- @Test
- public void testCopyModel3() throws Exception {
- Model model = getModelForFile("testFiles/complex_with_state.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- Model copy2 = serializeViaCellDesigner(copy);
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
- }
-
- @Test
- public void testCopyModel4() throws Exception {
- Model model = getModelForFile("testFiles/problematic_description.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- Model copy2 = serializeViaCellDesigner(copy);
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
- }
-
- @Test
- public void testCopyModelWithArtificialAliases() throws Exception {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- Model copy = new CopyCommand(model).execute();
-
- Model copy2 = serializeViaCellDesigner(copy);
-
- new CreateHierarchyCommand(copy2, 2, 2).execute();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
- }
-
@Test
public void testCopyModelWithSubmodels() throws Exception {
Model model = getModel();
@@ -389,16 +315,4 @@ public class CopyCommandTest extends CommandTestFunctions {
}
}
-
- @Test
- public void testCopyModelWithProject() throws Exception {
- Model originalModel = getModelForFile("testFiles/sample.xml", false);
- Project project = new Project();
- project.addModel(originalModel);
-
- Model colorModel = new CopyCommand(originalModel).execute();
-
- assertNotEquals(originalModel.getProject(), colorModel.getProject());
- }
-
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
index 323d0ad0eb31da3a306e22afe24db1cd6f471129..32dc9dbba304d7fda63c5f9df8cb6554075bd9f3 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CreateHierarchyCommandTest.java
@@ -1,38 +1,19 @@
package lcsb.mapviewer.commands;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.exception.InvalidStateException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
-import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.layout.graphics.LayerRect;
import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
public class CreateHierarchyCommandTest extends CommandTestFunctions {
@@ -45,271 +26,11 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
}
@Test
- public void testCyclicComplexes() throws Exception {
- Model model = getModelForFile("testFiles/cyclic_hierarchy_problem.xml", false);
-
- new CreateHierarchyCommand(model, 8, 80).execute();
-
- Species alias = model.getElementByElementId("sa5033");
-
- Set<Element> parents = new HashSet<Element>();
- while (alias.getComplex() != null) {
- assertFalse("Cyclic nesting", parents.contains(alias.getComplex()));
- alias = alias.getComplex();
- parents.add(alias);
- }
-
- Set<String> levels = new HashSet<>();
- for (final Element a : model.getElements()) {
- levels.add(a.getVisibilityLevel());
- }
- assertTrue(levels.size() > 2);
- }
-
- @Test
- public void testCreateHierachy() throws Exception {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
- // check if second call will throw an exception...
- new CreateHierarchyCommand(model, 2, 2).execute();
- }
-
- @Test
- public void testCreateHierachy2() throws Exception {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- boolean artifitial = false;
- for (final Compartment a : model.getCompartments()) {
- if (a instanceof PathwayCompartment) {
- artifitial = true;
- }
- }
- assertTrue("No hierarchical structure element found", artifitial);
- }
-
- @Test
- public void testRecreateHierachy() throws Exception {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- int aliasSize0 = model.getCompartments().size();
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- int aliasSize = model.getCompartments().size();
-
- assertTrue(aliasSize0 != aliasSize);
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- int aliasSize2 = model.getCompartments().size();
-
- assertEquals(aliasSize, aliasSize2);
- }
-
- @Test
- public void testParenting() throws Exception {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- assertFalse(model.getElementByElementId("sa1").getCompartment() instanceof PathwayCompartment);
- }
-
- @Test
- public void testCreateComponentsMinVisibility() throws Exception {
- double zoomFactor = 39.0625;
- int levels = 6;
-
- Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
- new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
- for (final Compartment compartment : model.getCompartments()) {
- if (compartment.getCompartment() == null) {
- int visibilityLevel = Integer.valueOf(compartment.getVisibilityLevel());
- assertTrue("Alias " + compartment.getElementId() + " is not visible at levels highers than "
- + compartment.getVisibilityLevel(), visibilityLevel <= 1);
- }
- }
-
- for (final Species species : model.getSpeciesList()) {
- if (species.getCompartment() == null) {
- int visibilityLevel = Integer.valueOf(species.getVisibilityLevel());
- assertTrue("Alias " + species.getElementId() + " is not visible at levels highers than "
- + species.getVisibilityLevel(), visibilityLevel <= 1);
- }
- }
- }
-
- @Test
- public void testCreateComponentsMaxVisibility() throws Exception {
- double zoomFactor = 39.0625;
- int levels = 6;
-
- Model model = getModelForFile("testFiles/other_full/GSTP1 subnetwork_220214.xml", false);
-
- new CreateHierarchyCommand(model, levels, zoomFactor).execute();
-
- for (final Element element : model.getElements()) {
- int visibilityLevel = Integer.valueOf(element.getVisibilityLevel());
- assertTrue("Alias " + element.getElementId() + " is not visible even at the bottom level (visibility: "
- + element.getVisibilityLevel() + ") ", visibilityLevel <= levels);
- }
- }
-
- @Test
- public void testCompactComplexesInNestedView() throws Exception {
- Model model = getModelForFile("testFiles/problematic/compact_complex_view_problem.xml", false);
- Element alias = model.getElementByElementId("sa1");
- Object parent1 = alias.getCompartment();
- new CreateHierarchyCommand(model, 3, 16).execute();
- Object parent2 = alias.getCompartment();
- assertEquals(parent1, parent2);
- }
-
- @Test(expected = InvalidStateException.class)
- public void testRecallHierachyCreation() throws Exception {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
- command.execute();
- command.execute();
- }
-
- @Test
- public void testClear() throws Exception {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
- command.clean();
- for (final Element alias : model.getElements()) {
- assertNull(alias.getCompartment());
- }
- for (final Compartment alias : model.getCompartments()) {
- assertNull(alias.getCompartment());
- assertTrue(alias.getElements().isEmpty());
- }
- }
-
- @Test
- public void testNestedProblem() throws Exception {
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- Model model = parser
- .createModel(new ConverterParams().filename("testFiles/nested_test.xml").sizeAutoAdjust(true));
-
- double zoomFactor = Math.max(model.getHeight(), model.getWidth()) / (256);
- int zoomLevels = (int) Math.ceil(Math.log(zoomFactor) / Math.log(2));
-
- CreateHierarchyCommand command = new CreateHierarchyCommand(model, zoomLevels, zoomFactor);
- command.execute();
-
- for (final Element alias : model.getElements()) {
- Element parentAlias = alias.getCompartment();
- if (parentAlias != null) {
- int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
- int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
- assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
- }
- if (alias instanceof Species) {
- parentAlias = ((Species) alias).getComplex();
- if (parentAlias != null) {
- int parentVisibilityLevel = Integer.valueOf(parentAlias.getVisibilityLevel());
- int aliasVisibilityLevel = Integer.valueOf(alias.getVisibilityLevel());
- assertTrue(aliasVisibilityLevel >= parentVisibilityLevel);
- }
- }
- }
- }
-
- @Test
- public void testDisconnectedChildInComplex() throws Exception {
- Model model = getModelForFile("testFiles/problematic/disconnected_child_in_complex.xml", false);
-
- new CreateHierarchyCommand(model, 8, 80).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xmlString = parser.model2String(model);
-
- InputStream stream = new ByteArrayInputStream(xmlString.getBytes(StandardCharsets.UTF_8));
-
- parser.createModel(new ConverterParams().inputStream(stream));
- }
-
- @Test
- public void testHierarchyWithCustomSemanticZooming() throws Exception {
- Model model = getModelForFile("testFiles/custom_semantic_zooming.xml", false);
-
- Map<Element, String> visibilityLevels = new HashMap<>();
- for (final Element element : model.getElements()) {
- if (element.getVisibilityLevel() != null && !element.getVisibilityLevel().isEmpty()) {
- visibilityLevels.put(element, element.getVisibilityLevel());
- }
- }
-
- new CreateHierarchyCommand(model, 4, 80).execute();
-
- for (final Element element : model.getElements()) {
- if (visibilityLevels.get(element) != null) {
- assertEquals("Visibility level changed, but shouldn't", visibilityLevels.get(element),
- element.getVisibilityLevel());
- }
- }
- }
-
- @Test
- public void testHierarchyWithCustomSemanticZoomingPathwayLevels() throws Exception {
- ElementUtils eu = new ElementUtils();
- Model model = getModelForFile("testFiles/custom_semantic_zooming.xml", false);
-
- Map<Element, String> visibilityLevels = new HashMap<>();
- for (final Element element : model.getElements()) {
- if (element.getVisibilityLevel() != null && !element.getVisibilityLevel().isEmpty()) {
- visibilityLevels.put(element, element.getVisibilityLevel());
- }
- }
-
- new CreateHierarchyCommand(model, 4, 80).execute();
-
- for (final Element element : model.getElements()) {
- if (visibilityLevels.get(element) == null) {
- int visibilityLevel = Integer.parseInt(element.getVisibilityLevel());
- if (element.getCompartment() != null) {
- int parentTransparency = Integer.parseInt(element.getCompartment().getTransparencyLevel());
- assertEquals(
- eu.getElementTag(element) + eu.getElementTag(element.getCompartment())
- + "Element should be directly visible when parent is transparent",
- parentTransparency, visibilityLevel);
- } else if (element instanceof Species) {
- int parentTransparency = Integer.parseInt(((Species) element).getComplex().getTransparencyLevel());
- assertEquals(
- eu.getElementTag(element) + eu.getElementTag(((Species) element).getComplex())
- + "Element should be directly visible when parent is transparent",
- parentTransparency, visibilityLevel);
- }
- }
- }
- }
-
- @Test
- public void testLayerWithNotes() throws Exception {
- Model model = getModelForFile("testFiles/layer_text_with_notes.xml", false);
-
- new CreateHierarchyCommand(model, 4, 80).execute();
-
- PathwayCompartment pathway = (PathwayCompartment) model.getCompartments().get(0);
-
- assertEquals("test", pathway.getName());
- assertEquals("5", pathway.getVisibilityLevel());
- assertEquals((Integer) 11, pathway.getZ());
- }
-
- @Test
- public void testCreatePathwayFromRectangle() throws Exception {
+ public void testCreatePathwayFromRectangle() {
Model model = new ModelFullIndexed(null);
Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
LayerRect layerRect = createLayerRect();
layer.addLayerRect(layerRect);
model.addLayer(layer);
@@ -322,18 +43,12 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
assertEquals(pathway.getBorderColor(), pathway.getFontColor());
}
- private LayerRect createLayerRect() {
- LayerRect layerRect = new LayerRect();
- layerRect.setBorderColor(Color.BLUE);
- layerRect.setFillColor(Color.YELLOW);
- return layerRect;
- }
-
@Test
public void testCreatePathwayWhenIdIsTaken() throws Exception {
Model model = new ModelFullIndexed(null);
Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
LayerRect layerRect = createLayerRect();
layer.addLayerRect(layerRect);
LayerRect layerRect2 = createLayerRect();
@@ -362,6 +77,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
Model model = new ModelFullIndexed(null);
Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
LayerText layerText = new LayerText();
layerText.setNotes("colors check\n"
+ "SemanticZoomLevelVisibility: 3\n"
@@ -394,7 +110,7 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
Model model = new ModelFullIndexed(null);
Layer layer = new Layer();
- layer.setName(CreateHierarchyCommand.TEXT_LAYER_NAME);
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME + "blah");
LayerRect layerRect = createLayerRect();
layer.addLayerRect(layerRect);
model.addLayer(layer);
@@ -405,4 +121,40 @@ public class CreateHierarchyCommandTest extends CommandTestFunctions {
assertEquals(0, model.getCompartments().size());
}
+ @Test
+ public void deletePathwayLayer() {
+ Model model = new ModelFullIndexed(null);
+
+ Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME);
+ LayerRect layerRect = createLayerRect();
+ layer.addLayerRect(layerRect);
+ model.addLayer(layer);
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 4, 80);
+ command.createArtificials();
+
+ PathwayCompartment pathway = (PathwayCompartment) model.getCompartments().get(0);
+
+ assertEquals(0, model.getLayers().size());
+ }
+
+ @Test
+ public void testCreateImageFromText() {
+ Model model = new ModelFullIndexed(null);
+
+ Layer layer = new Layer();
+ layer.setName(CreateHierarchyCommand.PATHWAY_LAYER_NAME + "blah");
+ LayerText layerText = createLayerText();
+ layer.addLayerText(layerText);
+ model.addLayer(layer);
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 4, 80);
+ command.createArtificials();
+
+ assertEquals(0, model.getCompartments().size());
+ assertEquals(1, layer.getImages().size());
+ assertEquals(0, layer.getTexts().size());
+ }
+
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
deleted file mode 100644
index 1af849f468c5a51d974f2c0a79be9d8d04a82350..0000000000000000000000000000000000000000
--- a/model-command/src/test/java/lcsb/mapviewer/commands/MoveElementsCommandTest.java
+++ /dev/null
@@ -1,241 +0,0 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-
-public class MoveElementsCommandTest extends CommandTestFunctions {
-
- private ModelComparator modelComparator = new ModelComparator();
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testMoveAlias() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa2");
- Element alias2 = model.getElementByElementId("sa1");
- double anotherAliasX = alias2.getX();
- double anotherAliasY = alias2.getY();
-
- List<BioEntity> list = new ArrayList<>();
- list.add(alias);
- double x = alias.getX();
- double y = alias.getY();
-
- double dx = 10;
- double dy = 2;
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // check new coordinates
- assertEquals(x + dx, alias.getX(), Configuration.EPSILON);
- assertEquals(y + dy, alias.getY(), Configuration.EPSILON);
-
- // and check if another alias didn't change coordinates
- assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
- assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
- list = new ArrayList<>();
- list.add(model2.getElementByElementId("sa2"));
- MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
- moveCommand2.execute();
-
- // if we perform the same operator on the second model then they should be
- // equal
- assertEquals(0, modelComparator.compare(model, model2));
- }
-
- @Test(expected = InvalidArgumentException.class)
- public void testMoveSpecies() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- List<BioEntity> list = new ArrayList<>();
- list.add(Mockito.mock(BioEntity.class));
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, 10, 10);
- moveCommand.execute();
- }
-
- @Test
- public void testAliasWithReaction() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa1");
- Element alias2 = model.getElementByElementId("sa2");
- double anotherAliasX = alias2.getX();
- double anotherAliasY = alias2.getY();
- Reaction reaction = model.getReactionByReactionId("re1");
-
- List<BioEntity> list = new ArrayList<>();
- list.add(alias);
- double x = reaction.getReactants().get(0).getLine().getStartPoint().getX();
- double y = reaction.getReactants().get(0).getLine().getStartPoint().getY();
-
- double dx = 10;
- double dy = 2;
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // check new coordinates of reaction
- assertEquals(x + dx, reaction.getReactants().get(0).getLine().getStartPoint().getX(), Configuration.EPSILON);
- assertEquals(y + dy, reaction.getReactants().get(0).getLine().getStartPoint().getY(), Configuration.EPSILON);
-
- // and check if another alias didn't change coordinates
- assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
- assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
-
- list = new ArrayList<>();
- list.add(model2.getElementByElementId("sa1"));
- MoveElementsCommand moveCommand2 = new MoveElementsCommand(model2, list, dx, dy);
- moveCommand2.execute();
-
- // if we perform the same operator on the second model then they should be
- // equal
- assertEquals(0, modelComparator.compare(model, model2));
- }
-
- @Test
- public void testMoveReaction() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias2 = model.getElementByElementId("sa1");
- double anotherAliasX = alias2.getX();
- double anotherAliasY = alias2.getY();
- Reaction reaction = model.getReactionByReactionId("re1");
-
- List<BioEntity> list = new ArrayList<>();
- list.add(reaction);
- double x = reaction.getReactants().get(0).getLine().getStartPoint().getX();
- double y = reaction.getReactants().get(0).getLine().getStartPoint().getY();
-
- double x2 = reaction.getReactants().get(0).getLine().getEndPoint().getX();
- double y2 = reaction.getReactants().get(0).getLine().getEndPoint().getY();
-
- double dx = 10;
- double dy = 2;
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // check new coordinates of reaction (point attached to alias shouldn't
- // move, the one not attached should move)
- assertEquals(x, reaction.getReactants().get(0).getLine().getStartPoint().getX(), Configuration.EPSILON);
- assertEquals(y, reaction.getReactants().get(0).getLine().getStartPoint().getY(), Configuration.EPSILON);
- assertEquals(x2 + dx, reaction.getReactants().get(0).getLine().getEndPoint().getX(), Configuration.EPSILON);
- assertEquals(y2 + dy, reaction.getReactants().get(0).getLine().getEndPoint().getY(), Configuration.EPSILON);
-
- // and check if another alias didn't change coordinates
- assertEquals(anotherAliasX, alias2.getX(), Configuration.EPSILON);
- assertEquals(anotherAliasY, alias2.getY(), Configuration.EPSILON);
- }
-
- @Test
- public void testUndo() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Model model2 = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa2");
-
- List<BioEntity> list = new ArrayList<>();
- list.add(alias);
-
- double dx = 10;
- double dy = 2;
-
- // models should be equal before move
- assertEquals(0, modelComparator.compare(model, model2));
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- moveCommand.execute();
-
- // after move models should be different
- assertTrue(0 != modelComparator.compare(model, model2));
-
- // undo command
- moveCommand.undo();
-
- // after undo they should be the same again
- assertEquals(0, modelComparator.compare(model, model2));
-
- moveCommand.redo();
-
- // after redo they should be different again
- assertTrue(0 != modelComparator.compare(model, model2));
- }
-
- @Test
- public void testGetAffectedRegion() throws Exception {
- Model model = getModelForFile("testFiles/spliting_test_Case.xml", false);
- Element alias = model.getElementByElementId("sa2");
-
- List<BioEntity> list = new ArrayList<>();
- list.add(alias);
- double x = alias.getX();
- double y = alias.getY();
-
- double dx = 10;
- double dy = 2;
-
- double minx = x;
- double maxx = alias.getWidth() + x + dx;
-
- double miny = y;
- double maxy = alias.getHeight() + y + dy;
-
- MoveElementsCommand moveCommand = new MoveElementsCommand(model, list, dx, dy);
- assertNull(moveCommand.getAffectedRegion());
- moveCommand.execute();
- assertNotNull(moveCommand.getAffectedRegion());
- Rectangle2D affectedRegion = moveCommand.getAffectedRegion();
- assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
- assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
- assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
- assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
-
- moveCommand.undo();
-
- affectedRegion = moveCommand.getAffectedRegion();
- assertEquals(minx, affectedRegion.getX(), Configuration.EPSILON);
- assertEquals(miny, affectedRegion.getY(), Configuration.EPSILON);
- assertEquals(maxx, affectedRegion.getX() + affectedRegion.getWidth(), Configuration.EPSILON);
- assertEquals(maxy, affectedRegion.getY() + affectedRegion.getHeight(), Configuration.EPSILON);
- }
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteFieldTest.java b/model-command/src/test/java/lcsb/mapviewer/utils/NoteFieldTest.java
similarity index 85%
rename from converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteFieldTest.java
rename to model-command/src/test/java/lcsb/mapviewer/utils/NoteFieldTest.java
index ebdc23cfcefc0cdebc4d3186dee862592f5d48c8..70f45afb46046cebf0f63fefd8ad0135979c22c7 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteFieldTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/utils/NoteFieldTest.java
@@ -1,12 +1,12 @@
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
-
-import static org.junit.Assert.assertNotNull;
+package lcsb.mapviewer.utils;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import static org.junit.Assert.assertNotNull;
+
public class NoteFieldTest {
@AfterClass
@@ -22,7 +22,7 @@ public class NoteFieldTest {
}
@Test
- public void testVallues() {
+ public void testValues() {
for (final NoteField field : NoteField.values()) {
assertNotNull(NoteField.valueOf(field.toString()));
assertNotNull(field.getClazz());
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java b/model-command/src/test/java/lcsb/mapviewer/utils/RestAnnotationParserTest.java
similarity index 85%
rename from converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
rename to model-command/src/test/java/lcsb/mapviewer/utils/RestAnnotationParserTest.java
