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 bea9a303b24cd239b155046d87a999faf86e338e..c144284b07413796ecaf99673c8c3663486f94e1 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java
@@ -1,19 +1,19 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
+import lcsb.mapviewer.commands.layout.ModifierType;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerAnchor;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.ConnectScheme;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.EditPoints;
import lcsb.mapviewer.converter.model.celldesigner.structure.fields.LineProperties;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
@@ -689,8 +689,8 @@ public class ReactionFromXml {
reactant.setLine(reactant.getLine().reverse());
reactant.getLine().addLine(p2, p);
- reactant.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
- operator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ reactant.getLine().trimEnd(ReactionData.RECT_SIZE / 2 - 1);
+ operator.getLine().trimEnd(ReactionData.RECT_SIZE / 2 - 1);
result.addNode(operator);
@@ -889,7 +889,7 @@ public class ReactionFromXml {
andOperator.getLine().addLine(product.getLine().getLines().get(i));
}
andOperator.getLine().setEndPoint(p);
- andOperator.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ andOperator.getLine().trimEnd(ReactionData.RECT_SIZE / 2 - 1);
p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
@@ -897,7 +897,7 @@ public class ReactionFromXml {
product.getLine().removeLine(0);
}
product.getLine().setStartPoint(p);
- product.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ product.getLine().trimBegin(ReactionData.RECT_SIZE / 2 - 1);
product.getLine().getEndAtd().setArrowType(ArrowType.FULL);
@@ -1210,11 +1210,11 @@ public class ReactionFromXml {
Point2D p2 = ld.getLines().get(ld.getLines().size() - index - 1).getP2();
Point2D p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
reactantLine.setEndPoint(p);
- reactantLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ reactantLine.trimEnd(ReactionData.RECT_SIZE / 2 - 1);
p = new Point2D.Double((p2.getX() + p1.getX()) / 2, (p2.getY() + p1.getY()) / 2);
productLine.setStartPoint(p);
- productLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2 - 1);
+ productLine.trimBegin(ReactionData.RECT_SIZE / 2 - 1);
productLine.getEndAtd().setArrowType(ArrowType.FULL);
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 953b8ff4fb08368257e4b22d10ad59c4b3e29ccb..f51028bd81c02857009bc0302226e719ac5d9208 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -1,5 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.reaction;
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -10,7 +11,6 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerL
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.CellDesignerPointTransformation;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorType;
import lcsb.mapviewer.converter.model.celldesigner.types.OperatorTypeUtils;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
index d6a906b736987999c73cb3c42e66422c4de62422..21059567562f7f82932a4031607d576e1220d8b2 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtils.java
@@ -1,15 +1,10 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
+import lcsb.mapviewer.commands.layout.ModifierType;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -19,26 +14,29 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
/**
* Util class that helps in transformation of CellDesigner modifiers into
* {@link Modifier} object in our model.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ModifierTypeUtils {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Returns {@link ModifierType} that reference to the clazz.
- *
- * @param clazz
- * class type for which result is returned
+ *
+ * @param clazz class type for which result is returned
* @return {@link ModifierType} that reference to the clazz
*/
public ModifierType getModifierTypeForClazz(final Class<? extends Modifier> clazz) {
@@ -53,9 +51,8 @@ public class ModifierTypeUtils {
/**
* Returns {@link ModifierType} that reference to the CellDesigner string
* 'type'.
- *
- * @param type
- * CellDesigner string defining modifier type
+ *
+ * @param type CellDesigner string defining modifier type
* @return {@link ModifierType} that reference to the CellDesigner 'type'
*/
public ModifierType getModifierTypeForStringType(final String type) {
@@ -69,11 +66,9 @@ public class ModifierTypeUtils {
/**
* Creates {@link Modifier} for the CellDesigner type.
- *
- * @param type
- * CellDesigner type of the modifier
- * @param alias
- * alias to which modifier point to
+ *
+ * @param type CellDesigner type of the modifier
+ * @param alias alias to which modifier point to
* @return {@link Modifier} for the CellDesigner type
*/
public Modifier createModifierForStringType(final String type, final Species alias) {
@@ -91,9 +86,8 @@ public class ModifierTypeUtils {
/**
* Returns CellDesigner string used for modifier creation.
- *
- * @param modifier
- * modifier for which CellDesigner string is looked for
+ *
+ * @param modifier modifier for which CellDesigner string is looked for
* @return CellDesigner string used for modifier creation
*/
public String getStringTypeByModifier(final Modifier modifier) {
@@ -108,9 +102,8 @@ public class ModifierTypeUtils {
* Returns string that identfies TargetLine index for the modifier. TargetLine
* index is a CellDesigner String that identifies to which point on the
* rectangle in the center line modifier line is connected.
- *
- * @param modifier
- * modifier for target line
+ *
+ * @param modifier modifier for target line
* @return string that identfies TargetLine index for the modifier
*/
public String getTargetLineIndexByModifier(final Modifier modifier) {
@@ -130,9 +123,8 @@ public class ModifierTypeUtils {
* Returns string that identfies TargetLine index for the modifier operator.
* TargetLine index is a CellDesigner String that identifies to which point on
* the rectangle in the center line modifier line is connected.
- *
- * @param modifier
- * modifier operator for target line
+ *
+ * @param modifier modifier operator for target line
* @return string that identfies TargetLine index for the modifier
*/
public String getTargetLineIndexByModifier(final NodeOperator modifier) {
@@ -157,21 +149,17 @@ public class ModifierTypeUtils {
* Returns string that identfies TargetLine index for the modifier line
* connected to reaction (target line index is explained here:
* {@link #getTargetLineIndexByModifier(Modifier)}).
