diff --git a/CHANGELOG b/CHANGELOG
index 1412aa62f84c143aff1beb16b043ab98bd9ac51d..7470a35bba857a34e0550e4366d72126a3f662bd 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -7,6 +7,8 @@ minerva (18.1.0) stable; urgency=medium
* Bug fix: information about species pathway/compartment has not been
separated. This caused to export the model into incorrect SBML - species are
separated using compartment (#2169)
+ * Bug fix: exporting model should provide deterministic output for species and
+ compartments (#2187)
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Dec 2024 13:00:00 +0200
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 dff6f97af0094312578fb5c09a6d4bf02c6a7b62..d0bceeb60ee61462bcc2f7d95e989360a4834256 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
@@ -715,7 +715,7 @@ public class CellDesignerXmlParser extends Converter {
final List<Gene> genes = new ArrayList<>();
final List<Rna> rnas = new ArrayList<>();
final List<AntisenseRna> antisenseRnas = new ArrayList<>();
- for (final Element element : model.getElements()) {
+ for (final Element element : model.getSortedElements()) {
if (element instanceof Protein) {
proteins.add((Protein) element);
} else if (element instanceof Gene) {
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 321f5d8a44ac4e06591d0722efaae71b4fec1682..1aedbdef808958c52e258be2bc1e29f01b78d56d 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
@@ -211,7 +211,7 @@ public class SbgnmlXmlExporter {
final Sbgn sbgnData = new Sbgn();
- for (final Element element : model.getElements()) {
+ for (final Element element : model.getSortedElements()) {
if (element instanceof Species) {
if (((Species) element).getComplex() == null) {
final Glyph newGlyph = elementToGlyph(element);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ElementByIdComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementByIdComparator.java
new file mode 100644
index 0000000000000000000000000000000000000000..a59f3de08839fd0c05a9b11b5ba0cac761d7a702
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ElementByIdComparator.java
@@ -0,0 +1,18 @@
+package lcsb.mapviewer.model.map.model;
+
+import lcsb.mapviewer.common.comparator.StringComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+import java.util.Comparator;
+
+public class ElementByIdComparator implements Comparator<Element> {
+ private final StringComparator comparator = new StringComparator();
+
+ @Override
+ public int compare(final Element o1, final Element o2) {
+ if (comparator.compare(o1.getElementId(), o2.getElementId()) == 0) {
+ return o1.getId() - o2.getId();
+ }
+ return comparator.compare(o1.getElementId(), o2.getElementId());
+ }
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 0a694e9307b033c47adc5a9a39493d008385082a..b9c683193f3b421dbe0a78938610e3115966f65c 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -1,13 +1,6 @@
package lcsb.mapviewer.model.map.model;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Set;
-
import com.fasterxml.jackson.annotation.JsonIgnore;
-
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.Drawable;
@@ -25,13 +18,18 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.List;
+import java.util.Set;
+
/**
* This interface defines functionality that the model container class should
* implement to access data efficiently. It shouldn't be implemented by data
* model.
- *
+ *
* @author Piotr Gawron
- *
*/
public interface Model {
@@ -45,45 +43,38 @@ public interface Model {
/**
* Adds element to the model.
- *
- * @param element
- * element to add
+ *
+ * @param element element to add
*/
void addElement(final Element element);
/**
- *
* @return model width
*/
double getWidth();
/**
* Sets model width.
- *
- * @param width
- * new model width
+ *
+ * @param width new model width
*/
void setWidth(final double width);
/**
* Sets model width.
*
- * @param text
- * new model width
+ * @param text new model width
*/
@JsonIgnore
void setWidth(final String text);
/**
- *
- * @param width
- * new {@link ModelData#width}
+ * @param width new {@link ModelData#width}
*/
@JsonIgnore
void setWidth(final int width);
/**
- *
* @return model height
*/
double getHeight();
@@ -91,24 +82,20 @@ public interface Model {
/**
* Sets model height.
*
- * @param height
- * new model height
+ * @param height new model height
*/
void setHeight(final double height);
/**
* Sets model height.