index 1ab0102ac738e4bc4d7ab1b1516016ea8ae3263d..adf50fc910fa1b67ef315a979f28e33f985e0160 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/utils/RestAnnotationParserTest.java
@@ -1,19 +1,15 @@
-package lcsb.mapviewer.converter.model.celldesigner.annotation;
+package lcsb.mapviewer.utils;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.commands.CommandTestFunctions;
import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
-import org.apache.xerces.dom.DocumentImpl;
import org.junit.After;
+import org.junit.Assert;
import org.junit.Before;
import org.junit.Test;
import org.mockito.Mockito;
@@ -30,7 +26,7 @@ import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertTrue;
-public class RestAnnotationParserTest extends CellDesignerTestFunctions {
+public class RestAnnotationParserTest extends CommandTestFunctions {
@Before
public void setUp() throws Exception {
@@ -126,7 +122,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
assertEquals(1, protein.getSynonyms().size());
assertEquals(1, protein.getFormerSymbols().size());
- assertEquals(6, getWarnings().size());
+ Assert.assertEquals(6, getWarnings().size());
}
@Test
@@ -137,7 +133,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
Species proteinAlias = new GenericProtein("id");
parser.processNotes(node.getFirstChild(), proteinAlias);
- assertEquals(1, getWarnings().size());
+ Assert.assertEquals(1, getWarnings().size());
}
@Test
@@ -156,26 +152,9 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
parser.processNotes(node.getFirstChild(), reaction);
- assertEquals(8, getWarnings().size());
+ Assert.assertEquals(8, getWarnings().size());
}
- @Test
- public void testMoveAnnotationsFromNotes() throws Exception {
- Model model = getModelForFile("testFiles/copyingAnnotationModel.xml");
-
- Set<Element> elements = model.getElements();
- for (final Element element : elements) {
- if (element.getName().equals("blabla")) {
- assertEquals(2, element.getMiriamData().size());
- element.getMiriamData()
- .add(new MiriamData(MiriamType.PUBMED, "12345"));
- element.getMiriamData()
- .add(new MiriamData(MiriamType.PUBMED, "333666"));
- assertEquals(2, element.getMiriamData().size());
- }
- assertFalse(element.getNotes().contains("rdf:RDF"));
- }
- }
@Test
public void testProcessRdfDescription() throws Exception {
@@ -228,10 +207,9 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
boolean importOnly = rap.isFieldAnnotated(field, ImportOnly.class);
if (!deprecated && !importOnly) {
- if (field.getClazz().isAssignableFrom(element.getClass())
- || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
+ if (field.getClazz().isAssignableFrom(element.getClass())) {
assertTrue("Export string doesn't contain info about: " + field.getCommonName(),
- str.indexOf(field.getCommonName()) >= 0);
+ str.contains(field.getCommonName()));
}
} else {
assertEquals("Export string contains info about: " + field.getCommonName() + " but shouldn't",
@@ -248,10 +226,9 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
String str = rap.createAnnotationString(element, false);
for (final NoteField field : NoteField.values()) {
- if (field.getClazz().isAssignableFrom(element.getClass())
- || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
+ if (field.getClazz().isAssignableFrom(element.getClass())) {
assertFalse("Export string contain info about: " + field.getCommonName() + ". But shouldn't",
- str.indexOf(field.getCommonName()) >= 0);
+ str.contains(field.getCommonName()));
}
}
@@ -264,16 +241,6 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
assertEquals(0, rap.getFormerSymbols(null).size());
}
- @Test(expected = InvalidArgumentException.class)
- public void testGetNotesInvalid() throws Exception {
- RestAnnotationParser rap = new RestAnnotationParser();
-
- Document xmlDoc = new DocumentImpl();
- Node node = xmlDoc.createElement("bla");
-
- rap.getNotes(node);
- }
-
@Test
public void testGetNotesWithMissingBody() throws Exception {
RestAnnotationParser rap = new RestAnnotationParser();
@@ -324,7 +291,7 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
parser.processNotes(str, new GenericProtein("id"));
- assertEquals(1, getWarnings().size());
+ Assert.assertEquals(1, getWarnings().size());
}
@Test
diff --git a/model-command/testFiles/annotation/recon_annotation_example.xml b/model-command/testFiles/annotation/recon_annotation_example.xml
new file mode 100644
index 0000000000000000000000000000000000000000..78de9aec3cc93d5a139d505d9deb030091604ca1
--- /dev/null
+++ b/model-command/testFiles/annotation/recon_annotation_example.xml
@@ -0,0 +1,228 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="170.0" y="171.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="399.0" y="173.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>Symbol: S1_SYMB
+Abbreviation: ABREVIATION
+ChargedFormula: FORMULA
+Charge: 324
+Synonyms: syn44
+DESCRIPTION
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>s1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s1">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.compound:C05488"/>
+</rdf:Bag>
+</bqmodel:is>
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A28870"/>
+</rdf:Bag>
+</bqmodel:is>
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hmdb:HMDB03141"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>s2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>Symbol: SAW
+Abbreviation: ABREVIATION2
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+Synonyms: SYN1
+DESCRIPTION2
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diff --git a/model-command/testFiles/annotation/sampleDescription.txt b/model-command/testFiles/annotation/sampleDescription.txt
new file mode 100644
index 0000000000000000000000000000000000000000..156cd8860b63618ae22909f26d5a9df24c88b2a0
--- /dev/null
+++ b/model-command/testFiles/annotation/sampleDescription.txt
@@ -0,0 +1,31 @@
+HGNC_ID: 1464
+Symbol: CAMK4
+Name: calcium/calmodulin-dependent protein kinase IV
+Description: RecName: Full=Calcium/calmodulin-dependent protein kinase type IV; Short=CaMK IV; EC=2.7.11.17; AltName: Full=CaM kinase-GR;
+Previous Symbols:
+Synonyms: CAMK, CAMKIV, CAMK-GR
+Chromosome: 5q21-q23
+UniProtKB_Acc: Q16566
+RefSeq_ID: NP_001735.1
+EntrezGene_ID: 814
+Ensembl_ID: ENSP00000282356, ENSG00000152495 , ENST00000282356
+UCSC_ID: uc003kpf.1
+Reactome_ID: REACT_16116
+Pubmed_ID: 2536634
+EMBL_ID: AAA18251.1, AAA35639.1, AAH16695.2, AAH25687.1, BAA06403.1, BC016695, BC025687, CH471086, D30742, EAW49033.1, EAW49034.1, L17000, L24959
+IPI_ID: IPI00430411
+UniGene_ID: Hs.591269
+PDB_ID: 2W4O
+DIP_ID: DIP-41997N
+MINT_ID:
+KEGG_ID: hsa:814
+GeneCards_ID: GC05P110587
+PharmGKB_ID: PA26050
+Pathway_Interaction_DB: hdac_classii_pathway, nfat_3pathway, pi3kplctrkpathway
+GO_Function: GO:0004683[calmodulin-dependent protein kinase activity][IEA:EC. ], GO:0005516[calmodulin binding][IEA:UniProtKB-KW. ], GO:0005524[ATP binding][IEA:UniProtKB-KW. ]
+GO_Process: GO:0006954[inflammatory response][IEA:UniProtKB-KW. ], GO:0007202[activation of phospholipase C activity][TAS:Reactome. ], GO:0007268[synaptic transmission][TAS:Reactome. ], GO:0007616[long-term memory][IGI:UniProtKB. ], GO:0033081[regulation of T cell differentiation in thymus][TAS:UniProtKB. ], GO:0043011[myeloid dendritic cell differentiation][IMP:UniProtKB. ], GO:0045670[regulation of osteoclast differentiation][TAS:UniProtKB. ], GO:0045893[positive regulation of transcription, DNA-dependent][IDA:UniProtKB. ], GO:0048011[nerve growth factor receptor signaling pathway][TAS:Reactome. ]
+GO_Component: GO:0005654[nucleoplasm][TAS:Reactome. ], GO:0005829[cytosol][TAS:Reactome. ]
+InterPro: IPR000719, IPR002290, IPR008271, IPR011009, IPR017441, IPR017442, Kinase-like_dom. , Protein_kinase_ATP_BS. , Prot_kinase_cat_dom. , Ser/Thr_kinase_AS. , Ser/Thr_kinase_dom. , Se/Thr_kinase-like_dom.
+Pfam: PF00069, Pkinase
+PANTHER:
+HOVERGEN: HBG108055
\ No newline at end of file
diff --git a/model-command/testFiles/other_full/GSTP1 subnetwork_220214.xml b/model-command/testFiles/other_full/GSTP1 subnetwork_220214.xml
deleted file mode 100644
index 90b3cdce6bd4a26bacf38f8c78e5bd35ee8429e9..0000000000000000000000000000000000000000
--- a/model-command/testFiles/other_full/GSTP1 subnetwork_220214.xml
+++ /dev/null
@@ -1,12409 +0,0 @@
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-</celldesigner:protein>
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-<celldesigner:protein id="pr898" name="TRAF2" type="GENERIC"/>
-<celldesigner:protein id="pr899" name="MAP3K5" type="GENERIC"/>
-<celldesigner:protein id="pr902" name="GLUT?" type="GENERIC"/>
-<celldesigner:protein id="pr903" name="GLUT1" type="GENERIC"/>
-<celldesigner:protein id="pr904" name="CDK5R1" type="GENERIC"/>
-<celldesigner:protein id="pr905" name="CAPN1" type="GENERIC"/>
-<celldesigner:protein id="pr906" name="CDK5R1 (p25)" type="TRUNCATED"/>
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-<celldesigner:modificationResidue angle="0.96" id="rs1" name="T89" side="none"/>
-</celldesigner:listOfModificationResidues>
-</celldesigner:protein>
-<celldesigner:protein id="pr908" name="GLRX2" type="GENERIC"/>
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-<celldesigner:protein id="pr910" name="E1/E2 domain " type="GENERIC"/>
-<celldesigner:protein id="pr882" name="generic_br_ protein" type="GENERIC"/>
-<celldesigner:protein id="pr911" name="PSMA5" type="GENERIC"/>
-<celldesigner:protein id="pr912" name="PRDX6" type="GENERIC"/>
-<celldesigner:protein id="pr914" name="PRKAB2" type="GENERIC"/>
-<celldesigner:protein id="pr913" name="PRKAB1" type="GENERIC"/>
-<celldesigner:protein id="pr915" name="MAPK3K5" type="GENERIC"/>
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-<celldesigner:protein id="pr918" name="SLC25A11" type="GENERIC"/>
-</celldesigner:listOfProteins>
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-<celldesigner:gene id="gn5" name="TXN" type="GENE"/>
-</celldesigner:listOfGenes>
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-<celldesigner:RNA id="rn2" name="SLC1A1" type="RNA"/>
-<celldesigner:RNA id="rn3" name="GGT1" type="RNA"/>
-<celldesigner:RNA id="rn4" name="GSTP1" type="RNA"/>
-<celldesigner:RNA id="rn5" name="TXN" type="RNA"/>
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-<celldesigner:listOfAntisenseRNAs/>
-<celldesigner:listOfLayers/>
-<celldesigner:listOfBlockDiagrams/>
-</celldesigner:extension>
-</annotation>
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-<unitDefinition metaid="substance" id="substance" name="substance">
-<listOfUnits>
-<unit metaid="CDMT00278" kind="mole"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="volume" id="volume" name="volume">
-<listOfUnits>
-<unit metaid="CDMT00279" kind="litre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="area" id="area" name="area">
-<listOfUnits>
-<unit metaid="CDMT00280" kind="metre" exponent="2"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="length" id="length" name="length">
-<listOfUnits>
-<unit metaid="CDMT00281" kind="metre"/>
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-</unitDefinition>
-<unitDefinition metaid="time" id="time" name="time">
-<listOfUnits>
-<unit metaid="CDMT00282" kind="second"/>
-</listOfUnits>
-</unitDefinition>
-</listOfUnitDefinitions>
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-<annotation>
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-<celldesigner:name>Astrocyte</celldesigner:name>
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-<annotation>
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-<celldesigner:name>endothelial cell</celldesigner:name>
-</celldesigner:extension>
-</annotation>
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-<compartment metaid="c5" id="c5" name="blood vessel" size="1" units="volume" outside="default">
-<annotation>
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-<celldesigner:name>blood vessel</celldesigner:name>
-</celldesigner:extension>
-</annotation>
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-<compartment metaid="c1" id="c1" name="Neuron" size="1" units="volume" outside="c5">
-<annotation>
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-<celldesigner:name>Neuron</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-<compartment metaid="c7" id="c7" name="nucleus" size="1" units="volume" outside="c1">
-<annotation>
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-<celldesigner:name>nucleus</celldesigner:name>
-</celldesigner:extension>
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-<compartment metaid="c8" id="c8" name="Mitochondria" size="1" units="volume" outside="c1">
-<annotation>
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-<celldesigner:name>Mitochondria</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-</listOfCompartments>
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-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr867</celldesigner:proteinReference>
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-<celldesigner:catalyzed reaction="re3"/>
-<celldesigner:catalyzed reaction="re1"/>
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-</annotation>
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-<annotation>
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-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>yGluCys</celldesigner:name>
-</celldesigner:speciesIdentity>
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-<rdf:Description rdf:about="#s2157">
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-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17515"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
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-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
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-</annotation>
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-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr869</celldesigner:proteinReference>
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-<celldesigner:catalyzed reaction="re82"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
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-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr870</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re6"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
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-<annotation>
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-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>glutathione</celldesigner:name>
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-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16856"/>
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-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>glycine</celldesigner:name>
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-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A15428"/>
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-</bqmodel:is>
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-<annotation>
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-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>glutathione</celldesigner:name>
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-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16856"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
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-<annotation>
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-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr872</celldesigner:proteinReference>
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-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
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-<annotation>
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-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr873</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
-<celldesigner:catalyzed reaction="re8"/>
-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2167" id="s2167" name="CysGly" compartment="c5" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>CysGly</celldesigner:name>
-</celldesigner:speciesIdentity>
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-<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-<rdf:Description rdf:about="#s2167">
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-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A4047"/>
-</rdf:Bag>
-</bqmodel:is>
-</rdf:Description>
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-</annotation>
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-<annotation>
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-<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr875</celldesigner:proteinReference>
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-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s2173" id="s2173" name="cystine" compartment="c6" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>cystine</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
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-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A16283"/>
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-</bqmodel:is>
-</rdf:Description>
-</rdf:RDF>
-</annotation>
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-<annotation>
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-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
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-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>cystine</celldesigner:name>
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-</bqmodel:is>
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-</rdf:RDF>
-</annotation>
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-<annotation>
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-<celldesigner:name>L-cysteine</celldesigner:name>
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-</bqmodel:is>
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-<annotation>
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-</bqmodel:is>
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-</annotation>
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-<annotation>
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-<celldesigner:proteinReference>pr876</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-<celldesigner:listOfCatalyzedReactions>
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-</celldesigner:listOfCatalyzedReactions>
-</celldesigner:extension>
-</annotation>
-</species>
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-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
-<celldesigner:name>L-cysteine</celldesigner:name>
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-<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17561"/>
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diff --git a/model-command/testFiles/problematic/compact_complex_view_problem.xml b/model-command/testFiles/problematic/compact_complex_view_problem.xml
deleted file mode 100644
index d4dd9f7ba25954f2afc0b2b44c75e7a24ff61759..0000000000000000000000000000000000000000
--- a/model-command/testFiles/problematic/compact_complex_view_problem.xml
+++ /dev/null
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-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="205.0" y="53.0"/>
-<celldesigner:boxSize width="289.0" height="240.0"/>
-<celldesigner:singleLine width="2.0"/>
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-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:complexSpeciesAlias>
-<celldesigner:complexSpeciesAlias id="csa2" species="s3" compartmentAlias="ca3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="31.0" y="75.0" w="165.0" h="252.0"/>
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-<celldesigner:view state="usual"/>
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-<celldesigner:usualView>
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-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="80.0" height="60.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
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-</celldesigner:complexSpeciesAlias>
-<celldesigner:complexSpeciesAlias id="csa1" species="s1" complexSpeciesAlias="csa3">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="308.0" y="139.0" w="103.0" h="56.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="brief"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
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-<celldesigner:innerPosition x="92.0" y="35.5"/>
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-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
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-<celldesigner:briefView>
-<celldesigner:innerPosition x="89.0" y="60.0"/>
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-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
-</celldesigner:briefView>
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-</celldesigner:complexSpeciesAlias>
-</celldesigner:listOfComplexSpeciesAliases>
-<celldesigner:listOfSpeciesAliases>
-<celldesigner:speciesAlias id="sa1" species="s2" complexSpeciesAlias="csa1">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="308.0" y="139.0" w="103.0" h="56.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="brief"/>
-<celldesigner:usualView>
-<celldesigner:innerPosition x="10.0" y="7.0"/>
-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffccffcc" scheme="Color"/>
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-<celldesigner:briefView>
-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="103.0" height="56.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="3fff0000" scheme="Color"/>
-</celldesigner:briefView>
-<celldesigner:info state="empty" angle="-1.5707963267948966"/>
-</celldesigner:speciesAlias>
-</celldesigner:listOfSpeciesAliases>
-<celldesigner:listOfGroups/>