- *
- *
- * @param modType
- * type of modifier for the line
- * @param reaction
- * reaction on which target line index is looked for
- * @param originalLine
- * line that connects modifier to the reaction
+ *
+ * @param modType type of modifier for the line
+ * @param reaction reaction on which target line index is looked for
+ * @param originalLine line that connects modifier to the reaction
* @return string that identifies TargetLine index for modifier line
*/
private String getTragteLineIndex(final ModifierType modType, final Reaction reaction, final PolylineData originalLine) {
PolylineData line = new PolylineData(originalLine);
line.trimEnd(-modType.getTrimLength());
- String[] possibleValues = new String[] { "0,2", "0,3", "0,4", "0,5", "0,6", "0,7" };
+ String[] possibleValues = new String[]{"0,2", "0,3", "0,4", "0,5", "0,6", "0,7"};
Point2D closestPoint = new Point2D.Double(Double.MAX_VALUE, Double.MAX_VALUE);
Point2D checkedPoint = line.getEndPoint();
String result = "0,0";
@@ -189,11 +177,9 @@ public class ModifierTypeUtils {
* This method get anchor point on the reaction line (the center point of this
* line is given as a parameter). The anchor point depends on the line and
* lineConnectionType associated with the modification.
- *
- * @param reaction
- * reaction on which we are looking for a point
- * @param lineConnectionType
- * point of connection to the reaction center rectangle
+ *
+ * @param reaction reaction on which we are looking for a point
+ * @param lineConnectionType point of connection to the reaction center rectangle
* @return coordinates of point on the center rectangle
*/
public Point2D getAnchorPointOnReactionRect(final Reaction reaction, final String lineConnectionType) {
@@ -212,34 +198,34 @@ public class ModifierTypeUtils {
if (spr.length > 1) {
id = spr[1];
if (id.equals("2")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y -= ReactionData.RECT_SIZE / 2;
} else if (id.equals("3")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
} else if (id.equals("4")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y -= ReactionData.RECT_SIZE / 2;
+ x -= ReactionData.RECT_SIZE / 2;
} else if (id.equals("5")) {
- y -= ReactionCellDesignerConverter.RECT_SIZE / 2;
- x += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y -= ReactionData.RECT_SIZE / 2;
+ x += ReactionData.RECT_SIZE / 2;
} else if (id.equals("6")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- x -= ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
+ x -= ReactionData.RECT_SIZE / 2;
} else if (id.equals("7")) {
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
- x += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
+ x += ReactionData.RECT_SIZE / 2;
} else if (id.equals("0")) {
// this is only workaround...
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
} else if (id.equals("1")) {
// this is only workaround...
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
} else {
throw new InvalidArgumentException("Unknown targetLineIndex: " + id);
}
} else {
logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction), "Invalid targetLineIndex: " + id);
- y += ReactionCellDesignerConverter.RECT_SIZE / 2;
+ y += ReactionData.RECT_SIZE / 2;
}
Point2D p = new Point2D.Double(x, y);
PointTransformation pointTransformation = new PointTransformation();
@@ -249,9 +235,8 @@ public class ModifierTypeUtils {
/**
* Update line parameters to make it look like a proper modifier.
- *
- * @param modifier
- * modifier for which line will be modified
+ *
+ * @param modifier modifier for which line will be modified
*/
public void updateLineEndPoint(final Modifier modifier) {
ModifierType modType = getModifierTypeForClazz(modifier.getClass());
@@ -265,9 +250,8 @@ public class ModifierTypeUtils {
/**
* Updates line parameters of modifier operator to make it look like a proper
* modifier.
- *
- * @param operator
- * modifier operator for which line will be modified
+ *
+ * @param operator modifier operator for which line will be modified
*/
@SuppressWarnings("unchecked")
public void updateLineEndPoint(final NodeOperator operator) {
@@ -286,11 +270,9 @@ public class ModifierTypeUtils {
/**
* Updates line parameters to make it look like a proper modifier.
- *
- * @param modType
- * type of modifier
- * @param line
- * line to update
+ *
+ * @param modType type of modifier
+ * @param line line to update
*/
private void updateLineByType(final ModifierType modType, final PolylineData line) {
line.setEndAtd(modType.getAtd().copy());
@@ -300,9 +282,8 @@ public class ModifierTypeUtils {
/**
* Returns type of the modifier in modifier operator.
- *
- * @param modifierOperator
- * opertor for which type will be returned
+ *
+ * @param modifierOperator opertor for which type will be returned
* @return type of the modifier in modifier operator
*/
public ModifierType getModifierTypeForOperator(final NodeOperator modifierOperator) {
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java
deleted file mode 100644
index 11cae750b81fcdec6a41d8ed846df7a0a284b9ef..0000000000000000000000000000000000000000
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverterTest.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
-
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-
-public class ReactionCellDesignerConverterTest {
-
- @AfterClass
- public static void tearDownAfterClass() throws Exception {
- }
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testConstructor() {
- ReactionCellDesignerConverter onverter = new ReactionCellDesignerConverter();
- assertNotNull(onverter);
- }
-
-}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
index 2ba3323171ff82597c0bc5846d1babc63dbf264a..b4fae845cb49872b844fc677325bb95ad64fdbc5 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeTest.java
@@ -1,12 +1,13 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import static org.junit.Assert.assertNotNull;
-
+import lcsb.mapviewer.commands.layout.ModifierType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
+import static org.junit.Assert.assertNotNull;
+
public class ModifierTypeTest {
@AfterClass
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
index 618b51764663b91eade984b99c88bd1ffc63e916..5c3d102141a44a0ba848a101f22e7765bf88ae1c 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierTypeUtilsTest.java
@@ -1,17 +1,6 @@
package lcsb.mapviewer.converter.model.celldesigner.types;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-
-import java.awt.geom.Point2D;
-
-import org.junit.After;
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
import lcsb.mapviewer.model.graphics.PolylineData;
@@ -21,12 +10,23 @@ import lcsb.mapviewer.model.map.reaction.NodeOperator;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.awt.geom.Point2D;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
public class ModifierTypeUtilsTest extends CellDesignerTestFunctions {
- private ModifierTypeUtils utils = new ModifierTypeUtils();
+ private final ModifierTypeUtils utils = new ModifierTypeUtils();
- private Modifier invalidModifier = Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS);
+ private final Modifier invalidModifier = Mockito.mock(Modifier.class, Mockito.CALLS_REAL_METHODS);
@AfterClass
public static void tearDownAfterClass() throws Exception {
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java
index b5a6aa6121488755acb1ba45a78ea44bd4480ae2..03337681a024fddf737c4fea9ed9a6f686625e0b 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/parser/ReactionParser.java
@@ -1,12 +1,12 @@
package lcsb.mapviewer.converter.model.sbgnml.parser;
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.sbgnml.SbgnLogMarker;
import lcsb.mapviewer.converter.model.sbgnml.structures.Process;
import lcsb.mapviewer.model.LogMarker;
@@ -61,23 +61,23 @@ public class ReactionParser extends GlyphParser {
/**
* List of all logic operator glyphs parsed so far.