*
- * @param text
- * new model height
+ * @param text new model height
*/
@JsonIgnore
void setHeight(final String text);
/**
- *
- * @param height
- * new {@link ModelData#height}
+ * @param height new {@link ModelData#height}
*/
@JsonIgnore
void setHeight(final int height);
@@ -121,9 +108,7 @@ public interface Model {
Set<Element> getElements();
/**
- *
- * @param elements
- * new {@link ModelData#elements} collection
+ * @param elements new {@link ModelData#elements} collection
*/
void setElements(final Set<Element> elements);
@@ -131,10 +116,8 @@ public interface Model {
* Returns element with the given element identifier
* ({@link Element#elementId} ).
*
- * @param idElement
- * element identifier
- * @param <T>
- * type of the object to be returned
+ * @param idElement element identifier
+ * @param <T> type of the object to be returned
* @return {@link Element} with the given id
*/
<T extends Element> T getElementByElementId(final String idElement);
@@ -142,8 +125,7 @@ public interface Model {
/**
* Adds reaction to the model.
*
- * @param reaction
- * reaction to add
+ * @param reaction reaction to add
*/
void addReaction(final Reaction reaction);
@@ -162,13 +144,11 @@ public interface Model {
/**
* Adds layer to the model.
*
- * @param layer
- * object to add
+ * @param layer object to add
*/
void addLayer(final Layer layer);
/**
- *
* @return set of layers
*/
Set<Layer> getLayers();
@@ -176,13 +156,11 @@ public interface Model {
/**
* Adds list of elements into model.
*
- * @param elements
- * list of elements
+ * @param elements list of elements
*/
void addElements(final Collection<? extends Element> elements);
/**
- *
* @return short description of the model
*/
String getNotes();
@@ -190,16 +168,14 @@ public interface Model {
/**
* Sets new short description of the model.
*
- * @param notes
- * new short description
+ * @param notes new short description
*/
void setNotes(final String notes);
/**
* Returns reaction with the id given in the parameter.
*
- * @param idReaction
- * reaction identifier ({@link Reaction#idReaction})
+ * @param idReaction reaction identifier ({@link Reaction#idReaction})
* @return reaction with the id given in the parameter
*/
Reaction getReactionByReactionId(final String idReaction);
@@ -207,24 +183,21 @@ public interface Model {
/**
* Adds set of layers to the model.
*
- * @param layers
- * object to add
+ * @param layers object to add
*/
void addLayers(final Collection<Layer> layers);
/**
* Adds {@link ElementGroup} to the model.
*
- * @param elementGroup
- * object to add
+ * @param elementGroup object to add
*/
void addElementGroup(final ElementGroup elementGroup);
/**
* Adds {@link BlockDiagram} to the model.
*
- * @param blockDiagram
- * object to add
+ * @param blockDiagram object to add
*/
void addBlockDiagream(final BlockDiagram blockDiagram);
@@ -235,8 +208,7 @@ public interface Model {
String getIdModel();
/**
- * @param idModel
- * the idModel to set
+ * @param idModel the idModel to set
* @see Model#idModel
*/
void setIdModel(final String idModel);
@@ -248,8 +220,7 @@ public interface Model {
int getTileSize();
/**
- * @param tileSize
- * the tileSize to set
+ * @param tileSize the tileSize to set
* @see ModelData#tileSize
*/
void setTileSize(final int tileSize);
@@ -261,8 +232,7 @@ public interface Model {
int getZoomLevels();
/**
- * @param zoomLevels
- * the zoomLevels to set
+ * @param zoomLevels the zoomLevels to set
* @see ModelData#zoomLevels
*/
void setZoomLevels(final int zoomLevels);
@@ -270,16 +240,14 @@ public interface Model {
/**
* Removes reaction from model.
*
- * @param reaction
- * reaction to remove
+ * @param reaction reaction to remove
*/
void removeReaction(final Reaction reaction);
/**
* Removes {@link Element} from the model.
*
- * @param element
- * element to remove
+ * @param element element to remove
*/
void removeElement(final Element element);
@@ -307,16 +275,14 @@ public interface Model {
/**
* Adds reactions to model.