-<celldesigner:listOfProteins>
-<celldesigner:protein id="pr1" name="s2" type="GENERIC"/>
-</celldesigner:listOfProteins>
-<celldesigner:listOfGenes/>
-<celldesigner:listOfRNAs/>
-<celldesigner:listOfAntisenseRNAs/>
-<celldesigner:listOfLayers/>
-<celldesigner:listOfBlockDiagrams/>
-</celldesigner:extension>
-</annotation>
-<listOfUnitDefinitions>
-<unitDefinition metaid="substance" id="substance" name="substance">
-<listOfUnits>
-<unit metaid="CDMT00001" kind="mole"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="volume" id="volume" name="volume">
-<listOfUnits>
-<unit metaid="CDMT00002" kind="litre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="area" id="area" name="area">
-<listOfUnits>
-<unit metaid="CDMT00003" kind="metre" exponent="2"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="length" id="length" name="length">
-<listOfUnits>
-<unit metaid="CDMT00004" kind="metre"/>
-</listOfUnits>
-</unitDefinition>
-<unitDefinition metaid="time" id="time" name="time">
-<listOfUnits>
-<unit metaid="CDMT00005" kind="second"/>
-</listOfUnits>
-</unitDefinition>
-</listOfUnitDefinitions>
-<listOfCompartments>
-<compartment metaid="default" id="default" size="1" units="volume"/>
-<compartment metaid="c3" id="c3" name="c3" size="1" units="volume" outside="default">
-<annotation>
-<celldesigner:extension>
-<celldesigner:name>c3</celldesigner:name>
-</celldesigner:extension>
-</annotation>
-</compartment>
-</listOfCompartments>
-<listOfSpecies>
-<species metaid="s3" id="s3" name="s3" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s3</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-<species metaid="s5" id="s5" name="s5" compartment="c3" initialAmount="0">
-<annotation>
-<celldesigner:extension>
-<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
-<celldesigner:speciesIdentity>
-<celldesigner:class>COMPLEX</celldesigner:class>
-<celldesigner:name>s5</celldesigner:name>
-</celldesigner:speciesIdentity>
-</celldesigner:extension>
-</annotation>
-</species>
-</listOfSpecies>
-</model>
-</sbml>
diff --git a/model-command/testFiles/sample.xml b/model-command/testFiles/sample.xml
deleted file mode 100644
index 8a0755ad0a623095df8241ef97c1f3ab3a917807..0000000000000000000000000000000000000000
--- a/model-command/testFiles/sample.xml
+++ /dev/null
@@ -1,2420 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
-<model metaid="untitled" id="untitled">
-<annotation>
-<celldesigner:extension>
-<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
-<celldesigner:modelDisplay sizeX="1308" sizeY="600"/>
-<celldesigner:listOfIncludedSpecies>
-<celldesigner:species id="s14" name="s14">
-<celldesigner:notes>
-<html xmlns="http://www.w3.org/1999/xhtml">
-<head>
-<title/>
-</head>
-<body/>
-</html>
-</celldesigner:notes>
-<celldesigner:annotation>
-<celldesigner:complexSpecies>s12</celldesigner:complexSpecies>
-<celldesigner:speciesIdentity>
-<celldesigner:class>PROTEIN</celldesigner:class>
-<celldesigner:proteinReference>pr5</celldesigner:proteinReference>
-</celldesigner:speciesIdentity>
-</celldesigner:annotation>
-</celldesigner:species>
-</celldesigner:listOfIncludedSpecies>
-<celldesigner:listOfCompartmentAliases/>
-<celldesigner:listOfComplexSpeciesAliases>
-<celldesigner:complexSpeciesAlias id="csa1" species="s12">
-<celldesigner:activity>inactive</celldesigner:activity>
-<celldesigner:bounds x="271.0" y="207.0" w="101.0" h="164.0"/>
-<celldesigner:font size="12"/>
-<celldesigner:view state="usual"/>
-<celldesigner:backupSize w="0.0" h="0.0"/>
-<celldesigner:backupView state="none"/>
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-<celldesigner:innerPosition x="0.0" y="0.0"/>
-<celldesigner:boxSize width="101.0" height="164.0"/>
-<celldesigner:singleLine width="2.0"/>
-<celldesigner:paint color="fff7f7f7" scheme="Color"/>
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-</celldesigner:complexSpeciesAlias>
-</celldesigner:listOfComplexSpeciesAliases>
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-<celldesigner:activity>inactive</celldesigner:activity>
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-<celldesigner:font size="12"/>
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-<celldesigner:boxSize width="80.0" height="40.0"/>
-<celldesigner:singleLine width="1.0"/>
-<celldesigner:paint color="ffffffff" scheme="Color"/>
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-<celldesigner:singleLine width="1.0"/>
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-<celldesigner:speciesAlias id="sa2" species="s2">
-<celldesigner:activity>inactive</celldesigner:activity>
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-<celldesigner:font size="12"/>
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-<celldesigner:speciesAlias id="sa3" species="s3">
-<celldesigner:activity>inactive</celldesigner:activity>
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-<celldesigner:activity>inactive</celldesigner:activity>
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-<head>
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-</head>
-<body>notes for reaction
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diff --git a/model-command/testFiles/xmlNodeTestExamples/antisense_rna.xml b/model-command/testFiles/xmlNodeTestExamples/antisense_rna.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bba9ae5a93e6ecb12c66b18ec55a48c8f639c314
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/antisense_rna.xml
@@ -0,0 +1,15 @@
+<celldesigner:AntisenseRNA id="arn1" name="s1" type="ANTISENSE_RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+some notes
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" name="zzz" size="0.3" pos="0.29999999999999993" type="CodingRegion"/>
+</celldesigner:listOfRegions>
+</celldesigner:AntisenseRNA>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/block_diagrams.xml b/model-command/testFiles/xmlNodeTestExamples/block_diagrams.xml
new file mode 100644
index 0000000000000000000000000000000000000000..15d462cb5d4afada6184abc3ff55fd267bc22d20
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/block_diagrams.xml
@@ -0,0 +1,15 @@
+<celldesigner:listOfBlockDiagrams>
+<celldesigner:blockDiagram protein="pr1">
+<celldesigner:canvas height="312" width="476"/>
+<celldesigner:block height="90" nameOffsetX="-8.0" nameOffsetY="-8.0" width="140" x="100" y="50"/>
+<celldesigner:halo height="150" width="200" x="70" y="20"/>
+<celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:residueInBlockDiagram id="0" offsetX="-27.0" type="dontcare"/>
+</celldesigner:listOfResiduesInBlockDiagram>
+<celldesigner:listOfExternalNamesForResidue/>
+<celldesigner:listOfBindingSitesInBlockDiagram/>
+<celldesigner:listOfEffectSitesInBlockDiagram/>
+<celldesigner:listOfInternalOperatorsInBlockDiagram/>
+<celldesigner:listOfInternalLinksInBlockDiagram/>
+</celldesigner:blockDiagram>
+</celldesigner:listOfBlockDiagrams>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_antisense_rna_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_antisense_rna_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..36c6c6d596924d2e583c08bab474613963754bd4
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_antisense_rna_collection.xml
@@ -0,0 +1,4 @@
+<celldesigner:listOfAntisenseRNAs>
+<celldesigner:AntisenseRNA id="arn1" name="s6" type="ANTISENSE_RNA"/>
+<celldesigner:AntisenseRNA id="arn2" name="s8" type="ANTISENSE_RNA"/>
+</celldesigner:listOfAntisenseRNAs>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias.xml b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f2f9049128675f1554eef5a45b1bccc6532342dc
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias.xml
@@ -0,0 +1,8 @@
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a278e98f461fb39e7aa8d800dccba9290c72d938
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_compartment_alias_collection.xml
@@ -0,0 +1,26 @@
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="139.0" y="55.0" w="522.0" h="178.0"/>
+<celldesigner:namePoint x="392.5" y="196.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca2" compartment="c2">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="707.0" y="187.0" w="118.0" h="73.0"/>
+<celldesigner:namePoint x="758.5" y="223.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+<celldesigner:compartmentAlias id="ca3" compartment="c3">
+<celldesigner:class>OVAL</celldesigner:class>
+<celldesigner:bounds x="185.0" y="143.0" w="86.0" h="50.0"/>
+<celldesigner:namePoint x="220.5" y="156.11618483532334"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias.xml
new file mode 100644
index 0000000000000000000000000000000000000000..95ff9bf4150dea3462f9fdea40c4f624fe92da17
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias.xml
@@ -0,0 +1,21 @@
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..22c1ec5c43f6643cc0f7735c1111e13138c84a9d
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_collection.xml
@@ -0,0 +1,65 @@
+<celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa2" species="s2598">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="863.0" y="35.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa3" species="s2599" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="767.0" y="15.0" w="61.0" h="87.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="23.0" y="15.0"/>
+<celldesigner:boxSize width="61.0" height="87.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bf37613db890d17ecff3ec40fc57b012f9375caf
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_empty_state.xml
@@ -0,0 +1,21 @@
+<celldesigner:complexSpeciesAlias id="csa1" species="s2597">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="744.0" y="0.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml
new file mode 100644
index 0000000000000000000000000000000000000000..032fdf22b55c648f3eca0abdd340cfdc74d49c4e
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_complex_alias_with_parent.xml
@@ -0,0 +1,21 @@
+<celldesigner:complexSpeciesAlias id="csa2" species="s2" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="183.0" y="156.0" w="78.0" h="101.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="11.0" y="9.0"/>
+<celldesigner:boxSize width="78.0" height="101.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_gene_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_gene_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fc0f27d416abf059565bbc52b9ed08bb375b2964
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_gene_collection.xml
@@ -0,0 +1,4 @@
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s3" type="GENE"/>
+<celldesigner:gene id="gn2" name="s4" type="GENE"/>
+</celldesigner:listOfGenes>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_included_species_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_included_species_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..9ac2917c63c1656375360a9c9377dc439af91b25
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_included_species_collection.xml
@@ -0,0 +1,53 @@
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s10</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s9</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s10</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+</celldesigner:listOfIncludedSpecies>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_protein_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_protein_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..527d1e134c67dfff3e18e5dd5a15a5a46e758125
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_protein_collection.xml
@@ -0,0 +1,6 @@
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+<celldesigner:protein id="pr3" name="s11" type="GENERIC"/>
+<celldesigner:protein id="pr4" name="s12" type="GENERIC"/>
+</celldesigner:listOfProteins>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_rna_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_rna_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fdee0dee3d1ececd1dee0dd81eff83e58d79cf4a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_rna_collection.xml
@@ -0,0 +1,4 @@
+<celldesigner:listOfRNAs>
+<celldesigner:RNA id="rn1" name="s5" type="RNA"/>
+<celldesigner:RNA id="rn2" name="s7" type="RNA"/>
+</celldesigner:listOfRNAs>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_sbml_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_sbml_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3d9b3b4af1bdc66d333c5e41699d325b98e2dba2
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_sbml_collection.xml
@@ -0,0 +1,101 @@
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s3" id="s3" name="s3" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s4" id="s4" name="s4" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn2</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s5" id="s5" name="s5" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn1</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s7" id="s7" name="s7" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn2</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s8" id="s8" name="s8" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn2</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s9" id="s9" name="s9" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s9</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml b/model-command/testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8fe0e36940e95c81170c76f2c113eaac9c8b04da
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/cd_species_alias_collection.xml
@@ -0,0 +1,78 @@
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa8" species="s2594">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="510.83547998986796" y="449.34999999999997" w="261.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.6161980749753" y="5346.0"/>
+<celldesigner:boxSize width="261.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa9" species="s2506">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="506.33547998986796" y="613.8499999999999" w="262.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="1459.1161980749753" y="5539.5"/>
+<celldesigner:boxSize width="262.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa10" species="s2595">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="282.0" y="75.0" w="134.0" h="94.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="134.0" height="94.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa11" species="s2596">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="483.0" y="76.0" w="82.0" h="96.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="82.0" height="96.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
diff --git a/model-command/testFiles/xmlNodeTestExamples/compartment.xml b/model-command/testFiles/xmlNodeTestExamples/compartment.xml
new file mode 100644
index 0000000000000000000000000000000000000000..da23a06a1c93990b3bd370922022f60896674003
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/compartment.xml
@@ -0,0 +1,16 @@
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#c1">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:123"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</compartment>
diff --git a/model-command/testFiles/xmlNodeTestExamples/gene.xml b/model-command/testFiles/xmlNodeTestExamples/gene.xml
new file mode 100644
index 0000000000000000000000000000000000000000..82e893f865462671eead57c4acba8a31f9a551de
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/gene.xml
@@ -0,0 +1,12 @@
+<celldesigner:gene id="gn3" name="BCL6" type="GENE">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+B-cell CLL/lymphoma 6
+</body>
+</html>
+</celldesigner:notes>
+</celldesigner:gene>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/layer.xml b/model-command/testFiles/xmlNodeTestExamples/layer.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ac0718cca948429afc5b3d7381dea7892ae8dcc3
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/layer.xml
@@ -0,0 +1,34 @@
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
diff --git a/model-command/testFiles/xmlNodeTestExamples/layer_collection.xml b/model-command/testFiles/xmlNodeTestExamples/layer_collection.xml
new file mode 100644
index 0000000000000000000000000000000000000000..818cce79cf0462baba5b90542c379992fb1eac19
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/layer_collection.xml
@@ -0,0 +1,36 @@
+<celldesigner:listOfLayers>
+<celldesigner:layer id="1" name="Layer0001" locked="false" visible="true">
+<celldesigner:listOfTexts>
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
+</celldesigner:listOfTexts>
+<celldesigner:listOfSquares>
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
+</celldesigner:listOfSquares>
+<celldesigner:listOfFreeLines>
+<celldesigner:layerFreeLine isArrow="false" isDotted="false">
+<celldesigner:bounds sx="75.0" sy="349.0" ex="238.0" ey="279.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
+</celldesigner:listOfFreeLines>
+</celldesigner:layer>
+</celldesigner:listOfLayers>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/layer_line.xml b/model-command/testFiles/xmlNodeTestExamples/layer_line.xml
new file mode 100644
index 0000000000000000000000000000000000000000..54eed30828ebf78f052c9d9d0528a1f50637ded7
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/layer_line.xml
@@ -0,0 +1,4 @@
+<celldesigner:layerFreeLine isArrow="true" isDotted="false">
+<celldesigner:bounds sx="56.0" sy="270.0" ex="181.0" ey="193.0"/>
+<celldesigner:line width="5.0" color="ff000000"/>
+</celldesigner:layerFreeLine>
diff --git a/model-command/testFiles/xmlNodeTestExamples/layer_oval.xml b/model-command/testFiles/xmlNodeTestExamples/layer_oval.xml
new file mode 100644
index 0000000000000000000000000000000000000000..1ac57f3ae62d3d85bfdbf683fb3bf7dfcde6065f
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/layer_oval.xml
@@ -0,0 +1,5 @@
+<celldesigner:layerCompartmentAlias type="Oval">
+<celldesigner:bounds x="268.0" y="34.0" w="211.0" h="97.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/layer_square.xml b/model-command/testFiles/xmlNodeTestExamples/layer_square.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c1a7322b1526d7ebf6e30427ca77c1f62b813525
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/layer_square.xml
@@ -0,0 +1,5 @@
+<celldesigner:layerCompartmentAlias type="Square">
+<celldesigner:bounds x="271.0" y="169.0" w="227.0" h="95.0"/>
+<celldesigner:paint color="ff000000" scheme="Gradation"/>
+<celldesigner:ispaint inner="false"/>
+</celldesigner:layerCompartmentAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/layer_text.xml b/model-command/testFiles/xmlNodeTestExamples/layer_text.xml
new file mode 100644
index 0000000000000000000000000000000000000000..70e0c5a798136b222da097762b5fcf4ca2dd8ee2
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/layer_text.xml
@@ -0,0 +1,8 @@
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml b/model-command/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml
new file mode 100644
index 0000000000000000000000000000000000000000..68185b6d00a516db4d300ca2d6cd24028b22efbb
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml
@@ -0,0 +1,9 @@
+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+Z-Index: 19
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/nested_complex.xml b/model-command/testFiles/xmlNodeTestExamples/nested_complex.xml
new file mode 100644
index 0000000000000000000000000000000000000000..2b1edfd3d04d554c15a6122a3ff4f5b98fc45981
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/nested_complex.xml
@@ -0,0 +1,490 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfIncludedSpecies>
+<celldesigner:species id="s3" name="s3">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s1</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s3</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s4" name="s4">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s6</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s4</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s5" name="s5">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s6</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s5</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s7" name="s7">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s2</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s8" name="s8">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s2</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s9" name="s9">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s1</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>s9</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s10" name="s10">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s5</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr3</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s11" name="s11">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s5</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr4</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+<celldesigner:species id="s12" name="s12">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body/>
+</html>
+</celldesigner:notes>
+<celldesigner:annotation>
+<celldesigner:complexSpecies>s6</celldesigner:complexSpecies>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn1</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:annotation>
+</celldesigner:species>
+</celldesigner:listOfIncludedSpecies>
+<celldesigner:listOfCompartmentAliases/>
+<celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:complexSpeciesAlias id="csa1" species="s1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="49.0" y="33.0" w="100.0" h="120.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
+<celldesigner:backupView state="none"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="100.0" height="120.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="2.0"/>