*/
- private List<Glyph> logicOperators = new ArrayList<>();
+ private final List<Glyph> logicOperators = new ArrayList<>();
/**
* List of all processes to be parsed.
*/
- private List<Process> processes = new ArrayList<>();
+ private final List<Process> processes = new ArrayList<>();
/**
* List of all logic arcs parsed so far.
*/
- private List<Arc> logicArcs = new ArrayList<>();
+ private final List<Arc> logicArcs = new ArrayList<>();
private final PointTransformation pt = new PointTransformation();
- private RenderParser renderParser;
+ private final RenderParser renderParser;
- private Model model;
+ private final Model model;
public ReactionParser(final RenderParser renderParser, final Model model) {
this.renderParser = renderParser;
@@ -160,7 +160,7 @@ public class ReactionParser extends GlyphParser {
public Reaction parseProcess(final Process p) throws Exception {
if (p.getProductArcs().isEmpty()) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, p, model),
- "The process must have at least one outgoing arc.");
+ "The process must have at least one outgoing arc.");
return null;
}
@@ -223,7 +223,7 @@ public class ReactionParser extends GlyphParser {
for (final Arc a : p.getProductArcs()) {
if (Objects.equals(getSourcePort(a), p.getProductsPort()) && ports.size() == 2
- || reaction.getProducts().size() == 0) {
+ || reaction.getProducts().size() == 0) {
Glyph target = getTargetGlyph(a);
Product product = new Product(model.getElementByElementId(target.getId()));
List<Point2D> pointList = getLinePoints(a);
@@ -255,13 +255,13 @@ public class ReactionParser extends GlyphParser {
boolean shouldReverse = reaction.getProducts().size() > 1;
for (final Product product : reaction.getProducts()) {
if (product.getLine().getStartPoint().distance(firstProduct.getLine().getStartPoint()) < Configuration.EPSILON
- && product.getLine().getEndPoint().distance(firstProduct.getLine().getEndPoint()) > Configuration.EPSILON) {
+ && product.getLine().getEndPoint().distance(firstProduct.getLine().getEndPoint()) > Configuration.EPSILON) {
shouldReverse = false;
}
}
if (shouldReverse) {
logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "process-arcs", p.getCentralPoint().getId(),
- model.getIdModel()), "Product lines should be reversed");
+ model.getIdModel()), "Product lines should be reversed");
for (final Product product : reaction.getProducts()) {
List<Line2D> lines = new ArrayList<>(product.getLine().getLines());
product.getLine().removeLines();
@@ -371,10 +371,10 @@ public class ReactionParser extends GlyphParser {
Point2D portPoint;
if (p.getReagentArcs().size() > 1) {
portPoint = new Point2D.Double(p.getReagentArcs().get(0).getEnd().getX(),
- p.getReagentArcs().get(0).getEnd().getY());
+ p.getReagentArcs().get(0).getEnd().getY());
} else {
portPoint = new Point2D.Double(p.getRevReagentArcs().get(0).getStart().getX(),
- p.getRevReagentArcs().get(0).getStart().getY());
+ p.getRevReagentArcs().get(0).getStart().getY());
}
PolylineData line = new PolylineData(portPoint, centerOfReactionPoint);
ArrowTypeData atd = new ArrowTypeData();
@@ -400,10 +400,10 @@ public class ReactionParser extends GlyphParser {
Point2D portPoint;
if (!p.isReversible()) {
portPoint = new Point2D.Double(p.getProductArcs().get(0).getStart().getX(),
- p.getProductArcs().get(0).getStart().getY());
+ p.getProductArcs().get(0).getStart().getY());
} else {
portPoint = new Point2D.Double(p.getRevProductArcs().get(0).getStart().getX(),
- p.getRevProductArcs().get(0).getStart().getY());
+ p.getRevProductArcs().get(0).getStart().getY());
}
PolylineData line = new PolylineData(portPoint, centerOfReactionPoint);
ArrowTypeData atd = new ArrowTypeData();
@@ -423,7 +423,7 @@ public class ReactionParser extends GlyphParser {
* @throws Exception thrown when parsed logic operator is invalid
*/
private void parseLogicOperator(final Arc arc, final Reaction reaction, final NodeOperator targetOperator)
- throws Exception {
+ throws Exception {
Port operatorPort = (Port) arc.getSource();
Glyph logicOperator = null;
for (final Glyph lo : getLogicOperators()) {
@@ -439,8 +439,8 @@ public class ReactionParser extends GlyphParser {
// inputs of Species
final Glyph tempLogicOperator = logicOperator;
boolean isCellDesignerValidLogicOperator = logicArcs.stream()
- .filter(a -> tempLogicOperator.getPort().contains(a.getTarget()) && !(a.getSource() instanceof Port))
- .count() == 2;
+ .filter(a -> tempLogicOperator.getPort().contains(a.getTarget()) && !(a.getSource() instanceof Port))
+ .count() == 2;
if (!isCellDesignerValidLogicOperator) {
throw new InvalidArgumentException("Parsed operator is not valid for CellDesigner: " + logicOperator.getId());
}
@@ -455,7 +455,7 @@ public class ReactionParser extends GlyphParser {
break;
case NOT:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, logicOperator, model),
- "NOT gates are not implemented in the platform.");
+ "NOT gates are not implemented in the platform.");
return;
default:
throw new InvalidArgumentException("Wrong logic operator class.");