*
- * @param reactions2
- * list of reaction to add
+ * @param reactions2 list of reaction to add
*/
void addReactions(final List<Reaction> reactions2);
/**
* Returns list of elements with given name.
*
- * @param name
- * name of the element
+ * @param name name of the element
* @return list of elements with given name
*/
List<Element> getElementsByName(final String name);
@@ -324,8 +290,7 @@ public interface Model {
/**
* Returns {@link Element} for given database identifier.
*
- * @param dbId
- * element database identifier ({@link Element#id})
+ * @param dbId element database identifier ({@link Element#id})
* @return {@link Element} for a given id
*/
<T extends Element> T getElementByDbId(final Integer dbId);
@@ -333,8 +298,7 @@ public interface Model {
/**
* Returns {@link Reaction} for given database identifier.
*
- * @param dbId
- * reaction database identifier ({@link Reaction#id})
+ * @param dbId reaction database identifier ({@link Reaction#id})
* @return {@link Reaction} for a given id
*/
Reaction getReactionByDbId(final Integer dbId);
@@ -354,15 +318,12 @@ public interface Model {
List<Element> getElementsSortedBySize();
/**
- *
* @return {@link ModelData#project}
*/
Project getProject();
/**
- *
- * @param project
- * new {@link ModelData#project}
+ * @param project new {@link ModelData#project}
*/
void setProject(final Project project);
@@ -372,7 +333,6 @@ public interface Model {
ModelData getModelData();
/**
- *
* @return {@link ModelData#id}
*/
int getId();
@@ -380,16 +340,14 @@ public interface Model {
/**
* Sets database identifier of the model.
*
- * @param id
- * database identifier
+ * @param id database identifier
*/
void setId(final int id);
/**
* Adds submodel connection.
*
- * @param submodel
- * submodel to add
+ * @param submodel submodel to add
*/
void addSubmodelConnection(final ModelSubmodelConnection submodel);
@@ -410,8 +368,7 @@ public interface Model {
/**
* Sets name of the model.
*
- * @param name
- * name of the model
+ * @param name name of the model
*/
void setName(final String name);
@@ -419,19 +376,17 @@ public interface Model {
* Returns {@link Model submodel} by the {@link ModelData#id database
* identifier} given in the parameter.
*
- * @param idObject
- * the {@link ModelData#id database identifier} that identifies
- * submodel
+ * @param idObject the {@link ModelData#id database identifier} that identifies
+ * submodel
* @return {@link Model submodel} by the {@link ModelData#id database
- * identifier} given in the parameter
+ * identifier} given in the parameter
*/
Model getSubmodelById(final Integer idObject);
/**
* Returns submodel identified by submodel identifier.
*
- * @param identifier
- * identifier of the model
+ * @param identifier identifier of the model
* @return submodel identified by identifier
*/
Model getSubmodelById(final String identifier);
@@ -447,8 +402,7 @@ public interface Model {
/**
* Returns connection to a submodel identified by connection name.
*
- * @param name
- * name of the connection
+ * @param name name of the connection
* @return connection to a submodel identified by connection name
*/
Model getSubmodelByConnectionName(final String name);
@@ -456,8 +410,7 @@ public interface Model {
/**
* Returns connection to a submodel identified by connection identifier.
*
- * @param id
- * id of the connection
+ * @param id id of the connection
* @return connection to a submodel identified by connection identifier
*/
SubmodelConnection getSubmodelConnectionById(final Integer id);
@@ -473,17 +426,16 @@ public interface Model {
* Returns {@link Model submodel} identified by the {@link ModelData#name
* model name}. It returns this 'parent' object when the names matches.
*
- * @param name
- * name of the submodel that should be returned
+ * @param name name of the submodel that should be returned
* @return {@link Model submodel} identified by the {@link ModelData#name
- * model name}
+ * model name}
*/
Model getSubmodelByName(final String name);
/**
* Return list of all {@link BioEntity} in the map. This includes all
* {@link Reaction reactions} and {@link Element elements}.