+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+<celldesigner:complexSpeciesAlias id="csa6" species="s6">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="329.0" y="22.0" w="178.0" h="195.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:backupSize w="0.0" h="0.0"/>
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+<celldesigner:activity>inactive</celldesigner:activity>
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+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="445.0" y="35.0" w="56.0" h="68.0"/>
+<celldesigner:font size="12"/>
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+<celldesigner:paint color="fff7f7f7" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:complexSpeciesAlias>
+</celldesigner:listOfComplexSpeciesAliases>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s7" complexSpeciesAlias="csa2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="203.0" y="39.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
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+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
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+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s8" complexSpeciesAlias="csa2">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="204.0" y="94.0" w="80.0" h="40.0"/>
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+<celldesigner:usualView>
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+<celldesigner:boxSize width="80.0" height="40.0"/>
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+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
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+<celldesigner:innerPosition x="0.0" y="0.0"/>
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+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa3" species="s9" complexSpeciesAlias="csa1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="56.0" y="101.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="7.0" y="68.5"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa4" species="s10" complexSpeciesAlias="csa5">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="347.0" y="87.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="6.0" y="11.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa5" species="s11" complexSpeciesAlias="csa5">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="350.0" y="139.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="9.0" y="63.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffcccc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa6" species="s12" complexSpeciesAlias="csa6">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="339.0" y="35.5" w="70.0" h="25.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10.0" y="13.5"/>
+<celldesigner:boxSize width="70.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffffff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s7" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s8" type="GENERIC"/>
+<celldesigner:protein id="pr3" name="s10" type="GENERIC"/>
+<celldesigner:protein id="pr4" name="s11" type="TRUNCATED"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes>
+<celldesigner:gene id="gn1" name="s12" type="GENE"/>
+</celldesigner:listOfGenes>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
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+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
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+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
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+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
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+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s1</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s2</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s6" id="s6" name="s6" compartment="default" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>s6</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+</model>
+</sbml>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes.xml b/model-command/testFiles/xmlNodeTestExamples/notes.xml
new file mode 100644
index 0000000000000000000000000000000000000000..07e958faee7d9bb5fd682ca528679300524a2818
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes.xml
@@ -0,0 +1,10 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes2.xml b/model-command/testFiles/xmlNodeTestExamples/notes2.xml
new file mode 100644
index 0000000000000000000000000000000000000000..fe5db406a203836ada3d7592b72be7b174c84350
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes2.xml
@@ -0,0 +1,23 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: SNCA
+Previous Symbols: X1, X2, X3
+Synonyms: Y1, Y2, Y3
+Name: Synuclein alpha (or something)
+Abbreviation: SN
+Formula: form
+MechanicalConfidenceScore: 2
+LowerBound: 2
+UpperBound: 2
+Subsystem: 2
+GeneProteinReaction: 1
+ChargedFormula: 1
+Charge:15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes3.xml b/model-command/testFiles/xmlNodeTestExamples/notes3.xml
new file mode 100644
index 0000000000000000000000000000000000000000..68f0aadbf7ce91b973d5a570b05d3385e6d72f11
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes3.xml
@@ -0,0 +1,11 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes4.xml b/model-command/testFiles/xmlNodeTestExamples/notes4.xml
new file mode 100644
index 0000000000000000000000000000000000000000..444dade224bdda399f10283c4da4dec8f280c86f
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes4.xml
@@ -0,0 +1,11 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Description: some notes some notes Symbol: strange2
+some notes some notes Symbol: strange3
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes5.xml b/model-command/testFiles/xmlNodeTestExamples/notes5.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b4d6531235e9a014514bc722dc172b7c9226f549
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes5.xml
@@ -0,0 +1,43 @@
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdfa:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/></rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:PTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family:ADH_Sf_Zn"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml b/model-command/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
new file mode 100644
index 0000000000000000000000000000000000000000..8e2a9d5f76a483fecc5a5ff93c8f2859bfae17de
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/notes_invalid_charge.xml
@@ -0,0 +1,11 @@
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Charge:a15
+some notes
+</body>
+</html>
+</celldesigner:notes>
diff --git a/model-command/testFiles/xmlNodeTestExamples/protein.xml b/model-command/testFiles/xmlNodeTestExamples/protein.xml
new file mode 100644
index 0000000000000000000000000000000000000000..835d0522dc38d576d721da4db15daef26aaf0383
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/protein.xml
@@ -0,0 +1,16 @@
+<celldesigner:protein id="pr23" name="SDHA" type="GENERIC">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+UniProtKB P31040 SDHA GO:0005749 GO_REF:0000024|UniProtKB:Q0QF01 ISS UniProtKB:Q0QF01 C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20100125 UniProtKB
+UniProtKB P31040 SDHA GO:0005749 PMID:7550341 TAS C Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial A8K5J6|DHSA_HUMAN|IPI00305166|Q16395|Q9UMY5|SDH2|SDHA|SDHF protein taxon:9606 20060419 UniProtKB
+</body>
+</html>
+</celldesigner:notes>
+<celldesigner:listOfModificationResidues>
+<celldesigner:modificationResidue angle="3.141592653589793" name="S176 bla bla" id="rs1" side="none"/>
+</celldesigner:listOfModificationResidues>
+</celldesigner:protein>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml
new file mode 100644
index 0000000000000000000000000000000000000000..15b2c0852ad7302848f0eabbbdb5a128f1f0406a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_dissociation_with_addition.xml
@@ -0,0 +1,102 @@
+<reaction metaid="re1" id="re1" name="aloha" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>DISSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="SSE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="NNE"/>
+</celldesigner:baseProduct>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="NW"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s4" alias="sa4" targetLineIndex="0,0">
+<celldesigner:linkAnchor position="W"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="0,1">
+<celldesigner:linkAnchor position="WNW"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="3" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="4" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="5" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="3" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="4" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="5" num1="4" num2="3" tShapeIndex="4">0.24786965283331241,1.4184399101982113 -0.2596602279438036,1.409877231858308 -0.35727191415681503,1.804760442830816 -2.2937599753831828,2.3784995538158102 0.363430985846696,2.922639182307759 0.6907115513398443,-0.8263950664174549 2.4806278565589914,-0.4844627944362667 2.1882644295694513,0.7795393156288313 0.5889014911814525,0.4467636503788679 1.5935032940046754,-0.8321513746664665 2.865325410784639,0.40459762305228997 1.0122523879316598,0.7052996795089067 0.1856396292788527,0.3448028007035582</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00011" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00012" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f759f74c79c412a8fad4d6f0eda5f4bbbd5e8545
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer.xml
@@ -0,0 +1,54 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="0" num1="0" num2="0" tShapeIndex="0">0.3543143297380586,0.41502311248073964</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml
new file mode 100644
index 0000000000000000000000000000000000000000..83738af5929eef26384ac1b2595e82e4c817ae35
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_heterodimer_with_additions.xml
@@ -0,0 +1,101 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s4" alias="sa4" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="SSE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="SSW"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="3" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="4" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="5" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="6" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="7" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="8" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="1" num1="2" num2="8" tShapeIndex="6">0.6898190045248871,0.41493212669683266 0.3690344574394102,0.4436355655530426 0.4067830423940162,-0.618154613466328 0.2057070196067705,0.27418031666165343 0.5573109932903977,0.24900556265208795 0.24307206195228326,0.011601570519530924 0.32722922889758355,-0.3519683205847308 0.23631167935790365,-0.6299101283205016 0.4451161869205815,-0.42463489483307004 2.1976031495216395,-0.051531612298451046 2.125528547270494,0.29079378866696914 0.34738186462324405,0.46335826795596924</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00009" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00010" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_positive_influence.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_positive_influence.xml
new file mode 100644
index 0000000000000000000000000000000000000000..6f969cbb9a88aae0d26229fe3b8154f82f132936
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_positive_influence.xml
@@ -0,0 +1,41 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>POSITIVE_INFLUENCE</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transcription.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ce5e630ed7ea90d676ef2a968afda2b1a77c3e0a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription.xml
@@ -0,0 +1,41 @@
+<reaction metaid="re4" id="re4" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSCRIPTION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s4" alias="sa4">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5686ed88800d7fbcea292d09ea2a8ffafb2701ea
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transcription_with_additions.xml
@@ -0,0 +1,80 @@
+<reaction metaid="re4" id="re4" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSCRIPTION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s4" alias="sa4">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s6" alias="sa6" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="vertical"/>
+<celldesigner:lineDirection index="1" value="horizontal"/>
+<celldesigner:lineDirection index="2" value="vertical"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.3275574775411034,-0.25113523762663204 0.6977609748292235,0.23172381829317268</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00008" species="s6">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa6</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00009" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transition.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transition.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0f8edfbdda56b01e196837ebfcc7ec6012252d89
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transition.xml
@@ -0,0 +1,45 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="2">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+<celldesigner:lineDirection index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.24477145008979806,0.2737964196744106 0.3030703119434812,-0.2478987966128221 0.845451600125741,-0.29800234330419595</celldesigner:editPoints>
+<celldesigner:line width="2.0" color="ff120000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml
new file mode 100644
index 0000000000000000000000000000000000000000..2154bc1a73eccecc094cef9c641cf190b88f298f
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transitionWithAdditionalNodes.xml
@@ -0,0 +1,86 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s4" alias="sa4" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.2694923595421561,0.03113391403065835</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="N"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.5963993894126993,-0.05429989069902841 0.5448875616378848,-1.603902125616216</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="2">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+<celldesigner:lineDirection index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints>0.11233758456827642,0.12302432727767126 0.13628805800643468,-0.11389609817852006 0.7741123124570151,-0.15496432192880294</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00008" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00009" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml
new file mode 100644
index 0000000000000000000000000000000000000000..379f3cb93327774a9899e7d2f5ffd1315486890e
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transition_omitted.xml
@@ -0,0 +1,45 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>KNOWN_TRANSITION_OMITTED</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="1">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+<celldesigner:lineDirection index="2" value="unknown"/>
+<celldesigner:lineDirection index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints omittedShapeIndex="1">0.1395721196429789,-0.2928391360632283 0.7711466302645423,0.20147252877787603 1.0166295304909794,0.12192232640388895</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_translation.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_translation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a39da860607dc653a9611713aeb2af2da88c3558
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_translation.xml
@@ -0,0 +1,77 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSLATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s3" alias="sa3" targetLineIndex="-1,0">
+<celldesigner:linkAnchor position="NNE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s6" alias="sa5" targetLineIndex="-1,1">
+<celldesigner:linkAnchor position="N"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00003" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00004" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>csa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_transport.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_transport.xml
new file mode 100644
index 0000000000000000000000000000000000000000..99be4f10416a9eb3256e9d1c03b885f18c26845a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_transport.xml
@@ -0,0 +1,59 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>asd
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRANSPORT</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="E"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#re885">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_631.3"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_truncation.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_truncation.xml
new file mode 100644
index 0000000000000000000000000000000000000000..393d0347e4d590e041fdf7dab901951019e8c9a0
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_truncation.xml
@@ -0,0 +1,60 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRUNCATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="ESE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:baseProduct>
+<celldesigner:baseProduct species="s3" alias="sa3">
+<celldesigner:linkAnchor position="W"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
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+<celldesigner:lineDirection arm="0" index="1" value="unknown"/>
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+<celldesigner:lineDirection arm="1" index="1" value="unknown"/>
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+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="2" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="3" value="unknown"/>
+</celldesigner:listOfLineDirection>
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+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml
new file mode 100644
index 0000000000000000000000000000000000000000..dccad1d1d777b5512f8d847be4b1c70064d8c70f
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_truncationWithModifier.xml
@@ -0,0 +1,187 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>TRUNCATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
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+<celldesigner:baseProducts>
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+<modifierSpeciesReference metaid="CDMT00016" species="s12">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa12</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00017" species="s13">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa13</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00018" species="s14">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa14</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00019" species="s15">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa15</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+</listOfModifiers>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml
new file mode 100644
index 0000000000000000000000000000000000000000..546a2740e2bc5108d302ce0b0fa2f7261684d2e6
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_unknown_transition.xml
@@ -0,0 +1,41 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>UNKNOWN_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="S"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="N"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml
new file mode 100644
index 0000000000000000000000000000000000000000..aa32d43ad2c2cf980d62d53c64534afc0c32aa3f
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_with_modifiers.xml
@@ -0,0 +1,91 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+<celldesigner:listOfModification>
+<celldesigner:modification type="BOOLEAN_LOGIC_GATE_AND" modifiers="s3,s4" aliases="sa3,sa4" modificationType="CATALYSIS" targetLineIndex="-1,2" editPoints="190.66666666666666,117.66666666666667">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="CATALYSIS" modifiers="s3" aliases="sa3" editPoints="0.3546405445791134,0.4532624937738668">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s3" alias="sa3">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+<celldesigner:modification type="CATALYSIS" modifiers="s4" aliases="sa4" targetLineIndex="-1,0" editPoints="0.04371287754328368,-0.803475293820294">
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+<celldesigner:lineDirection index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:linkTarget species="s4" alias="sa4">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:linkTarget>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:modification>
+</celldesigner:listOfModification>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<listOfModifiers>
+<modifierSpeciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+<modifierSpeciesReference metaid="CDMT00004" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</modifierSpeciesReference>
+</listOfModifiers>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/reaction_with_operators.xml b/model-command/testFiles/xmlNodeTestExamples/reaction_with_operators.xml
new file mode 100644
index 0000000000000000000000000000000000000000..da5e508d960591dcd376126a97b8d40eb9cf9fc9
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/reaction_with_operators.xml
@@ -0,0 +1,91 @@
+<reaction metaid="re1" id="re1" reversible="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>HETERODIMER_ASSOCIATION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s2" alias="sa2">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+<celldesigner:baseReactant species="s1" alias="sa1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseReactant>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s4" alias="sa4">