@@ -463,8 +463,8 @@ public class ReactionParser extends GlyphParser {
// Parse line from arc and operator glyph
Point2D operatorCenterPoint = new Point2D.Double(
- logicOperator.getBbox().getX() + logicOperator.getBbox().getW() / 2,
- logicOperator.getBbox().getY() + logicOperator.getBbox().getH() / 2);
+ logicOperator.getBbox().getX() + logicOperator.getBbox().getW() / 2,
+ logicOperator.getBbox().getY() + logicOperator.getBbox().getH() / 2);
List<Point2D> linePoints = getLinePoints(arc);
new ArrayList<Point2D>();
@@ -507,7 +507,7 @@ public class ReactionParser extends GlyphParser {
if (logicArc.getSource() instanceof Port) {
// The arc has source in logic operator
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, logicArc, model),
- "Logic operators trees are not compatible with CellDesigner. Therefore they are not supported.");
+ "Logic operators trees are not compatible with CellDesigner. Therefore they are not supported.");
continue;
// parseLogicOperator(logicArc, reaction, modifierClass,
// operator, model);
@@ -541,11 +541,11 @@ public class ReactionParser extends GlyphParser {
switch (ac) {
case ABSOLUTE_INHIBITION:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model),
- ac + " modifier is not supported. Changing to " + Inhibition.class.getSimpleName());
+ ac + " modifier is not supported. Changing to " + Inhibition.class.getSimpleName());
return new Inhibition(element);
case ABSOLUTE_STIMULATION:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model),
- ac + " modifier is not supported. Changing to " + PhysicalStimulation.class.getSimpleName());
+ ac + " modifier is not supported. Changing to " + PhysicalStimulation.class.getSimpleName());
return new PhysicalStimulation(element);
case CATALYSIS:
return new Catalysis(element);
@@ -628,7 +628,7 @@ public class ReactionParser extends GlyphParser {
switch (ArcClazz.fromClazz(arc.getClazz())) {
case PRODUCTION:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, arc, model),
- "Activity flow arc type is invalid. Changing to " + StateTransitionReaction.class.getSimpleName());
+ "Activity flow arc type is invalid. Changing to " + StateTransitionReaction.class.getSimpleName());
result = new StateTransitionReaction(arc.getId());
break;
default:
@@ -797,7 +797,7 @@ public class ReactionParser extends GlyphParser {
if (productPointList.size() == 3) {
if (productPointList.get(0).distance(productPointList.get(1)) > productPointList.get(1)
- .distance(productPointList.get(2))) {
+ .distance(productPointList.get(2))) {
Point2D newPoint = pt.getPointOnLine(productPointList.get(0), productPointList.get(1), 0.5);
productPointList.add(1, newPoint);
} else {
@@ -816,12 +816,12 @@ public class ReactionParser extends GlyphParser {
reactant.setLine(reactantLine);
PolylineData centerLine = new PolylineData(productPointList.subList(reactantPointEnds, productPointStarts + 1))
- .copy();
+ .copy();
reaction.setLine(centerLine);
ArrowTypeData productAtd = extractArrowTypeDataFromArc(arc);
PolylineData productLine = new PolylineData(
- productPointList.subList(productPointStarts, productPointList.size())).copy();
+ productPointList.subList(productPointStarts, productPointList.size())).copy();
productLine.setEndAtd(productAtd);
product.setLine(productLine);
@@ -935,19 +935,19 @@ public class ReactionParser extends GlyphParser {
return parsePhenotypeArc(a);
} catch (Exception e) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model), "Probelm with importing arc",
- e);
+ e);
}
break;
}
if (a.getSource() instanceof Glyph) {
Glyph sourceGlyph = (Glyph) a.getSource();
if (GlyphClazz.fromClazz(sourceGlyph.getClazz()).equals(GlyphClazz.PHENOTYPE)
- && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
+ && (model.getElementByElementId(targetGlyph.getId()) instanceof Species)) {
try {
return parsePhenotypeArc(a);
} catch (InvalidArgumentException ex) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "The arc is not a valid reduced notation arc.", ex);
+ "The arc is not a valid reduced notation arc.", ex);
}
break;
}
@@ -962,7 +962,7 @@ public class ReactionParser extends GlyphParser {
}
if (!found) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "Expected PHENOTYPE in reduced notation arc. Arc skipped.");
+ "Expected PHENOTYPE in reduced notation arc. Arc skipped.");
}
break;
} else {
@@ -984,13 +984,13 @@ public class ReactionParser extends GlyphParser {
}
if (!found) {
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "Cannot find a target for arc: " + a.getId() + ". Skipping");
+ "Cannot find a target for arc: " + a.getId() + ". Skipping");
}
}
break;
default:
logger.warn(new SbgnLogMarker(ProjectLogEntryType.PARSING_ISSUE, a, model),
- "The arc has not been parsed, since it is invalid for SBGN PD map.");
+ "The arc has not been parsed, since it is invalid for SBGN PD map.");
}
return null;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index cf6e21fcd562237486f7c03f1f3fb93d82d8efac..5f28eaeace3356ed1a6bca4fd3a575c942db5ad8 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
@@ -1,5 +1,7 @@
package lcsb.mapviewer.converter.model.sbml.reaction;
