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/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..a732c0d83ebe015d7e0c1fb6b81522066288e867 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));
@@ -739,7 +739,7 @@ public class CellDesignerXmlParser extends Converter {
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..4195ae9f81f2e306b3d5386b394fd6b231b06eba 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
@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.celldesigner;
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.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -15,6 +14,7 @@ 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;
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..bea9a303b24cd239b155046d87a999faf86e338e 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
@@ -4,10 +4,7 @@ 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;
@@ -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);
@@ -696,8 +695,8 @@ public class ReactionFromXml {
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) {
@@ -905,7 +904,7 @@ public class ReactionFromXml {
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);
@@ -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..953b8ff4fb08368257e4b22d10ad59c4b3e29ccb 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
@@ -1,25 +1,9 @@
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.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;
@@ -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/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..4c4c32c882828ab2d6aa05e3d41151a6a5e8f937
--- /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/artifitial_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..b09534c889b1e3bcb09f10924f4304248223bdc1
--- /dev/null
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CreateHierarchyCommandForProblematicCDTest.java
@@ -0,0 +1,300 @@
+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<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 testCreateHierarchy() throws Exception {
+ Model model = getModelForFile("testFiles/artifitial_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/artifitial_compartments.xml");
+
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ boolean artifitial = false;
+ for (final Compartment a : model.getCompartments()) {
+ if (a instanceof PathwayCompartment) {
+ artifitial = true;
+ break;
+ }
+ }
+ assertTrue("No hierarchical structure element found", artifitial);
+ }
+
+ @Test
+ public void testRecreateHierachy() throws Exception {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml");
+
+ 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");
+
+ 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.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");
+
+ 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");
+ 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");
+
+ CreateHierarchyCommand command = new CreateHierarchyCommand(model, 2, 2);
+ command.execute();
+ command.execute();
+ }
+
+ @Test
+ public void testClear() throws Exception {
+ Model model = getModelForFile("testFiles/artifitial_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.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");
+
+ 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("5", pathway.getVisibilityLevel());
+ assertEquals((Integer) 11, pathway.getZ());
+ }
+}
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
index 8b04264dc6408bb3fae74b1101250d4b3b018cd8..dded4298bdca5eaf2d5480d40ed5ded68117e3bf 100644
--- 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
@@ -2,18 +2,18 @@ package lcsb.mapviewer.converter.model.celldesigner;
import lcsb.mapviewer.converter.ComplexZipConverter;
import lcsb.mapviewer.converter.ComplexZipConverterParams;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
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.InconsistentModelException;
+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.Element;
+import lcsb.mapviewer.model.map.species.Protein;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
@@ -70,7 +70,24 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
testSerializationOverZip(project);
}
- private void testSerializationOverZip(final Project project) throws IOException, ConverterException, InconsistentModelException, InvalidInputDataExecption {
+ @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);
+ }
+
+ private void testSerializationOverZip(final Project project) throws Exception {
File tempFile = File.createTempFile("CD-", ".zip");
try (FileOutputStream outputStream = new FileOutputStream(tempFile)) {
byte[] data = projectFactory.project2zip(project);
@@ -84,6 +101,10 @@ public class ProjectExportTest extends CellDesignerTestFunctions {
}
for (ModelData model : project2.getModels()) {
clearModelFromZ(model);
+
+ for (Element element : model.getElements()) {
+ logger.debug(element.getSubmodel());
+ }
}
assertEquals(0, projectComparator.compare(project, project2));
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-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..8584db5f3caa63173ffd569968103e46dcac584f 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;
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-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/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/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/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/ProjectFactory.java b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
index 812e84783a70cdeabf3b011b43a71eaafe17e914..b42db99a4bf4325e344cd1837b988942e64904b2 100644
--- a/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
+++ b/converter/src/main/java/lcsb/mapviewer/converter/ProjectFactory.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter;
+import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.zip.GlyphZipEntryFile;
import lcsb.mapviewer.converter.zip.ImageZipEntryFile;
@@ -10,10 +11,19 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.layout.graphics.Glyph;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
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 org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -44,6 +54,15 @@ public class ProjectFactory {
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());
}
@@ -164,17 +183,85 @@ public class ProjectFactory {
addModelFileToZip(model.getModel(), "submaps/" + model.getName() + "." + converter.getFileExtensions().get(0), converter, zos);
}
}
+ Model mapping = createMappingModel(project.getModels());
+
+ addModelFileToZip(mapping, "submaps/mapping." + converter.getFileExtensions().get(0), converter, zos);
+
} catch (IOException ioe) {
throw new ConverterException(ioe);
}
return byteArrayOutputStream.toByteArray();
}
- 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();
+ 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);
+ }
+ }
+ }
+ 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 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;
}
}
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/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..9a6046aa981320eed0701fb8d773150340b812bc 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -3,7 +3,6 @@ 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;
@@ -15,6 +14,7 @@ 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;
@@ -127,7 +127,7 @@ 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);
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..9afa407aebda37e577d7fffe91b6042966dc3b99 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;
@@ -348,7 +347,6 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
line.setStartPoint(startPoint);
}
modifier.setLine(line);
- new ModifierTypeUtils().updateLineEndPoint(modifier);
}
}
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..5d2fdaadc98bb325e3952ee48b079112c7847e80 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() 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 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 = 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);
+ 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"));
@@ -94,7 +281,12 @@ public class ColorModelCommandTest extends CommandTestFunctions {
@Test
public void testColorTheSameElementTwiceUsingDifferentSelector() throws Exception {
- Model model = getModelForFile("testFiles/coloring_model.xml", true);
+ 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"));
@@ -108,66 +300,92 @@ 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>();
+ 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");
+ 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>();
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");
+ 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>();
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");
+ 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>();
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.addMiriamData(new MiriamData(MiriamType.PUBMED, "12345"));
@@ -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);
+ 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 +420,20 @@ 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");
@@ -227,10 +454,17 @@ public class ColorModelCommandTest extends CommandTestFunctions {
@Test
public void testColoredReactions() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ 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");
@@ -244,10 +478,17 @@ public class ColorModelCommandTest extends CommandTestFunctions {
@Test
public void testColoredReactions2() throws Exception {
- Model model = getModelForFile("testFiles/sample.xml", false);
+ 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 +500,23 @@ 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);
+ 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 +525,21 @@ 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);
+ 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 +548,15 @@ 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);
+ Model model = createSimpleModel();
+ Protein p1 = createProtein();
+ p1.setName("CNC");
+ model.addElement(p1);
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setName("CNC");
@@ -420,12 +567,15 @@ 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);
+ Model model = createSimpleModel();
+ Protein p1 = createProtein();
+ p1.setName("CNC");
+ model.addElement(p1);
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setName("CNC");
@@ -436,11 +586,13 @@ 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 +602,13 @@ 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);
+ Model model = createSimpleModel();
+ model.addElement(createProtein());
DataOverlayEntry schema = new GenericDataOverlayEntry();
schema.setElementId(model.getElements().iterator().next().getElementId());
@@ -465,59 +618,7 @@ 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..3b9ab3f51bafcdaab226fe9370bc18442b8d3e1f 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 +1,11 @@
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.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.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.reaction.Product;
@@ -24,15 +21,13 @@ 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.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 +38,9 @@ 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 +66,6 @@ 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 +73,18 @@ 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 +94,15 @@ 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;
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..246adc24a19e3ac76a9bcf5489dcfba040d88586 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 +1,21 @@
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 java.awt.Color;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
public class CreateHierarchyCommandTest extends CommandTestFunctions {
@@ -45,268 +28,7 @@ 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();
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/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;