- *
+ *
* @return list of all {@link BioEntity} in the map
*/
List<BioEntity> getBioEntities();
@@ -532,25 +484,27 @@ public interface Model {
void addMiriamData(final Collection<MiriamData> parseRdfNode);
- public void addAuthor(final Author author);
+ void addAuthor(final Author author);
void addAuthors(final Collection<Author> authorsFromRdf);
- public List<Author> getAuthors();
+ List<Author> getAuthors();
- public Calendar getCreationDate();
+ Calendar getCreationDate();
- public void setCreationDate(final Calendar creationDate);
+ void setCreationDate(final Calendar creationDate);
- public void addModificationDate(final Calendar modificationDate);
+ void addModificationDate(final Calendar modificationDate);
- public List<Calendar> getModificationDates();
+ List<Calendar> getModificationDates();
void addModificationDates(final Collection<Calendar> modificationDatesFromRdf);
- void removeBioEntity(final BioEntity bioEntitiy);
+ void removeBioEntity(final BioEntity bioEntity);
Set<Drawable> getDrawables();
Set<Drawable> getDrawables(boolean onlyVisible);
+
+ Collection<Element> getSortedElements();
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index 2301de3071c32efbab8e4bdab8b44a885708fb5b..ffa13ff0832c8ee05f30e028ec815bcff95b131e 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -1,18 +1,5 @@
package lcsb.mapviewer.model.map.model;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.BioEntity;
@@ -30,14 +17,25 @@ import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
/**
* This class implements {@link Model} interface. It's is very simple
* implementation containing structures that index the data from
* {@link ModelData} structure and provide access method to this indexed data.
- *
+ *
* @author Piotr Gawron
- *
*/
public class ModelFullIndexed implements Model {
@@ -45,31 +43,31 @@ public class ModelFullIndexed implements Model {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* Object that map {@link Element#elementId element identifier} into
* {@link Element}.
*/
- private Map<String, Element> elementByElementId = new HashMap<>();
+ private final Map<String, Element> elementByElementId = new HashMap<>();
/**
* Object that map {@link Element#id element database identifier} into
* {@link Element}.
*/
- private Map<Integer, Element> elementByDbId = new HashMap<>();
+ private final Map<Integer, Element> elementByDbId = new HashMap<>();
/**
* Object that map {@link Reaction#idReaction reaction identifier} into
* {@link Reaction}.
*/
- private Map<String, Reaction> reactionByReactionId = new HashMap<>();
+ private final Map<String, Reaction> reactionByReactionId = new HashMap<>();
/**
* Object that map {@link Reaction#id reaction database identifier} into
* {@link Reaction}.
*/
- private Map<Integer, Reaction> reactionByDbId = new HashMap<>();
+ private final Map<Integer, Reaction> reactionByDbId = new HashMap<>();
/**
* {@link ModelData} object containing "raw" data about the model.
@@ -78,9 +76,8 @@ public class ModelFullIndexed implements Model {
/**
* Default constructor.
- *
- * @param model
- * {@link ModelData} object containing "raw" data about the model
+ *
+ * @param model {@link ModelData} object containing "raw" data about the model
*/
public ModelFullIndexed(final ModelData model) {
if (model == null) {
@@ -202,6 +199,7 @@ public class ModelFullIndexed implements Model {
result.add((Compartment) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -322,6 +320,7 @@ public class ModelFullIndexed implements Model {
result.add((Species) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -333,6 +332,7 @@ public class ModelFullIndexed implements Model {
result.add((Species) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -344,6 +344,7 @@ public class ModelFullIndexed implements Model {
result.add((Complex) element);
}
}
+ result.sort(new ElementByIdComparator());
return result;
}
@@ -700,13 +701,13 @@ public class ModelFullIndexed implements Model {
}
@Override
- public void removeBioEntity(final BioEntity bioEntitiy) {
- if (bioEntitiy instanceof Reaction) {
- removeReaction((Reaction) bioEntitiy);
- } else if (bioEntitiy instanceof Element) {
- removeElement((Element) bioEntitiy);
+ public void removeBioEntity(final BioEntity bioEntity) {
+ if (bioEntity instanceof Reaction) {
+ removeReaction((Reaction) bioEntity);
+ } else if (bioEntity instanceof Element) {