+import lcsb.mapviewer.commands.layout.ModifierType;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
@@ -9,8 +11,6 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.common.exception.NotImplementedException;
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
import lcsb.mapviewer.converter.model.sbml.SbmlModelUtils;
import lcsb.mapviewer.converter.model.sbml.SbmlParameterParser;
@@ -72,14 +72,14 @@ import java.util.Map;
import java.util.Set;
public class SbmlReactionParser extends SbmlBioEntityParser {
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
- private ElementUtils eu = new ElementUtils();
+ private final ElementUtils eu = new ElementUtils();
- private SbmlSpeciesParser speciesParser;
- private SbmlCompartmentParser compartmentParser;
+ private final SbmlSpeciesParser speciesParser;
+ private final SbmlCompartmentParser compartmentParser;
- private PointTransformation pt = new PointTransformation();
+ private final PointTransformation pt = new PointTransformation();
public SbmlReactionParser(final Model sbmlModel, final lcsb.mapviewer.model.map.model.Model minervaModel,
final SbmlSpeciesParser speciesParser, final SbmlCompartmentParser compartmentParser) {
@@ -325,8 +325,8 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
// if there is no layout don't create center line
if (startNode.getLine() != null && startNode.getLine().length() > Configuration.EPSILON
&& endNode.getLine() != null && endNode.getLine().length() > Configuration.EPSILON) {
- startNode.getLine().trimEnd(ReactionCellDesignerConverter.RECT_SIZE);
- endNode.getLine().trimBegin(ReactionCellDesignerConverter.RECT_SIZE);
+ startNode.getLine().trimEnd(ReactionData.RECT_SIZE);
+ endNode.getLine().trimBegin(ReactionData.RECT_SIZE);
line.addLine(pt.copyPoint(startNode.getLine().getEndPoint()), pt.copyPoint(endNode.getLine().getStartPoint()));
line.setType(startNode.getLine().getType());
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
index bb2acde6f338b0ac3b09436348e999fd8f803ebe..b43073d0c40be477b8b65fac284631dcdc588a80 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -3,7 +3,6 @@ package lcsb.mapviewer.converter.model.sbml;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import org.junit.Test;
@@ -58,8 +57,7 @@ public class GenericSbmlToXmlParserTest extends SbmlTestFunctions {
testSbmlSerialization(model);
}
- private void testSbmlSerialization(final Model model) throws InconsistentModelException,
- IOException, ConverterException, InvalidInputDataExecption {
+ private void testSbmlSerialization(final Model model) throws ConverterException, InvalidInputDataExecption {
final SbmlParser converter = new SbmlParser();
converter.setProvideDefaults(false);
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index 9afa407aebda37e577d7fffe91b6042966dc3b99..dc27092f8fb434681a7d9f91a68209899576a035 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -346,6 +346,13 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
if (startPoint != null) {
line.setStartPoint(startPoint);
}
+ for (final ModifierType mt : ModifierType.values()) {
+ if (mt.getClazz().equals(modifier.getClass())) {
+ line.setEndAtd(mt.getAtd());
+ line.setType(mt.getLineType());
+ }
+ }
+
modifier.setLine(line);
}
}
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ModifierType.java
similarity index 72%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
rename to model-command/src/main/java/lcsb/mapviewer/commands/layout/ModifierType.java
index 24696c519e645025d4519d25c1a2f5f07573e0bc..49e8cf069db513c92b218abc7cc776244d1c260f 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ModifierType.java
@@ -1,6 +1,5 @@
-package lcsb.mapviewer.converter.model.celldesigner.types;
+package lcsb.mapviewer.commands.layout;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.LineType;
@@ -16,9 +15,8 @@ import lcsb.mapviewer.model.map.reaction.Modifier;
/**
* This enum defines how different types of CellDesigner modifiers should be
* translated into the reaction {@link Modifier} class.
- *
+ *
* @author Piotr Gawron
- *
*/
public enum ModifierType {
@@ -30,7 +28,7 @@ public enum ModifierType {
/**
* Inhibition.
*/
- INHIBITION("INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0, ReactionCellDesignerConverter.RECT_SIZE / 2 - 1),
+ INHIBITION("INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0, ReactionData.RECT_SIZE / 2 - 1),
/**
* Unknown catalysis.
@@ -41,7 +39,7 @@ public enum ModifierType {
* Unknown inhibition.
*/
UNKNOWN_INHIBITION("UNKNOWN_INHIBITION", UnknownInhibition.class, ArrowType.CROSSBAR, 8.0,
- ReactionCellDesignerConverter.RECT_SIZE / 2 - 1, LineType.DASHED),
+ ReactionData.RECT_SIZE / 2 - 1, LineType.DASHED),
/**
* Physical stimulation.
@@ -57,32 +55,32 @@ public enum ModifierType {
* Trigger.
*/
TRIGGER_STRING("TRIGGER", Trigger.class, ArrowType.BLANK_CROSSBAR),
-
+
/**
* CellDesigner 2.5 modification type.
*/
TRANSCRIPTIONAL_ACTIVATION("TRANSCRIPTIONAL_ACTIVATION", Trigger.class, ArrowType.BLANK_CROSSBAR),
-
+
/**
* CellDesigner 2.5 modification type.
