From 605b2066a431051895fbc51e74dfabb0fc0f31ab Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 20 Nov 2017 16:41:34 +0100
Subject: [PATCH] allow filtering by protein class (that is super class for all
types of proteins)
---
.../mapviewer/commands/ColorModelCommand.java | 742 +++++++++---------
.../commands/ColorModelCommandTest.java | 703 +++++++++--------
2 files changed, 742 insertions(+), 703 deletions(-)
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
index ceb5a31f73..534d8432b4 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/ColorModelCommand.java
@@ -1,365 +1,377 @@
-package lcsb.mapviewer.commands;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.ArrowTypeData;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamRelationType;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Product;
-import lcsb.mapviewer.model.map.reaction.Reactant;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
-import lcsb.mapviewer.modelutils.map.ElementUtils;
-
-/**
- * This {@link ModelCommand} colors a model (nodes and reactions) according to
- * set of {@link ColorSchema rules}.
- *
- * @author Piotr Gawron
- *
- */
-public class ColorModelCommand extends ModelCommand {
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private Logger logger = Logger.getLogger(ColorModelCommand.class);
-
- /**
- * Set of color schemas used in this command to color model.
- */
- private Collection<ColorSchema> schemas;
-
- /**
- * Object that helps to convert {@link ColorSchema} values into colors.
- *
- */
- private ColorExtractor colorExtractor;
-
- /**
- * Util class for all {@link BioEntity} elements.
- */
- private ElementUtils eu = new ElementUtils();
-
- /**
- * Default constructor.
- *
- * @param colorExtractor
- * object that helps to convert {@link ColorSchema} values into
- * colors
- * @param model
- * original model
- * @param schemas
- * set of color schemas used in this command to color model.
- */
- public ColorModelCommand(Model model, Collection<ColorSchema> schemas, ColorExtractor colorExtractor) {
- super(model);
- this.schemas = schemas;
- this.colorExtractor = colorExtractor;
- }
-
- /**
- * Applies color schema into the reaction.
- *
- * @param reaction
- * object to be colored
- * @param schema
- * color schema to be used
- * @throws InvalidColorSchemaException
- * thrown when {@link Reaction} was already colored by other schema
- */
- private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
- if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
- throw new InvalidColorSchemaException("At least two rows try to set color to reaction: " + reaction.getIdReaction());
- }
-
- Color color = colorExtractor.getNormalizedColor(schema);
- for (AbstractNode node : reaction.getNodes()) {
- node.getLine().setColor(color);
- if (schema.getLineWidth() != null) {
- node.getLine().setWidth(schema.getLineWidth());
- }
- }
- if (schema.getReverseReaction() != null && schema.getReverseReaction()) {
- ArrowTypeData atdBegining = reaction.getReactants().get(0).getLine().getBeginAtd();
- ArrowTypeData atdEnd = reaction.getProducts().get(0).getLine().getEndAtd();
- for (Reactant reactant : reaction.getReactants()) {
- reactant.getLine().setBeginAtd(atdEnd);
- }
- for (Product product : reaction.getProducts()) {
- product.getLine().setEndAtd(atdBegining);
- }
- }
- }
-
- /**
- * Checks if the coloring schema should be used for the reaction.
- *
- * @param reaction
- * reaction to which coloring schema is checked
- * @param schema
- * coloring schema
- * @return <code>true</code> if coloring schema should be used for
- * {@link Reaction}, <code>false</code> otherwise
- */
- private boolean match(Reaction reaction, ColorSchema schema) {
- if (schema.getName() != null) {
- return false;
- }
-
- if (schema.getReactionIdentifier() != null && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
- return true;
- }
- if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
- MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
- if (reaction.getMiriamData().contains(md)) {
- return true;
- }
- }
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().equals("")) {
-
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
- if (reaction.getMiriamData().contains(md)) {
- return true;
- }
- }
- }
-
- return false;
- }
-
- /**
- * Applies color schema into the {@link Element}.