+ removeElement((Element) bioEntity);
} else {
- throw new InvalidArgumentException("Unknown class type:" + bioEntitiy);
+ throw new InvalidArgumentException("Unknown class type:" + bioEntity);
}
}
@@ -731,4 +732,11 @@ public class ModelFullIndexed implements Model {
}
return result;
}
+
+ @Override
+ public Collection<Element> getSortedElements() {
+ List<Element> result = new ArrayList<>(getElements());
+ result.sort(new ElementByIdComparator());
+ return result;
+ }
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index c2fffd96d1f5f1f0deff454fca5711a2bf2f91aa..e868f83a9385a5a1d23a5975a5a5122eade8be26 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -1,21 +1,5 @@
package lcsb.mapviewer.model.map.model;
-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.util.ArrayList;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.mockito.Mockito;
-
import lcsb.mapviewer.ModelTestFunctions;
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
@@ -36,6 +20,21 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.field.StructuralState;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.mockito.Mockito;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertNull;
+import static org.junit.Assert.assertTrue;
public class ModelFullIndexedTest extends ModelTestFunctions {
@@ -543,4 +542,24 @@ public class ModelFullIndexedTest extends ModelTestFunctions {
assertTrue(model.getDrawables().contains(state));
}
+ @Test
+ public void testGetSortedElements() {
+ ModelFullIndexed model = new ModelFullIndexed(null);
+
+ Protein protein1 = new GenericProtein("1");
+ Protein protein2 = new GenericProtein("3");
+ Protein protein3 = new GenericProtein("2");
+ Protein protein4 = new GenericProtein("4");
+
+ model.addElement(protein1);
+
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ model.addElement(protein2);
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ model.addElement(protein3);
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ model.addElement(protein4);
+ assertEquals(protein1, model.getSortedElements().iterator().next());
+ }
+
}
diff --git a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java
index 33366ea4f4a148ffb604c598c5de7b9fa98d6a79..7efeeb482288e4cb08877a062b244c6a84e65e50 100644
--- a/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java
+++ b/pathvisio/src/main/java/lcsb/mapviewer/wikipathway/xml/ModelToGPML.java
@@ -1,23 +1,5 @@
package lcsb.mapviewer.wikipathway.xml;
-import java.awt.Color;
-import java.awt.Polygon;
-import java.awt.Shape;
-import java.awt.geom.Ellipse2D;
-import java.awt.geom.Line2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.commons.text.StringEscapeUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.geometry.ColorParser;
@@ -60,12 +42,28 @@ import lcsb.mapviewer.wikipathway.model.GpmlLineType;
import lcsb.mapviewer.wikipathway.model.InteractionMapping;
import lcsb.mapviewer.wikipathway.model.ShapeMapping;
import lcsb.mapviewer.wikipathway.utils.Geo;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.text.StringEscapeUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.awt.Color;
+import java.awt.Polygon;
+import java.awt.Shape;
+import java.awt.geom.Ellipse2D;
+import java.awt.geom.Line2D;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
/**
* Class contains methods for ModelToGPML conversion.
- *
+ *
* @author Jan Badura
- *
*/
public class ModelToGPML {
@@ -104,15 +102,15 @@ public class ModelToGPML {
/**
* Parser used to convert from/to xml {@link MiriamData} annotations.
*/
- private ReferenceParser referenceParser;
+ private final ReferenceParser referenceParser;
/**
* Parser used to convert from/to xml (in BioPAX format) {@link MiriamData}
* annotations.
*/
- private BiopaxParser biopaxParser;
+ private final BiopaxParser biopaxParser;
- private ColorParser colorParser = new ColorParser();
+ private final ColorParser colorParser = new ColorParser();
public ModelToGPML(final String mapName) {
referenceParser = new ReferenceParser(mapName);
@@ -121,7 +119,7 @@ public class ModelToGPML {
/**
* Returns new unique identifier for the model.
- *
+ *
* @return new unique identifier for the model
*/
private String getNewId() {
@@ -133,9 +131,8 @@ public class ModelToGPML {
* This function returns GPML Species type based on class. If it can not
* recognize one of (Rna,GeneProduct,Protein,Metabolite) it will throw
* {@link InvalidArgumentException}.