*/
- TRANSCRIPTIONAL_INHIBITION("TRANSCRIPTIONAL_INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0,
- ReactionCellDesignerConverter.RECT_SIZE / 2 - 1),
-
+ TRANSCRIPTIONAL_INHIBITION("TRANSCRIPTIONAL_INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0,
+ ReactionData.RECT_SIZE / 2 - 1),
+
;
/**
* CellDesigner string describing this type.
*/
- private String stringName;
+ private final String stringName;
/**
* Which class should be used for this type.
*/
- private Class<? extends Modifier> clazz;
+ private final Class<? extends Modifier> clazz;
/**
* How the arrow head of the line should look like.
*/
- private ArrowTypeData atd = new ArrowTypeData();
+ private final ArrowTypeData atd = new ArrowTypeData();
/**
* How much should be the arrow line trimmed.
*/
@@ -94,13 +92,10 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at) {
this(string, clazz, at, null, null, null);
@@ -108,15 +103,11 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
+ * @param arrowLength length of the arrow
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at, final Double arrowLength) {
this(string, clazz, at, arrowLength, null, null);
@@ -124,17 +115,12 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
- * @param trimLength
- * {@link #trimLength}
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
+ * @param arrowLength length of the arrow
+ * @param trimLength {@link #trimLength}
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at, final Double arrowLength, final Double trimLength) {
this(string, clazz, at, arrowLength, trimLength, null);
@@ -142,22 +128,16 @@ public enum ModifierType {
/**
* Constructor used to create and initialize this enum.
- *
- * @param string
- * {@link #stringName}
- * @param clazz
- * {@link #clazz}
- * @param at
- * type of the arrow
- * @param arrowLength
- * length of the arrow
- * @param trimLength
- * {@link #trimLength}
- * @param lt
- * {@link #lineType}
+ *
+ * @param string {@link #stringName}
+ * @param clazz {@link #clazz}
+ * @param at type of the arrow
+ * @param arrowLength length of the arrow
+ * @param trimLength {@link #trimLength}
+ * @param lt {@link #lineType}
*/
ModifierType(final String string, final Class<? extends Modifier> clazz, final ArrowType at, final Double arrowLength, final Double trimLength,
- final LineType lt) {
+ final LineType lt) {
stringName = string;
this.clazz = clazz;
if (at != null) {
@@ -176,7 +156,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #stringName}
*/
public String getStringName() {
@@ -184,7 +163,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #clazz}
*/
public Class<? extends Modifier> getClazz() {
@@ -192,7 +170,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #atd}
*/
public ArrowTypeData getAtd() {
@@ -200,7 +177,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #trimLength}
*/
public double getTrimLength() {
@@ -208,7 +184,6 @@ public enum ModifierType {
}
/**
- *
* @return {@link #lineType}
*/
public LineType getLineType() {
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ReactionData.java
similarity index 70%
rename from converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java
rename to model-command/src/main/java/lcsb/mapviewer/commands/layout/ReactionData.java
index 3c412c80daf0d34ea354342ad66954ac8f0a014b..4b4781f5404160dcef8687fd47ddc2eb418e1586 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/geometry/ReactionCellDesignerConverter.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ReactionData.java
@@ -1,13 +1,12 @@
-package lcsb.mapviewer.converter.model.celldesigner.geometry;
+package lcsb.mapviewer.commands.layout;
/**
* Class that provides CellDesigner specific graphical information for Reaction.
* It's used for conversion from xml to normal x,y coordinates.
- *
+ *
* @author Piotr Gawron
- *
*/
-public final class ReactionCellDesignerConverter {
+public final class ReactionData {
/**
* What is the size of rectangle that is drawn in center point of the reaction.
*/
@@ -16,7 +15,7 @@ public final class ReactionCellDesignerConverter {
/**
* Default constructor that prevents instantiation.
*/
- protected ReactionCellDesignerConverter() {
+ ReactionData() {
}
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
index 5c1dbdd87533991c929af53a79e00d5a13f3ff73..be9eb77da23132592b61099c3efd8ff11cdce9c0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/ArrowTypeDataComparator.java
@@ -1,35 +1,32 @@
package lcsb.mapviewer.model.graphics;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for ArrowTypeData. It compares the
* content, but skip database identifier.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ArrowTypeDataComparator extends Comparator<ArrowTypeData> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public ArrowTypeDataComparator(final double epsilon) {
super(ArrowTypeData.class);
@@ -48,22 +45,22 @@ public class ArrowTypeDataComparator extends Comparator<ArrowTypeData> {
DoubleComparator doubleComparator = new DoubleComparator(epsilon);
if (arg0.getArrowType().compareTo(arg1.getArrowType()) != 0) {
- logger.debug("Different arrow type: " + arg0.getArrowType() + ", " + arg1.getArrowType());
+ logger.debug("Different arrow type: {}, {}", arg0.getArrowType(), arg1.getArrowType());
return arg0.getArrowType().compareTo(arg1.getArrowType());
}
if (arg0.getArrowLineType().compareTo(arg1.getArrowLineType()) != 0) {
- logger.debug("Different arrow line type: " + arg0.getArrowLineType() + ", " + arg1.getArrowLineType());
+ logger.debug("Different arrow line type: {}, {}", arg0.getArrowLineType(), arg1.getArrowLineType());
return arg0.getArrowLineType().compareTo(arg1.getArrowLineType());
}
if (doubleComparator.compare(arg0.getLen(), arg1.getLen()) != 0) {
- logger.debug("Different length: " + arg0.getLen() + ", " + arg1.getLen());
+ logger.debug("Different length: {}, {}", arg0.getLen(), arg1.getLen());
return doubleComparator.compare(arg0.getLen(), arg1.getLen());
}
if (doubleComparator.compare(arg0.getAngle(), arg1.getAngle()) != 0) {
- logger.debug("Different angle: " + arg0.getAngle() + ", " + arg1.getAngle());
+ logger.debug("Different angle: {}, {}", arg0.getAngle(), arg1.getAngle());
return doubleComparator.compare(arg0.getAngle(), arg1.getAngle());
}
return 0;
diff --git a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
index f74203ca56a54aabb4d82a22266c0e16e44bc03f..63e6fc9f589354a7b4e709000ed78ffbed991639 100644
--- a/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/graphics/PolylineDataComparator.java
@@ -1,36 +1,33 @@
package lcsb.mapviewer.model.graphics;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.comparator.IntegerComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for {@link PolylineData}. It
* compares the content, but skip database identifier.