+<celldesigner:linkAnchor position="INACTIVE"/>
+</celldesigner:baseProduct>
+</celldesigner:baseProducts>
+<celldesigner:listOfReactantLinks>
+<celldesigner:reactantLink reactant="s3" alias="sa3" targetLineIndex="2,0">
+<celldesigner:linkAnchor position="INACTIVE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:reactantLink>
+</celldesigner:listOfReactantLinks>
+<celldesigner:listOfProductLinks>
+<celldesigner:productLink product="s5" alias="sa5" targetLineIndex="2,1">
+<celldesigner:linkAnchor position="INACTIVE"/>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000" type="Straight"/>
+</celldesigner:productLink>
+</celldesigner:listOfProductLinks>
+<celldesigner:connectScheme connectPolicy="direct">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection arm="0" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="1" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="0" value="unknown"/>
+<celldesigner:lineDirection arm="2" index="1" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:editPoints num0="0" num1="0" num2="1" tShapeIndex="1">0.0339412438306228,-0.1656317895311532 0.7249666221628845,0.4813084112149532</celldesigner:editPoints>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00002" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00003" species="s3">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa3</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00004" species="s4">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa4</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+<speciesReference metaid="CDMT00005" species="s5">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa5</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+</reaction>
diff --git a/model-command/testFiles/xmlNodeTestExamples/rna.xml b/model-command/testFiles/xmlNodeTestExamples/rna.xml
new file mode 100644
index 0000000000000000000000000000000000000000..c6cf0548471445776f352e8fb19c38a280a075d2
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/rna.xml
@@ -0,0 +1,12 @@
+<celldesigner:RNA id="rn36" name="BCL6" type="RNA">
+<celldesigner:notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+B-cell CLL/lymphoma 6
+</body>
+</html>
+</celldesigner:notes>
+</celldesigner:RNA>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/rna_with_region.xml b/model-command/testFiles/xmlNodeTestExamples/rna_with_region.xml
new file mode 100644
index 0000000000000000000000000000000000000000..52566ea024fa319f50e1dde5d0c1d75d1ac8b94a
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/rna_with_region.xml
@@ -0,0 +1,5 @@
+<celldesigner:RNA id="rn49" name="TRNAU1" type="RNA">
+<celldesigner:listOfRegions>
+<celldesigner:region id="tr1" size="0.0" pos="0.10569105691056911" type="Modification Site"/>
+</celldesigner:listOfRegions>
+</celldesigner:RNA>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_antisense_rna.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_antisense_rna.xml
new file mode 100644
index 0000000000000000000000000000000000000000..b3a9173dc8eb8d2477e9424bd3c7224c5277af57
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_antisense_rna.xml
@@ -0,0 +1,11 @@
+<species metaid="s1" id="s2" name="s3" compartment="default" initialAmount="2" hasOnlySubstanceUnits="true" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ANTISENSE_RNA</celldesigner:class>
+<celldesigner:antisensernaReference>arn1</celldesigner:antisensernaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_complex.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_complex.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d51eb1284575a60f5dfef88d6fcded8c73ac1eca
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_complex.xml
@@ -0,0 +1,11 @@
+<species metaid="s6549" id="s6549" name="LC3-II" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>COMPLEX</celldesigner:class>
+<celldesigner:name>LC3-II</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_degraded.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_degraded.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0e8b347258fdf30f3cc03e0d03a263fdcfe6d13e
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_degraded.xml
@@ -0,0 +1,11 @@
+<species metaid="s1275" id="s1275" name="s1275" compartment="c20" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>DEGRADED</celldesigner:class>
+<celldesigner:name>s1275</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_drug.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_drug.xml
new file mode 100644
index 0000000000000000000000000000000000000000..ebb8c4a7a95e64a33cf960c6702d34c4fa195d12
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_drug.xml
@@ -0,0 +1,11 @@
+<species metaid="s6104" id="s6104" name="geldanamycin" compartment="c1" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>DRUG</celldesigner:class>
+<celldesigner:name>geldanamycin</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_gene.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_gene.xml
new file mode 100644
index 0000000000000000000000000000000000000000..3d176259f8c172c99f0fff8d06bd5a6d5fc58c1c
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_gene.xml
@@ -0,0 +1,73 @@
+<species metaid="s5916" id="s5916" name="Ptgr1" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: PTGR1
+Name: prostaglandin reductase 1
+Description: RecName: Full=Prostaglandin reductase 1; Short=PRG-1; EC=1.3.1.-; AltName: Full=15-oxoprostaglandin 13-reductase; EC=1.3.1.48; AltName: Full=NADP-dependent leukotriene B4 12-hydroxydehydrogenase; EC=1.3.1.74;
+Previous Symbols: LTB4DH
+Synonyms: LTB4DH
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>GENE</celldesigner:class>
+<celldesigner:geneReference>gn95</celldesigner:geneReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5916">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:18429"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11695"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_036344.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139580.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AADH_Sf_Zn"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A22949"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001139581.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_ion.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_ion.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5c2222a435b30b39aa5a3d4375f4f8b2bf1e9901
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_ion.xml
@@ -0,0 +1,124 @@
+<species metaid="s6029" id="s6029" name="Pi" compartment="c1" initialConcentration="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Long Name: PiSynonym: Synonym not specifiedAccession: U02720
+Symbol: SERPINA1
+Name: serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1
+Description: RecName: Full=Alpha-1-antitrypsin; AltName: Full=Alpha-1 protease inhibitor; AltName: Full=Alpha-1-antiproteinase; AltName: Full=Serpin A1; Contains: RecName: Full=Short peptide from AAT; Short=SPAAT; Flags: Precursor;
+Previous Symbols: PI
+Synonyms: AAT, PI
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>ION</celldesigner:class>
+<celldesigner:name>Pi</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6029">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121172.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3AProt_inh_serpin"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA35509"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:panther.family%3APTHR11461"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121174.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:8941"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002235.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121175.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121176.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121179.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121173.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121177.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_3705"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001121178.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002236.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_000286.3"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A5265"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_phenotype.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_phenotype.xml
new file mode 100644
index 0000000000000000000000000000000000000000..62bbee07b09e23caf5a6d59fd02c9bd373fb2aa5
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_phenotype.xml
@@ -0,0 +1,15 @@
+<species metaid="s5462" id="s5462" name="Neuronal damage and death" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PHENOTYPE</celldesigner:class>
+<celldesigner:name>Neuronal damage and death</celldesigner:name>
+</celldesigner:speciesIdentity>
+<celldesigner:listOfCatalyzedReactions>
+<celldesigner:catalyzed reaction="re1435"/>
+<celldesigner:catalyzed reaction="re1434"/>
+</celldesigner:listOfCatalyzedReactions>
+</celldesigner:extension>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_protein.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_protein.xml
new file mode 100644
index 0000000000000000000000000000000000000000..0f8d55a9f69c7fe05edd1eff4180ce09e5b5692c
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_protein.xml
@@ -0,0 +1,63 @@
+<species metaid="s5456" id="s5456" name="PTPRC" compartment="c27" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>protein tyrosine phosphatase, receptor type, C
+also known as CED45
+Symbol: PTPRC
+Name: protein tyrosine phosphatase, receptor type, C
+Description: RecName: Full=Receptor-type tyrosine-protein phosphatase C; EC=3.1.3.48; AltName: Full=Leukocyte common antigen; Short=L-CA; AltName: Full=T200; AltName: CD_antigen=CD45; Flags: Precursor;
+Previous Symbols: CD45
+Synonyms: CD45
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:entrez.gene:5788"/></rdf:Bag>
+</bqbiol:is>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_002829.2"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_13296"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>transmembrane</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1116</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5456">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_563578.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA34011"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:9666"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_rna.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_rna.xml
new file mode 100644
index 0000000000000000000000000000000000000000..a848f327dc38d38126e832a04b89f039b7d817a0
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_rna.xml
@@ -0,0 +1,78 @@
+<species metaid="s5914" id="s5914" name="Fmo3" compartment="c20" initialAmount="0" charge="0">
+<notes>
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<title/>
+</head>
+<body>
+Symbol: FMO3
+Name: flavin containing monooxygenase 3
+Description: RecName: Full=Dimethylaniline monooxygenase [N-oxide-forming] 3; EC=1.14.13.8; AltName: Full=Dimethylaniline oxidase 3; AltName: Full=FMO II; AltName: Full=FMO form 2; AltName: Full=Hepatic flavin-containing monooxygenase 3; Short=FMO 3;
+Previous Symbols:
+Synonyms:
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s6095">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:ncbigene:2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</body>
+</html>
+</notes>
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>RNA</celldesigner:class>
+<celldesigner:rnaReference>rn101</celldesigner:rnaReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s5914">
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:8486388"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_001002294.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_5740"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pharmgkb.pathways:PA166"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:kegg.genes:hsa%3A2328"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:refseq:NP_008825.4"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:hgnc:3771"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+<bqbiol:isVersionOf>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:pubmed:9417913"/>
+</rdf:Bag>
+</bqbiol:isVersionOf>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml
new file mode 100644
index 0000000000000000000000000000000000000000..db9afbef0800f907e06a8b5367023fc5954f1b9c
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_simple_molecule.xml
@@ -0,0 +1,11 @@
+<species metaid="s5463" id="s5463" name="Peroxides" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>SIMPLE_MOLECULE</celldesigner:class>
+<celldesigner:name>Peroxides</celldesigner:name>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
diff --git a/model-command/testFiles/xmlNodeTestExamples/sbml_unknown.xml b/model-command/testFiles/xmlNodeTestExamples/sbml_unknown.xml
new file mode 100644
index 0000000000000000000000000000000000000000..e8891db4fbdfd8654c5fb96c248232bac23e6056
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/sbml_unknown.xml
@@ -0,0 +1,23 @@
+<species metaid="s1356" id="s1356" name="unidentified caspase acting on Occludin" compartment="c1" initialAmount="0" charge="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>UNKNOWN</celldesigner:class>
+<celldesigner:name>unidentified caspase acting on Occludin</celldesigner:name>
+</celldesigner:speciesIdentity>
+<celldesigner:listOfCatalyzedReactions>
+<celldesigner:catalyzed reaction="re514"/>
+</celldesigner:listOfCatalyzedReactions>
+</celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#s1356">
+<bqbiol:hasVersion>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:reactome:REACT_21584.1"/>
+</rdf:Bag>
+</bqbiol:hasVersion>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+</species>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias.xml
new file mode 100644
index 0000000000000000000000000000000000000000..f3e98a79102afd980f9876205615e4f0be22fdc9
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias_with_font.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
new file mode 100644
index 0000000000000000000000000000000000000000..893947c964229bd2c87122606ce6871170ac4f9c
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_font.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa1" species="s78">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="78.0" y="207.0" w="307.0" h="110.0"/>
+<celldesigner:font size="30"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="307.0" height="110.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias_with_state.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_state.xml
new file mode 100644
index 0000000000000000000000000000000000000000..86a9a4163397e8007edcdf4e3e046fe60557ed55
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias_with_state.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa1" species="s78">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="69.0" y="75.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="0.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="open" prefix="free input" label="test" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
diff --git a/model-command/testFiles/xmlNodeTestExamples/species_alias_without_state.xml b/model-command/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
new file mode 100644
index 0000000000000000000000000000000000000000..267d16430a0c9bc1636be7798c2387a24fdd4e0c
--- /dev/null
+++ b/model-command/testFiles/xmlNodeTestExamples/species_alias_without_state.xml
@@ -0,0 +1,19 @@
+<celldesigner:speciesAlias id="sa36" species="s78" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="11813.0" y="2840.5" w="80.0" h="25.0"/>
+<celldesigner:font size="16"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="10416.0" y="2424.5"/>
+<celldesigner:boxSize width="80.0" height="25.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccff66" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..c11a06102de6742aba62ab93fed73425569b183c
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/ProjectComparator.java
@@ -0,0 +1,67 @@
+package lcsb.mapviewer.model;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
+import lcsb.mapviewer.model.map.layout.graphics.GlyphComparator;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelDataComparator;
+import lcsb.mapviewer.model.overlay.DataOverlay;
+import lcsb.mapviewer.model.overlay.DataOverlayComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.HashSet;
+
+public class ProjectComparator extends Comparator<Project> {
+
+ private static final Logger logger = LogManager.getLogger();
+
+ private final ModelComparator modelComparator;
+ private final SetComparator<ModelData> modelDataSetComparator;
+ private final SetComparator<DataOverlay> dataOverlaySetComparator;
+ private final SetComparator<Glyph> glyphSetComparator;
+
+ public ProjectComparator(final double epsilon) {
+ super(Project.class);
+ modelComparator = new ModelComparator(epsilon);
+ modelDataSetComparator = new SetComparator<>(new ModelDataComparator(epsilon));
+ glyphSetComparator = new SetComparator<>(new GlyphComparator());
+ dataOverlaySetComparator = new SetComparator<>(new DataOverlayComparator(epsilon));
+ }
+
+ public ProjectComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(final Project arg0, final Project arg1) {
+ int compareResult = glyphSetComparator.compare(new HashSet<>(arg0.getGlyphs()), new HashSet<>(arg1.getGlyphs()));
+ if (compareResult != 0) {
+ logger.debug("Glyphs different");
+ return compareResult;
+ }
+
+ compareResult = modelComparator.compare(arg0.getTopModel(), arg1.getTopModel());
+ if (compareResult != 0) {
+ logger.debug("Top model different: {}, {}", arg0.getTopModel(), arg1.getTopModel());
+ return compareResult;
+ }
+
+ if (modelDataSetComparator.compare(arg0.getModels(), arg1.getModels()) != 0) {
+ logger.debug("Models different");
+ return modelDataSetComparator.compare(arg0.getModels(), arg1.getModels());
+ }
+
+ int status = dataOverlaySetComparator.compare(new HashSet<>(arg0.getDataOverlays()), new HashSet<>(arg1.getDataOverlays()));
+ if (status != 0) {
+ logger.debug("Data overlays different");
+ return status;
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntryComparator.java b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntryComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..2dda81abcb2ae007c29ca5aaba6f5ad1e1f87e4c
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/cache/UploadedFileEntryComparator.java
@@ -0,0 +1,32 @@
+package lcsb.mapviewer.model.cache;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+import java.util.Arrays;
+
+public class UploadedFileEntryComparator extends Comparator<UploadedFileEntry> {
+
+ public UploadedFileEntryComparator() {
+ super(UploadedFileEntry.class, true);
+ }
+
+
+ @Override
+ protected int internalCompare(final UploadedFileEntry arg0, final UploadedFileEntry arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ if (stringComparator.compare(arg0.getOriginalFileName(), arg1.getOriginalFileName()) != 0) {
+ logger.debug("Original file name is different: {} != {}", arg0.getOriginalFileName(), arg1.getOriginalFileName());
+ return stringComparator.compare(arg0.getOriginalFileName(), arg1.getOriginalFileName());
+ }
+
+ if (!Arrays.equals(arg0.getFileContent(), arg1.getFileContent())) {
+ logger.debug("Glyph content different for file {}.", arg0.getOriginalFileName());
+ return -1;
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
index 5c1dbdd87533991c929af53a79e00d5a13f3ff73..be9eb77da23132592b61099c3efd8ff11cdce9c0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
@@ -1,35 +1,32 @@
package lcsb.mapviewer.model.graphics;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for ArrowTypeData. It compares the
* content, but skip database identifier.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ArrowTypeDataComparator extends Comparator<ArrowTypeData> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public ArrowTypeDataComparator(final double epsilon) {
super(ArrowTypeData.class);
@@ -48,22 +45,22 @@ public class ArrowTypeDataComparator extends Comparator<ArrowTypeData> {
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
if (arg0.getArrowType().compareTo(arg1.getArrowType()) != 0) {
- logger.debug("Different arrow type: " + arg0.getArrowType() + ", " + arg1.getArrowType());
+ logger.debug("Different arrow type: {}, {}", arg0.getArrowType(), arg1.getArrowType());
return arg0.getArrowType().compareTo(arg1.getArrowType());
}
if (arg0.getArrowLineType().compareTo(arg1.getArrowLineType()) != 0) {
- logger.debug("Different arrow line type: " + arg0.getArrowLineType() + ", " + arg1.getArrowLineType());
+ logger.debug("Different arrow line type: {}, {}", arg0.getArrowLineType(), arg1.getArrowLineType());
return arg0.getArrowLineType().compareTo(arg1.getArrowLineType());
}
if (doubleComparator.compare(arg0.getLen(), arg1.getLen()) != 0) {
- logger.debug("Different length: " + arg0.getLen() + ", " + arg1.getLen());
+ logger.debug("Different length: {}, {}", arg0.getLen(), arg1.getLen());
return doubleComparator.compare(arg0.getLen(), arg1.getLen());
}
if (doubleComparator.compare(arg0.getAngle(), arg1.getAngle()) != 0) {
- logger.debug("Different angle: " + arg0.getAngle() + ", " + arg1.getAngle());
+ logger.debug("Different angle: {}, {}", arg0.getAngle(), arg1.getAngle());
return doubleComparator.compare(arg0.getAngle(), arg1.getAngle());
}
return 0;
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
index f74203ca56a54aabb4d82a22266c0e16e44bc03f..63e6fc9f589354a7b4e709000ed78ffbed991639 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
@@ -1,36 +1,33 @@
package lcsb.mapviewer.model.graphics;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for {@link PolylineData}. It
* compares the content, but skip database identifier.