- *
- * @param species
- * species for which GPML type will be returned
+ *
+ * @param species species for which GPML type will be returned
* @return String - type
*/
private String getType(final Species species) {
@@ -171,9 +168,8 @@ public class ModelToGPML {
* Since in pathvisio it is impossible to set the size of group rectangle this
* function calculates new rectangle for complex based on contents of this
* complex.
- *
- * @param alias
- * alias for which rectangle border is calculated
+ *
+ * @param alias alias for which rectangle border is calculated
* @return rectangle border for alias
*/
Shape getShape(final Element alias) {
@@ -237,11 +233,9 @@ public class ModelToGPML {
* This function calculates {@link PolylineData} based on start {@link Reactant}
* and end {@link Product}. If end or start points are to far away from their
* rectangles new points are added.
- *
- * @param start
- * reactant from which polyline starts
- * @param end
- * product where polyline ends
+ *
+ * @param start reactant from which polyline starts
+ * @param end product where polyline ends
* @return {@link PolylineData} between start and end
*/
private PolylineData getPolyline(final Reactant start, final Product end) {
@@ -280,11 +274,9 @@ public class ModelToGPML {
/**
* This function calculates PolylineData based on ReactionNode.
- *
- * @param rn
- * reaction node for which polyline is calculated
- * @param mainLine
- * main line to which polyline is attached
+ *
+ * @param rn reaction node for which polyline is calculated
+ * @param mainLine main line to which polyline is attached
* @return polyline for {@link ReactionNode}
*/
PolylineData getPolyline(final ReactionNode rn, final PolylineData mainLine) {
@@ -328,13 +320,12 @@ public class ModelToGPML {
/**
* This function transform Compartments into Shapes (final Oval or Rectangle)
* from PathVisio.
- *
- * @param model
- * model where compartments are placed
+ *
+ * @param model model where compartments are placed
* @return String that encodes all compartments in GPML format
*/
private String getComparments(final Model model) {
- StringBuilder result = new StringBuilder("");
+ StringBuilder result = new StringBuilder();
for (final Compartment compartment : model.getCompartments()) {
result.append(compartmentToXml(compartment));
}
@@ -342,7 +333,7 @@ public class ModelToGPML {
}
String compartmentToXml(final Compartment ca) {
- StringBuilder comparments = new StringBuilder("");
+ StringBuilder comparments = new StringBuilder();
double x = ca.getCenterX();
double y = ca.getCenterY();
double h = ca.getHeight();
@@ -374,23 +365,18 @@ public class ModelToGPML {
* This function creates Interaction for other product, reactant or modifier
* from main reaction. This is support function for getInteractions(Model
* model).
- *
- * @param rn
- * object representing reactant/product/modifier
- * @param anchId
- * identifier of the anchor where it will be connected
- * @param anchors
- * string builder where anchors are stored (it will be modified to add
- * anchor for this element)
- * @param mainLine
- * line used for connecting this element
+ *
+ * @param rn object representing reactant/product/modifier
+ * @param anchId identifier of the anchor where it will be connected
+ * @param anchors string builder where anchors are stored (it will be modified to add
+ * anchor for this element)
+ * @param mainLine line used for connecting this element
* @return string representing connection of this element to reaction
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * @throws ConverterException thrown when there is a problem with conversion
*/
private String getInteractionForAnchor(final ReactionNode rn, final String anchId, final StringBuilder anchors, final PolylineData mainLine)
throws ConverterException {
- StringBuilder interaction = new StringBuilder("");
+ StringBuilder interaction = new StringBuilder();
PolylineData line = getPolyline(rn, mainLine);
Point2D ps = line.getStartPoint();
@@ -486,16 +472,14 @@ public class ModelToGPML {
/**
* This function encode Species into DataNodes from GPML format. Empty complexes
* are also transformed into DataNodes.