- *
+ *
* @author Piotr Gawron
- *
*/
public class PolylineDataComparator extends Comparator<PolylineData> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public PolylineDataComparator(final double epsilon) {
super(PolylineData.class, true);
@@ -51,7 +48,7 @@ public class PolylineDataComparator extends Comparator<PolylineData> {
ArrowTypeDataComparator atdComparator = new ArrowTypeDataComparator(epsilon);
if (integerComparator.compare(arg0.getLines().size(), arg1.getLines().size()) != 0) {
- logger.debug("Lines have different segments number: " + arg0.getLines().size() + ", " + arg1.getLines().size());
+ logger.debug("Lines have different segments number: {}, {}", arg0.getLines().size(), arg1.getLines().size());
return integerComparator.compare(arg0.getLines().size(), arg1.getLines().size());
}
// TODO this should be fixed
@@ -68,27 +65,27 @@ public class PolylineDataComparator extends Comparator<PolylineData> {
// }
if (atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd()) != 0) {
- logger.debug("Lines have different begin adt: " + arg0.getBeginAtd() + ", " + arg1.getBeginAtd());
+ logger.debug("Lines have different begin atd: {}, {}", arg0.getBeginAtd(), arg1.getBeginAtd());
return atdComparator.compare(arg0.getBeginAtd(), arg1.getBeginAtd());
}
if (atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd()) != 0) {
- logger.debug("Lines have different end adt: " + arg0.getEndAtd() + ", " + arg1.getEndAtd());
+ logger.debug("Lines have different end atd: {}, {}", arg0.getEndAtd(), arg1.getEndAtd());
return atdComparator.compare(arg0.getEndAtd(), arg1.getEndAtd());
}
if (doubleComparator.compare(arg0.getWidth(), arg1.getWidth()) != 0) {
- logger.debug("Lines have different width: " + arg0.getWidth() + ", " + arg1.getWidth());
+ logger.debug("Lines have different width: {}, {}", arg0.getWidth(), arg1.getWidth());
return doubleComparator.compare(arg0.getWidth(), arg1.getWidth());
}
if (integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB()) != 0) {
- logger.debug("Lines have different color: " + arg0.getColor() + ", " + arg1.getColor());
+ logger.debug("Lines have different color: {}, {}", arg0.getColor(), arg1.getColor());
return integerComparator.compare(arg0.getColor().getRGB(), arg1.getColor().getRGB());
}
if (arg0.getType().compareTo(arg1.getType()) != 0) {
- logger.debug("Lines have different type: " + arg0.getType() + ", " + arg1.getType());
+ logger.debug("Lines have different type: {}, {}", arg0.getType(), arg1.getType());
return arg0.getType().compareTo(arg1.getType());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
index e29bd2f9ac45a4dfd52316bfc08a1282ab85c373..518e95b87768d8c02c742036f81012d576c9dfb0 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/ReactionComparator.java
@@ -1,8 +1,5 @@
package lcsb.mapviewer.model.map.reaction;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.comparator.BooleanComparator;
@@ -16,31 +13,31 @@ import lcsb.mapviewer.model.graphics.PolylineDataComparator;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.MiriamDataComparator;
import lcsb.mapviewer.model.map.kinetics.SbmlKineticsComparator;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
/**
* This class implements comparator interface for {@link Reaction}.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ReactionComparator extends Comparator<Reaction> {
/**
* Default class logger.
*/
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Epsilon value used for comparison of doubles.
*/
- private double epsilon;
+ private final double epsilon;
- private boolean ignoreLayout;
+ private final boolean ignoreLayout;
/**
* Constructor that requires {@link #epsilon} parameter.