- *
+ *
* @author Piotr Gawron
- *
*/
public class PolylineDataComparator extends Comparator<PolylineData> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public PolylineDataComparator(final double epsilon) {
super(PolylineData.class, true);
@@ -51,7 +48,7 @@ public class PolylineDataComparator extends Comparator<PolylineData> {
ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
if (integerComparator.compare(arg0.getLines().size(), arg1.getLines().size()) != 0) {
- logger.debug("Lines have different segments number: " + arg0.getLines().size() + ", " + arg1.getLines().size());
+ logger.debug("Lines have different segments number: {}, {}", arg0.getLines().size(), arg1.getLines().size());
return integerComparator.compare(arg0.getLines().size(), arg1.getLines().size());
}
// TODO this should be fixed
@@ -68,27 +65,27 @@ public class PolylineDataComparator extends Comparator<PolylineData> {
// }
if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
- logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
+ logger.debug("Lines have different begin atd: {}, {}", arg0.getBeginAtd(), arg1.getBeginAtd());
return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
}
if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
- logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
+ logger.debug("Lines have different end atd: {}, {}", arg0.getEndAtd(), arg1.getEndAtd());
return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
}
if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
+ logger.debug("Lines have different width: {}, {}", arg0.getWidth(), arg1.getWidth());
return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
}
if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
- logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
+ logger.debug("Lines have different color: {}, {}", arg0.getColor(), arg1.getColor());
return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
}
if (arg0.getType().compareTo(arg1.getType()) != 0) {
- logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
+ logger.debug("Lines have different type: {}, {}", arg0.getType(), arg1.getType());
return arg0.getType().compareTo(arg1.getType());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
index ce6428dd066b246d9d00f121c2c6cda15809ef3f..b3e03db228d5f922fcd896393e8b7f33741951c4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/MiriamType.java
@@ -4248,7 +4248,7 @@ public enum MiriamType {
new Class<?>[]{}, "MIR:00000127",
new Class<?>[]{},
"obi",
- "OBI:0000070"),
+ "OBI_0000070"),
OMA_GROUP("OMA Group",
"https://omabrowser.org/cgi-bin/gateway.pl",
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/GlyphComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/GlyphComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..e217a4bc5d86d30bfb5e4fe12435bf3c95fea74e
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/GlyphComparator.java
@@ -0,0 +1,24 @@
+package lcsb.mapviewer.model.map.layout.graphics;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.model.cache.UploadedFileEntryComparator;
+
+public class GlyphComparator extends Comparator<Glyph> {
+
+
+ public GlyphComparator() {
+ super(Glyph.class, true);
+ }
+
+ @Override
+ protected int internalCompare(final Glyph arg0, final Glyph arg1) {
+ UploadedFileEntryComparator fileComparator = new UploadedFileEntryComparator();
+
+ if (fileComparator.compare(arg0.getFile(), arg1.getFile()) != 0) {
+ return fileComparator.compare(arg0.getFile(), arg1.getFile());
+ }
+
+ return 0;
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
index 7ccf3708f6c06f557926eeebff97ae13a2b1e206..fd635e43dae7aff8c2ab93436af79fbbbead22a7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
@@ -434,6 +434,7 @@ public class Layer implements MinervaEntity {
result.addAll(ovals);
result.addAll(rectangles);
result.addAll(texts);
+ result.addAll(images);
return result;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerImageComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerImageComparator.java
index 1849718e2111159baf115ef83277056a4bf566c3..9c45516173d42374815022e853a3ebc2505aade2 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerImageComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerImageComparator.java
@@ -23,23 +23,29 @@ public class LayerImageComparator extends Comparator<LayerImage> {
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
IntegerComparator integerComparator = new IntegerComparator();
- if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ int status = doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
+ if (status != 0) {
+ logger.debug("Image width different: {} != {}", arg0.getWidth(), arg1.getWidth());
+ return status;
}
if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
+ logger.debug("Image Height different: {} != {}", arg0.getHeight(), arg1.getHeight());
return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
}
if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
+ logger.debug("Image X different: {} != {}", arg0.getX(), arg1.getX());
return doubleComparator.compare(arg0.getX(), arg1.getX());
}
if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
+ logger.debug("Image Y different: {} != {}", arg0.getY(), arg1.getY());
return doubleComparator.compare(arg0.getY(), arg1.getY());
}
if (integerComparator.compare(arg0.getZ(), arg1.getZ()) != 0) {
+ logger.debug("Image Z different: {} != {}", arg0.getZ(), arg1.getZ());
return integerComparator.compare(arg0.getZ(), arg1.getZ());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
index e6e6be49e6dc342833516e2b5826050656ddd3ce..3cb94de59267845468099013216c6abdd173397a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerText.java
@@ -43,7 +43,7 @@ public class LayerText implements MinervaEntity, Drawable {
/**
* Default font size of the text.
*/
- private static final double DEFAULT_LAYER_FONT_SIZE = 11.0;
+ public static final double DEFAULT_LAYER_FONT_SIZE = 11.0;
/**
* Default class logger.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index b9c683193f3b421dbe0a78938610e3115966f65c..d3525bfdb0dd8f169020e033f9a7b5ce1b82b2a9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -507,4 +507,6 @@ public interface Model {
Set<Drawable> getDrawables(boolean onlyVisible);
Collection<Element> getSortedElements();
+
+ void removeLayer(Layer pathwayLayer);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
index 16f6065ca420fe5e99e1da9463be5cddcb51962b..f31d8915ffc0f3f0d8e8eab2952584f5060f4049 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelComparator.java
@@ -1,14 +1,5 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.CalendarComparator;
@@ -33,22 +24,24 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.ElementComparator;
import lcsb.mapviewer.modelutils.map.ElementUtils;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
/**
* Comparator for {@link Model} class.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ModelComparator extends Comparator<Model> {
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
private SetComparator<SbmlUnit> unitSetComparator = new SetComparator<>(new SbmlUnitComparator());
@@ -56,13 +49,12 @@ public class ModelComparator extends Comparator<Model> {
private ElementComparator elementComparator;
- private ElementUtils eu = new ElementUtils();
+ private final ElementUtils eu = new ElementUtils();
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public ModelComparator(final double epsilon) {
super(Model.class);
@@ -121,11 +113,20 @@ public class ModelComparator extends Comparator<Model> {
int status = compareElements(arg0.getElements(), arg1.getElements());
if (status != 0) {
- logger.debug("Set of elements different");
+ Set<String> model0ids = new HashSet<>();
+ Set<String> model1ids = new HashSet<>();
+
+ for (Element element : arg0.getElements()) {
+ model0ids.add(element.getElementId());
+ }
+ for (Element element : arg1.getElements()) {
+ model1ids.add(element.getElementId());
+ }
+ logger.debug("Set of elements different: {}, {}", model1ids, model0ids);
return status;
}
- SetComparator<Layer> layerSetComparator = new SetComparator<Layer>(new LayerComparator(epsilon));
+ SetComparator<Layer> layerSetComparator = new SetComparator<Layer>(new LayerComparator(epsilon));
status = layerSetComparator.compare(arg0.getLayers(), arg1.getLayers());
if (status != 0) {
@@ -202,13 +203,10 @@ public class ModelComparator extends Comparator<Model> {
/**
* Compares two sets of elements.
- *
- * @param elements
- * first set of elements
- * @param elements2
- * second set of elements
- * @return if sets are equal then returns 0. If they are different then -1/1
- * is returned.
+ *
+ * @param elements first set of elements
+ * @param elements2 second set of elements
+ * @return if sets are equal then returns 0. If they are different then -1/1 is returned.
*/
private int compareElements(final Set<Element> elements, final Set<Element> elements2) {
@@ -216,8 +214,8 @@ public class ModelComparator extends Comparator<Model> {
Map<String, Element> map2 = new HashMap<>();
if (elements.size() != elements2.size()) {
- logger.debug("Number of elements different: " + elements.size() + ", " + elements2.size());
- return ((Integer) elements.size()).compareTo(elements2.size());
+ logger.debug("Number of elements different: {}, {}", elements.size(), elements2.size());
+ return Integer.compare(elements.size(), elements2.size());
}
for (final Element element : elements) {
@@ -248,15 +246,13 @@ public class ModelComparator extends Comparator<Model> {
/**
* Compares two collection of models.
- *
- * @param collection1
- * first collection to compare
- * @param collection2
- * second collection to compare
+ *
+ * @param collection1 first collection to compare
+ * @param collection2 second collection to compare
* @return 0 if the collections are identical, -1/1 otherwise
*/
private int compareSubmodels(final Collection<ModelSubmodelConnection> collection1,
- final Collection<ModelSubmodelConnection> collection2) {
+ final Collection<ModelSubmodelConnection> collection2) {
IntegerComparator integerComparator = new IntegerComparator();
if (integerComparator.compare(collection1.size(), collection2.size()) != 0) {
logger.debug("collection of submodels doesn't match: " + collection1.size() + ", " + collection2.size());
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index 9258dcedb579239edc6c703a61d23e89e7992222..996edbb7250bdfc94a6ed954e61e4b3c7df2aa21 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -793,4 +793,8 @@ public class ModelData implements MinervaEntity {
public EntityType getEntityType() {
throw new NotImplementedException();
}
+
+ public void removeLayer(final Layer pathwayLayer) {
+ this.layers.remove(pathwayLayer);
+ }
}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelDataComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..21ca1415b96e2c351b1a9cf14ddfdf45374c3188
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelDataComparator.java
@@ -0,0 +1,26 @@
+package lcsb.mapviewer.model.map.model;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+
+public class ModelDataComparator extends Comparator<ModelData> {
+
+ private final ModelComparator modelComparator;
+
+ public ModelDataComparator(final double epsilon) {
+ super(ModelData.class);
+ modelComparator = new ModelComparator(epsilon);
+ }
+
+ /**
+ * Default constructor.
+ */
+ public ModelDataComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(final ModelData arg0, final ModelData arg1) {
+ return modelComparator.compare(new ModelFullIndexed(arg0), new ModelFullIndexed(arg1));
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index ffa13ff0832c8ee05f30e028ec815bcff95b131e..3a672046de4fe8e9fa4b2a159d1e652971b9214a 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -739,4 +739,9 @@ public class ModelFullIndexed implements Model {
result.sort(new ElementByIdComparator());
return result;
}
+
+ @Override
+ public void removeLayer(final Layer pathwayLayer) {
+ modelData.removeLayer(pathwayLayer);
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
index ecbd93fbacf95a2d0426fcdbaf3e5f387fc33a92..2cb72be7eb3a052f3ae0a2b080bc03925106adc9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/SubmodelConnectionComparator.java
@@ -1,36 +1,33 @@
package lcsb.mapviewer.model.map.model;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.StringComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for {@link SubmodelConnection}. It
* handles comparison of subclasses of {@link SubmodelConnection} class.
- *
+ *
* @author Piotr Gawron
- *
*/
public class SubmodelConnectionComparator extends Comparator<SubmodelConnection> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public SubmodelConnectionComparator(final double epsilon) {
super(SubmodelConnection.class, true);
@@ -60,7 +57,7 @@ public class SubmodelConnectionComparator extends Comparator<SubmodelConnection>
}
if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
return stringComparator.compare(arg0.getName(), arg1.getName());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
index c84733e90ae90e6cbf1d43fd4463275c85fd191b..68a975713ffec544e13837667119da71fc6ba096 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/AbstractNodeComparator.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.model.map.reaction;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.model.graphics.PolylineDataComparator;
@@ -10,28 +7,22 @@ import lcsb.mapviewer.model.graphics.PolylineDataComparator;
/**
* This class implements comparator interface for AbstractNode. It also handles
* comparison of subclasses of AbstractNode class.
- *
+ *
* @author Piotr Gawron
- *
*/
public class AbstractNodeComparator extends Comparator<AbstractNode> {
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
- private boolean ignoreLayout;
+ private final boolean ignoreLayout;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public AbstractNodeComparator(final double epsilon, final boolean ignoreLayout) {
super(AbstractNode.class, true);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index e29bd2f9ac45a4dfd52316bfc08a1282ab85c373..518e95b87768d8c02c742036f81012d576c9dfb0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.model.map.reaction;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.BooleanComparator;
@@ -16,31 +13,31 @@ import lcsb.mapviewer.model.graphics.PolylineDataComparator;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamDataComparator;
import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for {@link Reaction}.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ReactionComparator extends Comparator<Reaction> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
- private boolean ignoreLayout;
+ private final boolean ignoreLayout;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public ReactionComparator(final double epsilon, final boolean ignoreLayout) {
super(Reaction.class);
@@ -66,12 +63,12 @@ public class ReactionComparator extends Comparator<Reaction> {
AbstractNodeComparator nodeComparator = new AbstractNodeComparator(epsilon, ignoreLayout);
if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
return stringComparator.compare(arg0.getName(), arg1.getName());
}
if (stringComparator.compare(arg0.getNotes().trim(), arg1.getNotes().trim()) != 0) {
- logger.debug("Notes different: " + arg0.getNotes() + ", " + arg1.getNotes());
+ logger.debug("Notes different: {}, {}", arg0.getNotes(), arg1.getNotes());
return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index cb649f940f8beeb37a06082ba79c0e60009df8c6..7858e94c4ac26510f2e9ffc100829d109c9e24a7 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -366,6 +366,7 @@ public abstract class Element implements BioEntity, MinervaEntity, SbmlArgument
setGlyph(new Glyph(original.getGlyph()));
}
setBorderColor(original.getBorderColor());
+ setImmediateLink(original.getImmediateLink());
}
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
index b5bf17b05a83eb3592fbdfdb78892a8ffef38c1e..e4cd56e75133735ca72d43f0461967a92b483846 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/ElementComparator.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.model.map.species;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.ColorComparator;
@@ -17,30 +14,25 @@ import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamDataComparator;
import lcsb.mapviewer.model.map.compartment.CompartmentComparator;
+import lcsb.mapviewer.model.map.layout.graphics.GlyphComparator;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnectionComparator;
/**
* Comparator class used for comparing {@link Element} objects.
- *
- * @author Piotr Gawron
*
+ * @author Piotr Gawron
*/
public class ElementComparator extends Comparator<Element> {
- /**
- * Default class logger.