- *
- * @param model
- * model where aliases are placed
+ *
+ * @param model model where aliases are placed
* @return string representing {@link lcsb.mapviewer.wikipathway.model.DataNode
- * data nodes}
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * data nodes}
+ * @throws ConverterException thrown when there is a problem with conversion
*/
protected String getDataNodes(final Model model) throws ConverterException {
- StringBuilder dataNodes = new StringBuilder("");
+ StringBuilder dataNodes = new StringBuilder();
for (final Species species : model.getNotComplexSpeciesList()) {
if (!(species instanceof Complex) && !(species instanceof Degraded)) {
@@ -657,13 +641,12 @@ public class ModelToGPML {
/**
* This function encode ComplexAliases into Groups from GPML format.
- *
- * @param model
- * model where aliases are placed
+ *
+ * @param model model where aliases are placed
* @return string representing groups in GPML format
*/
protected String getGroups(final Model model) {
- StringBuilder groups = new StringBuilder("");
+ StringBuilder groups = new StringBuilder();
for (final Complex complex : model.getComplexList()) {
if (complex.getElements().size() > 0) {
@@ -685,15 +668,13 @@ public class ModelToGPML {
/**
* This function encode Reactions into Interactions from GPML format.
- *
- * @param model
- * model where reactions are placed
+ *
+ * @param model model where reactions are placed
* @return string with interactions in GPML format
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * @throws ConverterException thrown when there is a problem with conversion
*/
protected String getInteractions(final Model model) throws ConverterException {
- StringBuilder interactions = new StringBuilder("");
+ StringBuilder interactions = new StringBuilder();
for (final Reaction reaction : model.getReactions()) {
String reactionArrowHead = InteractionMapping.getGpmlInteractionTypeForMinervaReactionClass(reaction.getClass())
@@ -701,8 +682,8 @@ public class ModelToGPML {
String lineStyle = GpmlLineType.getByLineType(reaction.getLine().getType()).getGpmlString();
- StringBuilder anchors = new StringBuilder("");
- StringBuilder tmp = new StringBuilder("");
+ StringBuilder anchors = new StringBuilder();
+ StringBuilder tmp = new StringBuilder();
interactions.append(" <Interaction GraphId=\"" + reaction.getIdReaction() + "\">\n");
if (reaction.getNotes() != null) {
@@ -767,12 +748,12 @@ public class ModelToGPML {
tmp.append(getInteractionForAnchor(modifier, getNewId(), anchors, line));
}
- interactions.append(anchors.toString());
+ interactions.append(anchors);
interactions.append(" </Graphics>\n");
interactions.append(
referenceParser.toXml(reaction.getMiriamData(), new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction)));
interactions.append(" </Interaction>\n");
- interactions.append(tmp.toString());
+ interactions.append(tmp);
}
return interactions.toString();
@@ -780,15 +761,13 @@ public class ModelToGPML {
/**
* This function returns Model in GPML format.
- *
- * @param model
- * model to transform
+ *
+ * @param model model to transform
* @return string in GPML format representing model
- * @throws ConverterException
- * thrown when there is a problem with conversion
+ * @throws ConverterException thrown when there is a problem with conversion
*/
public String getGPML(final Model model) throws ConverterException {
- StringBuilder gpml = new StringBuilder("");
+ StringBuilder gpml = new StringBuilder();
gpml.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
gpml.append("<Pathway xmlns=\"http://pathvisio.org/GPML/2013a\"");
if (model.getName() != null) {
@@ -845,7 +824,7 @@ public class ModelToGPML {
private String getStates(final Model model) throws ConverterException {
StringBuilder result = new StringBuilder();
- for (final Element element : model.getElements()) {
+ for (final Element element : model.getSortedElements()) {
if (element instanceof SpeciesWithModificationResidue) {
for (final ModificationResidue mr : ((SpeciesWithModificationResidue) element).getModificationResidues()) {
result.append(modifictionResidueToState(mr));
@@ -860,7 +839,7 @@ public class ModelToGPML {
}
protected String getShapes(final Model model) throws ConverterException {
- StringBuilder result = new StringBuilder("");
+ StringBuilder result = new StringBuilder();
result.append(getComparments(model));
for (final Species species : model.getNotComplexSpeciesList()) {