- *
- * @param epsilon
- * {@link #epsilon}
+ *
+ * @param epsilon {@link #epsilon}
*/
public ReactionComparator(final double epsilon, final boolean ignoreLayout) {
super(Reaction.class);
@@ -66,12 +63,12 @@ public class ReactionComparator extends Comparator<Reaction> {
AbstractNodeComparator nodeComparator = new AbstractNodeComparator(epsilon, ignoreLayout);
if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
- logger.debug("Name different: " + arg0.getName() + ", " + arg1.getName());
+ logger.debug("Name different: {}, {}", arg0.getName(), arg1.getName());
return stringComparator.compare(arg0.getName(), arg1.getName());
}
if (stringComparator.compare(arg0.getNotes().trim(), arg1.getNotes().trim()) != 0) {
- logger.debug("Notes different: " + arg0.getNotes() + ", " + arg1.getNotes());
+ logger.debug("Notes different: {}, {}", arg0.getNotes(), arg1.getNotes());
return stringComparator.compare(arg0.getNotes(), arg1.getNotes());
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
index f6bf6a4c3dd5836c8bd97867a5206e8e53edd928..ea330674da7974d55e721bb4d7e90e610d586746 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelContructor.java
@@ -1,13 +1,13 @@
package lcsb.mapviewer.wikipathway.xml;
import lcsb.mapviewer.commands.CreateHierarchyCommand;
+import lcsb.mapviewer.commands.layout.ModifierType;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.ConverterException;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.converter.model.celldesigner.reaction.ReactionLineData;
-import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierTypeUtils;
import lcsb.mapviewer.model.LogMarker;
import lcsb.mapviewer.model.ProjectLogEntryType;
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java
index 6a8a3ba912f8edbcb12dd4f6cc44605a34a8ed20..fea5c243fbf1392960aa049457866ea4b4282088 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ReactionLayoutFinder.java
@@ -1,24 +1,12 @@
package lcsb.mapviewer.wikipathway.xml;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.comparator.DoubleComparator;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.LineTransformation;
import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.PolylineDataFactory;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.reaction.Modifier;
@@ -27,17 +15,28 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.wikipathway.model.Edge;
import lcsb.mapviewer.wikipathway.model.Interaction;
import lcsb.mapviewer.wikipathway.utils.Geo;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
class ReactionLayoutFinder {
- private Logger logger = LogManager.getLogger();
+ private final Logger logger = LogManager.getLogger();
- private LineTransformation lt = new LineTransformation();
- private PointTransformation pt = new PointTransformation();
+ private final LineTransformation lt = new LineTransformation();
+ private final PointTransformation pt = new PointTransformation();
private Interaction interaction;
- public static enum LineLocation {
+ public enum LineLocation {
PRODUCT,
MODIFIER,
REACTANT,
@@ -48,11 +47,10 @@ class ReactionLayoutFinder {
/**
* Return coordinates where all {@link Reactant} should end, all
* {@link Modifier} should end, and all {@link Product} should start.
- *
- * @param interaction
- * GPML {@link Interaction}
+ *
+ * @param interaction GPML {@link Interaction}
* @return map consisted of three entries for classes: {@link Product},
- * {@link Reactant}, {@link Modifier}
+ * {@link Reactant}, {@link Modifier}
*/
public Map<Class<?>, Point2D> getNodeStartPoints(final Interaction interaction) {
this.interaction = interaction;
@@ -78,12 +76,12 @@ class ReactionLayoutFinder {
points.get(Reactant.class));
PolylineData inputReactionLine = getSubline(interaction.getLine(), points.get(Reactant.class),
points.get(Modifier.class));
- inputReactionLine.trimEnd(ReactionCellDesignerConverter.RECT_SIZE / 2);
+ inputReactionLine.trimEnd(ReactionData.RECT_SIZE / 2);
PolylineData outputReactionLine = getSubline(interaction.getLine(),
points.get(Modifier.class), points.get(Product.class));
- outputReactionLine.trimBegin(ReactionCellDesignerConverter.RECT_SIZE / 2);
+ outputReactionLine.trimBegin(ReactionData.RECT_SIZE / 2);
PolylineData productLine = getSubline(interaction.getLine(),
points.get(Product.class), interaction.getLine().getEndPoint());
PolylineData modifierLine = new PolylineData(pt.copyPoint(inputReactionLine.getEndPoint()),
@@ -320,7 +318,6 @@ class ReactionLayoutFinder {
PolylineData result = new PolylineData(originalPolylineData);
List<Line2D> lines = new ArrayList<>(result.getLines().subList(start, end + 1));
result.removeLines();
- ;
result.addLines(lines);
result.setStartPoint(pt.copyPoint(startPoint));
diff --git a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
index 908bc74ddbe876471a2dc6f16ec71a36c94f9a76..c591c36b99ab27b490305f2a9d18eb57ac897315 100644
--- a/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
+++ b/pathvisio/src/test/java/lcsb/mapviewer/wikipathway/GPMLToModelTest.java
@@ -1,7 +1,7 @@
package lcsb.mapviewer.wikipathway;
+import lcsb.mapviewer.commands.layout.ReactionData;
import lcsb.mapviewer.common.geometry.PointTransformation;
-import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
import lcsb.mapviewer.model.graphics.HorizontalAlign;
import lcsb.mapviewer.model.graphics.VerticalAlign;
import lcsb.mapviewer.model.map.Drawable;
@@ -37,7 +37,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
private ModelComparator mc;
- private PointTransformation pt = new PointTransformation();
+ private final PointTransformation pt = new PointTransformation();
@Before
public void setUp() {
@@ -278,6 +278,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
for (final Complex species : model.getComplexList()) {
if ("p70 S6 Kinases".equals(species.getName())) {
nameFound = true;
+ break;
}
}
assertTrue("Complex parsed from gpml should have a valid name", nameFound);
@@ -381,7 +382,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/small/protein_with_modification.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- Gene gene = (Gene) model1.getElementByElementId("be3de");
+ Gene gene = model1.getElementByElementId("be3de");
assertNotNull(gene);
assertEquals(2, gene.getModificationResidues().size());
for (ModificationResidue mr : gene.getModificationResidues()) {
@@ -398,7 +399,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
String fileName = "testFiles/small/protein_with_modification_2.gpml";
Model model1 = new GPMLToModel().getModel(fileName);
- Gene protein = (Gene) model1.getElementByElementId("be3de");
+ Gene protein = model1.getElementByElementId("be3de");
assertNotNull(protein);
assertEquals(2, protein.getModificationResidues().size());
@@ -418,7 +419,7 @@ public class GPMLToModelTest extends WikipathwaysTestFunctions {
double distance = pt.getPointOnLine(centerLine.getP1(), centerLine.getP2(), 0.5)
.distance(reaction.getModifiers().get(0).getLine().getEndPoint());
assertTrue("Modifier is too far from center point: " + distance,
- distance < ReactionCellDesignerConverter.RECT_SIZE);
+ distance < ReactionData.RECT_SIZE);
assertEquals(0, getWarnings().size());
}