- */
- private static Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public ElementComparator(final double epsilon) {
super(Element.class, true);
@@ -72,99 +64,100 @@ public class ElementComparator extends Comparator<Element> {
StringComparator stringComparator = new StringComparator();
ColorComparator colorComparator = new ColorComparator();
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
+ GlyphComparator glyphComparator = new GlyphComparator();
if (stringComparator.compare(arg0.getElementId(), arg1.getElementId()) != 0) {
- logger.debug("ElementId different: " + arg0.getElementId() + ", " + arg1.getElementId());
+ logger.debug("ElementId different: {}, {}", arg0.getElementId(), arg1.getElementId());
return stringComparator.compare(arg0.getElementId(), arg1.getElementId());
}
if (doubleComparator.compare(arg0.getX(), arg1.getX()) != 0) {
- logger.debug("X different: " + arg0.getX() + ", " + arg1.getX());
+ logger.debug("X different: {}, {}", arg0.getX(), arg1.getX());
return doubleComparator.compare(arg0.getX(), arg1.getX());
}
if (doubleComparator.compare(arg0.getY(), arg1.getY()) != 0) {
- logger.debug("Y different: " + arg0.getY() + ", " + arg1.getY());
+ logger.debug("Y different: {}, {}", arg0.getY(), arg1.getY());
return doubleComparator.compare(arg0.getY(), arg1.getY());
}
IntegerComparator integerComparator = new IntegerComparator();
if (integerComparator.compare(arg0.getZ(), arg1.getZ()) != 0) {
- logger.debug("Z-index different: " + arg0.getZ() + ", " + arg1.getZ());
+ logger.debug("Z-index different: {}, {}", arg0.getZ(), arg1.getZ());
return integerComparator.compare(arg0.getZ(), arg1.getZ());
}
if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Width different: " + arg0.getWidth() + ", " + arg1.getWidth());
+ logger.debug("Width different: {}, {}", arg0.getWidth(), arg1.getWidth());
return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
}
if (doubleComparator.compare(arg0.getHeight(), arg1.getHeight()) != 0) {
- logger.debug("Height different: " + arg0.getHeight() + ", " + arg1.getHeight());
+ logger.debug("Height different: {}, {}", arg0.getHeight(), arg1.getHeight());
return doubleComparator.compare(arg0.getHeight(), arg1.getHeight());
}
if (doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize()) != 0) {
- logger.debug("Font size different: " + arg0.getFontSize() + ", " + arg1.getFontSize());
+ logger.debug("Font size different: {}, {}", arg0.getFontSize(), arg1.getFontSize());
return doubleComparator.compare(arg0.getFontSize(), arg1.getFontSize());
}
if (stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel()) != 0) {
- logger.debug("Visibility level different: " + arg0.getVisibilityLevel() + ", " + arg1.getVisibilityLevel());
+ logger.debug("Visibility level different: {}, {}", arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
return stringComparator.compare(arg0.getVisibilityLevel(), arg1.getVisibilityLevel());
}
if (colorComparator.compare(arg0.getFillColor(), arg1.getFillColor()) != 0) {
- logger.debug("Fill color different: " + arg0.getFillColor() + ", " + arg1.getFillColor());
+ logger.debug("Fill color different: {}, {}", arg0.getFillColor(), arg1.getFillColor());
return colorComparator.compare(arg0.getFillColor(), arg1.getFillColor());
}
if (colorComparator.compare(arg0.getBorderColor(), arg1.getBorderColor()) != 0) {
- logger.debug("Border color different: " + arg0.getBorderColor() + ", " + arg1.getBorderColor());
+ logger.debug("Border color different: {}, {}", arg0.getBorderColor(), arg1.getBorderColor());
return colorComparator.compare(arg0.getBorderColor(), arg1.getBorderColor());
}
if (colorComparator.compare(arg0.getFontColor(), arg1.getFontColor()) != 0) {
- logger.debug("Font color different: " + arg0.getFontColor() + ", " + arg1.getFontColor());
+ logger.debug("Font color different: {}, {}", arg0.getFontColor(), arg1.getFontColor());
return colorComparator.compare(arg0.getFontColor(), arg1.getFontColor());
}
// this should be somehow modified, because it can create a situation where
// comparison will fall into infinite loop (in cyclic submodels)
- ElementSubmodelConnectionComparator ascc = new ElementSubmodelConnectionComparator(epsilon);
- int status = ascc.compare(arg0.getSubmodel(), arg1.getSubmodel());
+ ElementSubmodelConnectionComparator connectionComparator = new ElementSubmodelConnectionComparator(epsilon);
+ int status = connectionComparator.compare(arg0.getSubmodel(), arg1.getSubmodel());
if (status != 0) {
- logger.debug("Element submodel different: " + arg0.getSubmodel() + ", " + arg1.getSubmodel());
+ logger.debug("Element submodel different: {}, {}", arg0.getSubmodel(), arg1.getSubmodel());
return status;
}
if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
return stringComparator.compare(arg0.getName(), arg1.getName());
}
if (stringComparator.compare(arg0.getNotes(), arg1.getNotes(), true) != 0) {
- logger.debug("notes different: \n\"" + arg0.getNotes() + "\"\n\"" + arg1.getNotes() + "\"");
+ logger.debug("notes different: \n\"{}\"\n\"{}\"", arg0.getNotes(), arg1.getNotes());
return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
}
if (stringComparator.compare(arg0.getSymbol(), arg1.getSymbol()) != 0) {
- logger.debug("symbol different: \"" + arg0.getSymbol() + "\", \"" + arg1.getSymbol() + "\"");
+ logger.debug("symbol different: \"{}\", \"{}\"", arg0.getSymbol(), arg1.getSymbol());
return stringComparator.compare(arg0.getSymbol(), arg1.getSymbol());
}
if (stringComparator.compare(arg0.getFullName(), arg1.getFullName()) != 0) {
- logger.debug("full name different: \"" + arg0.getFullName() + "\", \"" + arg1.getFullName() + "\"");
+ logger.debug("full name different: \"{}\", \"{}\"", arg0.getFullName(), arg1.getFullName());
return stringComparator.compare(arg0.getFullName(), arg1.getFullName());
}
if (stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation()) != 0) {
- logger.debug("Abbreviation different: \"" + arg0.getAbbreviation() + "\", \"" + arg1.getAbbreviation() + "\"");
+ logger.debug("Abbreviation different: \"{}\", \"{}\"", arg0.getAbbreviation(), arg1.getAbbreviation());
return stringComparator.compare(arg0.getAbbreviation(), arg1.getAbbreviation());
}
if (stringComparator.compare(arg0.getFormula(), arg1.getFormula()) != 0) {
- logger.debug("formula different: \"" + arg0.getFormula() + "\", \"" + arg1.getFormula() + "\"");
+ logger.debug("formula different: \"{}\", \"{}\"", arg0.getFormula(), arg1.getFormula());
return stringComparator.compare(arg0.getFormula(), arg1.getFormula());
}
@@ -184,46 +177,52 @@ public class ElementComparator extends Comparator<Element> {
status = miriamDataSetComparator.compare(arg0.getMiriamData(), arg1.getMiriamData());
if (status != 0) {
- logger.debug("miriam data different");
- logger.debug(arg0.getMiriamData());
- logger.debug(arg1.getMiriamData());
+ logger.debug("miriam data different:\n{}\n{}", arg0.getMiriamData(), arg1.getMiriamData());
return status;
}
if (doubleComparator.compare(arg0.getNameX(), arg1.getNameX()) != 0) {
- logger.debug("NameX different: " + arg0.getNameX() + ", " + arg1.getNameX());
+ logger.debug("NameX different: {}, {}", arg0.getNameX(), arg1.getNameX());
return doubleComparator.compare(arg0.getNameX(), arg1.getNameX());
}
if (doubleComparator.compare(arg0.getNameY(), arg1.getNameY()) != 0) {
- logger.debug("NameY different: " + arg0.getNameY() + ", " + arg1.getNameY());
+ logger.debug("NameY different: {}, {}", arg0.getNameY(), arg1.getNameY());
return doubleComparator.compare(arg0.getNameY(), arg1.getNameY());
}
if (doubleComparator.compare(arg0.getNameWidth(), arg1.getNameWidth()) != 0) {
- logger.debug("NameWidth different: " + arg0.getNameWidth() + ", " + arg1.getNameWidth());
+ logger.debug("NameWidth different: {}, {}", arg0.getNameWidth(), arg1.getNameWidth());
return doubleComparator.compare(arg0.getNameWidth(), arg1.getNameWidth());
}
if (doubleComparator.compare(arg0.getNameHeight(), arg1.getNameHeight()) != 0) {
- logger.debug("NameHeight different: " + arg0.getNameHeight() + ", " + arg1.getNameHeight());
+ logger.debug("NameHeight different: {}, {}", arg0.getNameHeight(), arg1.getNameHeight());
return doubleComparator.compare(arg0.getNameHeight(), arg1.getNameHeight());
}
EnumComparator<VerticalAlign> verticalAlignComparator = new EnumComparator<>();
if (verticalAlignComparator.compare(arg0.getNameVerticalAlign(), arg1.getNameVerticalAlign()) != 0) {
- logger.debug("Name vertical alignment different: " + arg0.getNameVerticalAlign() + ", "
- + arg1.getNameVerticalAlign());
+ logger.debug("Name vertical alignment different: {}, {}", arg0.getNameVerticalAlign(), arg1.getNameVerticalAlign());
return verticalAlignComparator.compare(arg0.getNameVerticalAlign(), arg1.getNameVerticalAlign());
}
EnumComparator<HorizontalAlign> horizontalAlignComparator = new EnumComparator<>();
if (horizontalAlignComparator.compare(arg0.getNameHorizontalAlign(), arg1.getNameHorizontalAlign()) != 0) {
- logger.debug("Name horizontal alignment different: " + arg0.getNameHorizontalAlign() + ", "
- + arg1.getNameHorizontalAlign());
+ logger.debug("Name horizontal alignment different: {}, {}", arg0.getNameHorizontalAlign(), arg1.getNameHorizontalAlign());
return horizontalAlignComparator.compare(arg0.getNameHorizontalAlign(), arg1.getNameHorizontalAlign());
}
+ if (stringComparator.compare(arg0.getImmediateLink(), arg1.getImmediateLink()) != 0) {
+ logger.debug("Immediate link different: {}, {}", arg0.getImmediateLink(), arg1.getImmediateLink());
+ return stringComparator.compare(arg0.getImmediateLink(), arg1.getImmediateLink());
+ }
+
+ if (glyphComparator.compare(arg0.getGlyph(), arg1.getGlyph()) != 0) {
+ logger.debug("Glyph different: {}, {}", arg0.getGlyph(), arg1.getGlyph());
+ return glyphComparator.compare(arg0.getGlyph(), arg1.getGlyph());
+ }
+
return 0;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayComparator.java b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..5937141f60786af39cbdc2cf1923d5b19886ce92
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayComparator.java
@@ -0,0 +1,59 @@
+package lcsb.mapviewer.model.overlay;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+
+import java.util.HashSet;
+
+public class DataOverlayComparator extends Comparator<DataOverlay> {
+
+ private final SetComparator<DataOverlayEntry> dataOverlayEntrySetComparator;
+
+ public DataOverlayComparator(final double epsilon) {
+ super(DataOverlay.class, true);
+ this.dataOverlayEntrySetComparator = new SetComparator<>(new DataOverlayEntryComparator(epsilon));
+ }
+
+ public DataOverlayComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(final DataOverlay arg0, final DataOverlay arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ int status = stringComparator.compare(arg0.getName(), arg1.getName());
+ if (status != 0) {
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getDescription(), arg1.getDescription());
+ if (status != 0) {
+ logger.debug("Description different: {}, {}", arg0.getDescription(), arg1.getDescription());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ if (status != 0) {
+ logger.debug("GenomeVersion different: {}, {}", arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ if (status != 0) {
+ logger.debug("GenomeVersion different: {}, {}", arg0.getGenomeVersion(), arg1.getGenomeVersion());
+ return status;
+ }
+
+ status = dataOverlayEntrySetComparator.compare(new HashSet<>(arg0.getEntries()), new HashSet<>(arg1.getEntries()));
+ if (status != 0) {
+ logger.debug("Entries different");
+ return status;
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntryComparator.java b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntryComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..8ab3b2deef71f2a44625ac8e39b3fd5187afcd59
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/overlay/DataOverlayEntryComparator.java
@@ -0,0 +1,107 @@
+package lcsb.mapviewer.model.overlay;
+
+import lcsb.mapviewer.common.Comparator;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.comparator.BooleanComparator;
+import lcsb.mapviewer.common.comparator.ColorComparator;
+import lcsb.mapviewer.common.comparator.DoubleComparator;
+import lcsb.mapviewer.common.comparator.SetComparator;
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamDataComparator;
+import lcsb.mapviewer.modelutils.map.ClassNameComparator;
+
+public class DataOverlayEntryComparator extends Comparator<DataOverlayEntry> {
+
+ private final SetComparator<MiriamData> miriamDataSetComparator = new SetComparator<>(new MiriamDataComparator());
+
+ private final SetComparator<String> stringSetComparator = new SetComparator<>(new StringComparator());
+ private final SetComparator<Class<? extends BioEntity>> classSetComparator = new SetComparator<>(new ClassNameComparator<>());
+
+ private final ColorComparator colorComparator = new ColorComparator();
+ private final BooleanComparator booleanComparator = new BooleanComparator();
+ private final DoubleComparator doubleComparator;
+
+ public DataOverlayEntryComparator(final double epsilon) {
+ super(DataOverlayEntry.class);
+ doubleComparator = new DoubleComparator(epsilon);
+ }
+
+ public DataOverlayEntryComparator() {
+ this(Configuration.EPSILON);
+ }
+
+ @Override
+ protected int internalCompare(final DataOverlayEntry arg0, final DataOverlayEntry arg1) {
+ StringComparator stringComparator = new StringComparator();
+
+ int status = stringComparator.compare(arg0.getName(), arg1.getName());
+ if (status != 0) {
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getDescription(), arg1.getDescription());
+ if (status != 0) {
+ logger.debug("Description different: {}, {}", arg0.getDescription(), arg1.getDescription());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getElementId(), arg1.getElementId());
+ if (status != 0) {
+ logger.debug("ElementId different: {}, {}", arg0.getElementId(), arg1.getElementId());
+ return status;
+ }
+
+ status = stringComparator.compare(arg0.getModelName(), arg1.getModelName());
+ if (status != 0) {
+ logger.debug("ModelName different: {}, {}", arg0.getModelName(), arg1.getModelName());
+ return status;
+ }
+
+ status = colorComparator.compare(arg0.getColor(), arg1.getColor());
+ if (status != 0) {
+ logger.debug("Color different: {}, {}", arg0.getColor(), arg1.getColor());
+ return status;
+ }
+
+ status = miriamDataSetComparator.compare(arg0.getMiriamData(), arg1.getMiriamData());
+ if (status != 0) {
+ logger.debug("MiriamData different: {}, {}", arg0.getMiriamData(), arg1.getMiriamData());
+ return status;
+ }
+
+ status = stringSetComparator.compare(arg0.getCompartments(), arg1.getCompartments());
+ if (status != 0) {
+ logger.debug("Compartments different: {}, {}", arg0.getCompartments(), arg1.getCompartments());
+ return status;
+ }
+
+ status = doubleComparator.compare(arg0.getLineWidth(), arg1.getLineWidth());
+ if (status != 0) {
+ logger.debug("LineWidth different: {}, {}", arg0.getLineWidth(), arg1.getLineWidth());
+ return status;
+ }
+
+ status = booleanComparator.compare(arg0.getReverseReaction(), arg1.getReverseReaction());
+ if (status != 0) {
+ logger.debug("ReverseReaction different: {}, {}", arg0.getReverseReaction(), arg1.getReverseReaction());
+ return status;
+ }
+
+ status = doubleComparator.compare(arg0.getValue(), arg1.getValue());
+ if (status != 0) {
+ logger.debug("Value different: {}, {}", arg0.getValue(), arg1.getValue());
+ return status;
+ }
+
+ status = classSetComparator.compare(arg0.getTypes(), arg1.getTypes());
+ if (status != 0) {
+ logger.debug("Types different: {}, {}", arg0.getTypes(), arg1.getTypes());
+ return status;
+ }
+
+ return 0;
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
index f88c513a5b0cf88965dc9449d84420229e517fc6..a25bcd8764fcbc2d7b94d0f8dc1636e62c5b4519 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ClassNameComparator.java
@@ -4,14 +4,13 @@ import java.util.Comparator;
/**
* Class used to compare classes using class names (SimpleName).
- *
+ *
* @author Piotr Gawron
- *
*/
-public class ClassNameComparator implements Comparator<Class<?>> {
+public class ClassNameComparator<T> implements Comparator<Class<? extends T>> {
@Override
- public int compare(final Class<?> o1, final Class<?> o2) {
+ public int compare(final Class<? extends T> o1, final Class<? extends T> o2) {
return o1.getSimpleName().compareTo(o2.getSimpleName());
}
diff --git a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
index 019eb8ff2f6ec2c9d2a6b792c8605bb27debbe8e..d47c340960a78094ec732900ca32aa14b00e3b77 100644
--- a/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
+++ b/model/src/main/java/lcsb/mapviewer/modelutils/map/ElementUtils.java
@@ -1,5 +1,15 @@
package lcsb.mapviewer.modelutils.map;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.field.ModificationResidue;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.reflections.Reflections;
+
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
@@ -11,22 +21,10 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.reflections.Reflections;
-
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.Drawable;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.field.ModificationResidue;
-
/**
* Class with some util method for {@link BioEntity} objects.
- *
+ *
* @author Piotr Gawron
- *
*/
public final class ElementUtils {
@@ -52,23 +50,21 @@ public final class ElementUtils {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
- * @param elementClasses
- * the elementClasses to set
+ * @param elementClasses the elementClasses to set
* @see #elementClasses
*/
- protected static void setElementClasses(final Map<String, Class<? extends Element>> elementClasses) {
+ static void setElementClasses(final Map<String, Class<? extends Element>> elementClasses) {
ElementUtils.elementClasses = elementClasses;
}
/**
- * @param reactionClasses
- * the reactionClasses to set
+ * @param reactionClasses the reactionClasses to set
* @see #reactionClasses
*/
- protected static void setReactionClasses(final Map<String, Class<? extends Reaction>> reactionClasses) {
+ static void setReactionClasses(final Map<String, Class<? extends Reaction>> reactionClasses) {
ElementUtils.reactionClasses = reactionClasses;
}
@@ -76,8 +72,7 @@ public final class ElementUtils {
* This method return tag that identifies {@link BioEntity}. This tag should
* be used in warning messages.
*
- * @param element
- * tag for this element is created
+ * @param element tag for this element is created
* @return tag that identifies element
*/
public String getElementTag(final Drawable element) {
@@ -88,11 +83,9 @@ public final class ElementUtils {
* This method return tag that identifies {@link BioEntity}. This tag should
* be used in warning messages.
*
- * @param element
- * tag for this element is created
- * @param annotator
- * this object identifies class that will produce warning. it can be
- * null (in such situation it will be skipped in the tag)
+ * @param element tag for this element is created
+ * @param annotator this object identifies class that will produce warning. it can be
+ * null (in such situation it will be skipped in the tag)
* @return tag that identifies element
*/
public String getElementTag(final Drawable element, final Object annotator) {
@@ -182,8 +175,7 @@ public final class ElementUtils {
* Returns list of classes that extends {@link Element} class, but don't have
* children (leaves in the hierarchy tree).
*
- * @return list of classes that extends {@link Element} class, but don't have
- * children (leaves in the hierarchy tree)
+ * @return list of classes that extends {@link Element} class, but don't have children (leaves in the hierarchy tree)
*/
public List<Class<? extends Element>> getAvailableElementSubclasses() {
List<Class<? extends Element>> result = new ArrayList<>();
@@ -191,14 +183,14 @@ public final class ElementUtils {
refreshClasses();
}
result.addAll(elementClasses.values());
- Collections.sort(result, new ClassNameComparator());
+ Collections.sort(result, new ClassNameComparator<>());
return result;
}
/**
* Refresh list of known implementation of {@link Element} class.
*/
- protected void refreshClasses() {
+ private void refreshClasses() {
bioEntityClassByStringName = new HashMap<>();
List<Class<? extends Element>> tmp = new ArrayList<>();
@@ -270,8 +262,7 @@ public final class ElementUtils {
/**
* Returns a {@link Class} that extends {@link BioEntity} for a given name.
*
- * @param name
- * name of the class
+ * @param name name of the class
* @return {@link Class} that extends {@link BioEntity} for a given name
*/
public Class<?> getClassByName(final String name) {
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
index 4c8e741187274935a4dce99945ce97f07576396e..b6408a09ad8ada8b70afaba745bc784b52ec5199 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementComparatorTest.java
@@ -307,4 +307,24 @@ public class ElementComparatorTest extends ModelTestFunctions {
assertEquals(0, comparator.compare(species2, species1));
}
+ @Test
+ public void testCompareImmediateLink() throws Exception {
+ SimpleMolecule species1 = createSimpleMolecule();
+ SimpleMolecule species2 = new SimpleMolecule(species1);
+
+ species1.setImmediateLink(faker.internet().url());
+ assertTrue(comparator.compare(species1, species2) != 0);
+ assertTrue(comparator.compare(species2, species1) != 0);
+
+ species1 = createSimpleMolecule();
+ species2 = createSimpleMolecule();
+
+ species1.setImmediateLink(faker.internet().url());
+ species2.setImmediateLink(species1.getImmediateLink());
+
+ assertEquals(0, comparator.compare(species1, species2));
+ assertEquals(0, comparator.compare(species2, species1));
+
+ }
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
index 1a5e038d828f02de032647013a10f83af4b726e6..2bab07e31452439d40bbf76528192763045a83bb 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/species/ElementTest.java
@@ -1,22 +1,5 @@
package lcsb.mapviewer.model.map.species;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -30,10 +13,27 @@ import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
public class ElementTest extends ModelTestFunctions {
- private static double EPSILON = Configuration.EPSILON;
+ private static final double EPSILON = Configuration.EPSILON;
@Before
public void setUp() throws Exception {
@@ -103,9 +103,11 @@ public class ElementTest extends ModelTestFunctions {
GenericProtein protein = new GenericProtein();
protein.setId(-17);
protein.setSubmodel(new ElementSubmodelConnection());
+ protein.setImmediateLink(faker.internet().url());
Element copy = new GenericProtein(protein);
assertNotNull(copy);
assertEquals(protein.getId(), copy.getId());
+ assertEquals(protein.getImmediateLink(), copy.getImmediateLink());
}
@Test
@@ -350,7 +352,7 @@ public class ElementTest extends ModelTestFunctions {
synonyms = new ArrayList<>();
synonyms.add(syn);
element.addSynonyms(synonyms);
- assertFalse(syn.equals(element.getSynonyms().get(1)));
+ assertNotEquals(syn, element.getSynonyms().get(1));
}
@Test
@@ -369,7 +371,7 @@ public class ElementTest extends ModelTestFunctions {
formerSymbols = new ArrayList<>();
formerSymbols.add(syn);
element.addFormerSymbols(formerSymbols);
- assertFalse(syn.equals(element.getFormerSymbols().get(1)));
+ assertNotEquals(syn, element.getFormerSymbols().get(1));
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
index f20dc52948b2e0496dd2b38203e222c178a849db..ea330674da7974d55e721bb4d7e90e610d586746 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
@@ -1,13 +1,13 @@
package lcsb.mapviewer.wikipathway.xml;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
@@ -106,7 +106,7 @@ public class ModelContructor {
*/
private static final double EPSILON = 1e-6;
/**
- * List of {@link Shape#shape shapes} that are not supported to be part of a
+ * List of shapes that are not supported to be part of a
* {@link Complex complex}.
*/
private static final Set<GpmlShape> INALID_COMPLEX_SHAPE_CHILDREN = new HashSet<>();
@@ -1252,7 +1252,7 @@ public class ModelContructor {
}
if (complex.getName() == null || (complex.getName().isEmpty())) {
for (final Layer layer : model.getLayers()) {
- if (layer.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
+ if (!layer.getName().equals(CreateHierarchyCommand.PATHWAY_LAYER_NAME)) {
LayerText toRemove = null;
for (final LayerText lt : layer.getTexts()) {
if (complex.contains(lt)) {
@@ -1297,7 +1297,7 @@ public class ModelContructor {
for (final Compartment compartment : model.getCompartments()) {
if (compartment.getName() == null || compartment.getName().isEmpty()) {
for (final Layer layer : model.getLayers()) {
- if (layer.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
+ if (!layer.getName().equals(CreateHierarchyCommand.PATHWAY_LAYER_NAME)) {
LayerText toRemove = null;
for (final LayerText lt : layer.getTexts()) {
if (compartment.contains(lt)) {
@@ -1322,12 +1322,6 @@ public class ModelContructor {
}
}
- /**
- * Creates list of {@link LayerLine} in the model from gpml model.
- *
- * @param graph gpml model
- * @return list of {@link LayerLine}
- */
private Collection<PolylineData> createLines(final Graph graph) {
final List<PolylineData> result = new ArrayList<PolylineData>();
for (final PolylineData pd : graph.getLines()) {
@@ -1398,7 +1392,7 @@ public class ModelContructor {
layer.setVisible(true);
layer.setLayerId(1);
layer.setZ(1);
- layer.setName(CreateHierarchyCommand.TEXT_LAYER_NAME);
+ layer.setName("text");
}
}
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java
index 6a8a3ba912f8edbcb12dd4f6cc44605a34a8ed20..fea5c243fbf1392960aa049457866ea4b4282088 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java
@@ -1,24 +1,12 @@
package lcsb.mapviewer.wikipathway.xml;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -27,17 +15,28 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.wikipathway.model.Edge;
import lcsb.mapviewer.wikipathway.model.Interaction;
import lcsb.mapviewer.wikipathway.utils.Geo;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
class ReactionLayoutFinder {
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
- private LineTransformation lt = new LineTransformation();
- private PointTransformation pt = new PointTransformation();
+ private final LineTransformation lt = new LineTransformation();
+ private final PointTransformation pt = new PointTransformation();
private Interaction interaction;
- public static enum LineLocation {
+ public enum LineLocation {
PRODUCT,
MODIFIER,
REACTANT,
@@ -48,11 +47,10 @@ class ReactionLayoutFinder {
/**
* Return coordinates where all {@link Reactant} should end, all
* {@link Modifier} should end, and all {@link Product} should start.
- *
- * @param interaction
- * GPML {@link Interaction}
+ *
+ * @param interaction GPML {@link Interaction}
* @return map consisted of three entries for classes: {@link Product},
- * {@link Reactant}, {@link Modifier}
+ * {@link Reactant}, {@link Modifier}
*/
public Map<Class<?>, Point2D> getNodeStartPoints(final Interaction interaction) {
this.interaction = interaction;
@@ -78,12 +76,12 @@ class ReactionLayoutFinder {
points.get(Reactant.class));
PolylineData inputReactionLine = getSubline(interaction.getLine(), points.get(Reactant.class),
points.get(Modifier.class));
- inputReactionLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2);
+ inputReactionLine.trimEnd(ReactionData.RECT_SIZE / 2);
PolylineData outputReactionLine = getSubline(interaction.getLine(),
points.get(Modifier.class), points.get(Product.class));
- outputReactionLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2);
+ outputReactionLine.trimBegin(ReactionData.RECT_SIZE / 2);
PolylineData productLine = getSubline(interaction.getLine(),
points.get(Product.class), interaction.getLine().getEndPoint());
PolylineData modifierLine = new PolylineData(pt.copyPoint(inputReactionLine.getEndPoint()),
@@ -320,7 +318,6 @@ class ReactionLayoutFinder {
PolylineData result = new PolylineData(originalPolylineData);
List<Line2D> lines = new ArrayList<>(result.getLines().subList(start, end + 1));
result.removeLines();
- ;
result.addLines(lines);
result.setStartPoint(pt.copyPoint(startPoint));
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 908bc74ddbe876471a2dc6f16ec71a36c94f9a76..c591c36b99ab27b490305f2a9d18eb57ac897315 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.wikipathway;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.Drawable;
@@ -37,7 +37,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
private ModelComparator mc;
- private PointTransformation pt = new PointTransformation();
+ private final PointTransformation pt = new PointTransformation();
@Before
public void setUp() {
@@ -278,6 +278,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
for (final Complex species : model.getComplexList()) {
if ("p70 S6 Kinases".equals(species.getName())) {
nameFound = true;
+ break;
}
}
assertTrue("Complex parsed from gpml should have a valid name", nameFound);
@@ -381,7 +382,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/small/protein_with_modification.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- Gene gene = (Gene) model1.getElementByElementId("be3de");
+ Gene gene = model1.getElementByElementId("be3de");
assertNotNull(gene);
assertEquals(2, gene.getModificationResidues().size());
for (ModificationResidue mr : gene.getModificationResidues()) {
@@ -398,7 +399,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/small/protein_with_modification_2.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- Gene protein = (Gene) model1.getElementByElementId("be3de");
+ Gene protein = model1.getElementByElementId("be3de");
assertNotNull(protein);
assertEquals(2, protein.getModificationResidues().size());
@@ -418,7 +419,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
double distance = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5)
.distance(reaction.getModifiers().get(0).getLine().getEndPoint());
assertTrue("Modifier is too far from center point: " + distance,
- distance < ReactionCellDesignerConverter.RECT_SIZE);
+ distance < ReactionData.RECT_SIZE);
assertEquals(0, getWarnings().size());
}
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
index 87aa9ea10fa440b82d74bffad4800ee36d85c8fe..141626a385e1024b57ba177d697a671736d2b5af 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/WikipathwaysTestFunctions.java
@@ -5,7 +5,6 @@ import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ZIndexPopulator;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -23,6 +22,7 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.Unknown;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import lcsb.mapviewer.utils.ZIndexPopulator;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import org.junit.Rule;
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
index 11e01fb110b161a1daef817dfa9260062bbddf80..559cb14632fb65cf335bfdecb9da0fba0a200aa0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java
@@ -36,12 +36,12 @@ import lcsb.mapviewer.model.job.MinervaJob;
import lcsb.mapviewer.model.job.MinervaJobPriority;
import lcsb.mapviewer.model.job.MinervaJobType;
import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamType;
import lcsb.mapviewer.model.map.layout.ProjectBackground;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundImageLayer;
import lcsb.mapviewer.model.map.layout.ProjectBackgroundStatus;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
@@ -58,7 +58,6 @@ import lcsb.mapviewer.persist.dao.ProjectDao;
import lcsb.mapviewer.persist.dao.ProjectLogEntryDao;
import lcsb.mapviewer.persist.dao.ProjectLogEntryProperty;
import lcsb.mapviewer.persist.dao.ProjectProperty;
-import lcsb.mapviewer.persist.dao.graphics.LayerProperty;
import lcsb.mapviewer.persist.dao.map.ModelProperty;
import lcsb.mapviewer.persist.dao.user.UserAnnotationSchemaDao;
import lcsb.mapviewer.services.interfaces.ICommentService;
@@ -470,6 +469,18 @@ public class ProjectService implements IProjectService {
}
}
+ @Override
+ public byte[] getGeneratedSourceZipForProject(final Project project) throws ConverterException {
+ try {
+ ComplexZipConverter converter = new ComplexZipConverter(CellDesignerXmlParser.class);
+ Project dbProject = self.getProjectByProjectId(project.getProjectId());
+ ProjectFactory factory = new ProjectFactory(converter);
+ return factory.project2zip(dbProject);
+ } catch (ConverterException | InconsistentModelException e) {
+ throw new ConverterException(e);
+ }
+ }
+
@Override
public Set<MiriamData> getMiriamForProject(final String projectId) {
return new HashSet<>(self.getMiriamWithDuplicatesForProject(projectId));
@@ -602,16 +613,6 @@ public class ProjectService implements IProjectService {
self.createSimpleProject(params);
}
- Map<LayerProperty, Object> layerFilter = new HashMap<>();
- layerFilter.put(LayerProperty.PROJECT_ID, params.getProjectId());
- List<Layer> layers = layerService.getAll(layerFilter, Pageable.unpaged()).getContent();
- for (final Layer layer : layers) {
- if (!layer.getName().equals(CreateHierarchyCommand.TEXT_LAYER_NAME)) {
- layer.setVisible(false);
- layerService.update(layer);
- }
- }
-
self.updateProjectStatus(params.getProjectId(), ProjectStatus.UPLOADING_TO_DB, 0.0);
self.addBuiltInBackgrounds(params);
@@ -735,6 +736,7 @@ public class ProjectService implements IProjectService {
}
for (ModelData modelData : project.getModels()) {
project.addLogEntries(fixModelIssues(modelData));
+ modelData.setTileSize(MapGenerator.TILE_SIZE);
}
self.update(project);
} catch (final IOException | ConverterException e) {
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
index 0f73a7bcca41dc17fcdac39724d66f7593159904..904a308ddd4b0860041720e9fc022a3fb600cb44 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IProjectService.java
@@ -182,4 +182,8 @@ public interface IProjectService extends MinervaJobExecutor, CrudService<Project
void submitAnnotateProjectJob(final String projectId, final UserAnnotationSchema schema);
void submitRefreshChemicalInfoJobs(final String projectId);
+
+ @Transactional
+ byte[] getGeneratedSourceZipForProject(final Project project) throws ConverterException;
+
}
diff --git a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java
index 000a7709de727c9ec0257db9e571669131b4dacb..6de23de428a1ec2bed75aee1a3d6dc1bdb6b7571 100644
--- a/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java
+++ b/service/src/test/java/lcsb/mapviewer/services/impl/ProjectServiceNoTransactionTest.java
@@ -572,7 +572,7 @@ public class ProjectServiceNoTransactionTest extends TestUtils {
for (final ZipEntryFile entry : params.getZipEntries()) {
complexParams.entry(entry);
}
- Model model = parser.createModel(complexParams);
+ Model model = parser.createModel(complexParams, new Project());
assertNotNull(model);
assertEquals("main", model.getName());
diff --git a/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java b/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java
index c7bdce6b3c82fa2adf3741fdc7c3bb91c9925457..15716dc9964e963c25b035146ca436d9e4ec9d68 100644
--- a/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java
+++ b/web/src/main/java/lcsb/mapviewer/web/api/project/NewProjectController.java
@@ -4,6 +4,8 @@ import lcsb.mapviewer.api.OperationNotAllowedException;
import lcsb.mapviewer.api.QueryException;
import lcsb.mapviewer.api.UpdateConflictException;
import lcsb.mapviewer.api.minervanet.MinervaNetController;
+import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.job.MinervaJob;
import lcsb.mapviewer.model.security.Privilege;
@@ -27,6 +29,7 @@ import org.hibernate.validator.constraints.NotBlank;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
+import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
@@ -239,4 +242,21 @@ public class NewProjectController {
return serializer.prepareResponse(project, new ProjectResponseDecorator(minervaNetController.getSharedProjects(), meshService, taxonomyService));
}
+ @PreAuthorize("hasAnyAuthority('IS_ADMIN', 'READ_PROJECT:' + #projectId)")
+ @GetMapping(value = "/{projectId}:downloadGeneratedZip")
+ public ResponseEntity<?> downloadGeneratedZip(final @PathVariable(value = "projectId") String projectId)
+ throws ObjectNotFoundException, ConverterException {
+ Project project = projectService.getProjectByProjectId(projectId);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given projectId does not exist");
+ }
+
+ byte[] content = projectService.getGeneratedSourceZipForProject(project);
+ final HttpHeaders responseHeaders = new HttpHeaders();
+ responseHeaders.add("content-disposition", "attachment; filename=" + projectId + ".zip");
+ responseHeaders.add("Content-Type", MimeType.ZIP.getTextRepresentation());
+
+ return new ResponseEntity<>(content, responseHeaders, HttpStatus.OK);
+ }
+
}
\ No newline at end of file
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
index ad3c9406ca953663e2d65d5b662f2c727fe25061..b157a93fc5fc61d0a7185c38db8df4ddc85deb05 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
@@ -1315,6 +1315,10 @@ public class NewApiDocs {
fieldWithPath(prefix + "id")
.description("job id")
.type(JsonFieldType.NUMBER),
+ fieldWithPath(prefix + "progress")
+ .description("optional info about job progress (0-100)")
+ .optional()
+ .type(JsonFieldType.NUMBER),
fieldWithPath(prefix + "jobType")
.description("job type")
.type(JsonFieldType.STRING),
@@ -1329,6 +1333,14 @@ public class NewApiDocs {
.description("when the job execution finished")
.optional()
.type(JsonFieldType.STRING),
+ fieldWithPath(prefix + "externalObjectClass")
+ .description("if job is attached to object here is the type of the object")
+ .optional()
+ .type(JsonFieldType.STRING),
+ fieldWithPath(prefix + "externalObjectId")
+ .description("if job is attached to object here is the id of the object")
+ .optional()
+ .type(JsonFieldType.NUMBER),
fieldWithPath(prefix + "priority")
.description("job priority (1 is the highest priority)")
.type(JsonFieldType.NUMBER)
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java
index 7d7ad5c1023a5872cea9b14a65a2d51559d27e36..d4255f3975b9915ec29f4ee145ad50da25fc8190 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/plugin/NewPluginControllerTest.java
@@ -59,6 +59,7 @@ public class NewPluginControllerTest extends ControllerIntegrationTest {
public void setUp() throws Exception {
objectMapper = newApiResponseSerializer.getObjectMapper();
pluginHashes = new ArrayList<>();
+ pluginHashes.add(PLUGIN_HASH);
}
@After
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java
index 75c4b7c2ac308f498843ed909d3eca8898bd6620..a34b6578dfa3af2578ca7c9c34d8864c968a8eab 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/project/NewProjectControllerTest.java
@@ -599,4 +599,18 @@ public class NewProjectControllerTest extends ControllerIntegrationTest {
}
+ @Test
+ public void testGeneratedZip() throws Exception {
+ createProjectWithGlyph(TEST_PROJECT);
+
+ final MockHttpSession session = createSession(BUILT_IN_TEST_ADMIN_LOGIN, BUILT_IN_TEST_ADMIN_PASSWORD);
+
+ final RequestBuilder request = get("/minerva/new_api/projects/{projectId}:downloadGeneratedZip", TEST_PROJECT)
+ .session(session);
+
+ mockMvc.perform(request)
+ .andExpect(status().isOk())
+ .andExpect(status().is2xxSuccessful());
+ }
+
}