- *
- * @param element
- * object to be colored
- * @param schema
- * color schema to be used
- * @throws InvalidColorSchemaException
- * thrown when alias was already colored by other schema
- */
- private void applyColor(Element element, ColorSchema schema) throws InvalidColorSchemaException {
- if (element instanceof Species) {
- if (!element.getColor().equals(Color.WHITE)) {
- throw new InvalidColorSchemaException("At least two rows try to set color to element: " + element.getName());
- }
- element.setColor(colorExtractor.getNormalizedColor(schema));
- }
- }
-
- /**
- * Checks if the coloring schema should be used for the {@link Element}.
- *
- * @param element
- * {@link Element} for which coloring schema is checked
- * @param schema
- * coloring schema
- * @return <code>true</code> if coloring schema should be used for
- * {@link Element}, <code>false</code> otherwise
- */
- protected boolean match(Element element, ColorSchema schema) {
- if (element instanceof Species) {
- if (schema.getName() != null) {
- if (!element.getName().equalsIgnoreCase(schema.getName())) {
- return false;
- }
- }
- if (schema.getTypes().size() > 0) {
- if (!schema.getTypes().contains(element.getClass())) {
- return false;
- }
- }
- if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
- MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
-
- if (!element.getMiriamData().contains(md)) {
- return false;
- }
- }
- for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
- if (pair.getRight() != null && !pair.getRight().equals("")) {
- MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
- if (!element.getMiriamData().contains(md)) {
- return false;
- }
- }
- }
-
- if (schema.getCompartments().size() > 0) {
- boolean found = false;
- for (Compartment compartment : element.getModelData().getModel().getCompartments()) {
- for (String compartmentName : schema.getCompartments()) {
- if (compartment.getName().equalsIgnoreCase(compartmentName)) {
- if (compartment.cross(element)) {
- found = true;
- }
- }
- }
- }
- if (!found) {
- return false;
- }
- }
-
- // if we have reaction id to match then reject
- if (schema.getReactionIdentifier() != null) {
- return false;
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Checks which coloring schemas weren't used in the model coloring process.
- *
- * @return list of schemas that weren't used during coloring
- */
- public Collection<ColorSchema> getMissingSchema() {
- List<ColorSchema> result = new ArrayList<ColorSchema>();
- for (ColorSchema schema : schemas) {
- boolean found = false;
- for (Element element : getModel().getElements()) {
- if (match(element, schema)) {
- found = true;
- }
- }
- for (Reaction reaction : getModel().getReactions()) {
- if (match(reaction, schema)) {
- found = true;
- }
- }
- if (!found) {
- result.add(schema);
- }
- }
- return result;
- }
-
- /**
- * Returns list of elements ({@link Reaction reactions} and {@link Element
- * elements}) that are modified by the coloring command.
- *
- * @return {@link Map}, where key corresponds to modified {@link Reaction} or
- * {@link Element} and value is a {@link ColorSchema} that should be
- * used for coloring
- * @throws InvalidColorSchemaException
- * thrown when more than one {@link ColorSchema} match an element
- */
- public Map<Object, ColorSchema> getModifiedElements() throws InvalidColorSchemaException {
- Map<Object, ColorSchema> result = new HashMap<>();
-
- List<Model> models = new ArrayList<>();
- models.add(getModel());
- models.addAll(getModel().getSubmodels());
- for (Model model2 : models) {
- for (ColorSchema schema : schemas) {
- for (Element element : model2.getElements()) {
- if (match(element, schema)) {
- if (result.get(element) != null && !colorExtractor.getNormalizedColor(result.get(element)).equals(Color.WHITE)) {
- throw new InvalidColorSchemaException(eu.getElementTag(element) + "Element is colored by more than one rule.");
- }
- result.put(element, schema);
- }
- }
- for (Reaction reaction : model2.getReactions()) {
- if (match(reaction, schema)) {
- if (result.get(reaction) != null && !colorExtractor.getNormalizedColor(result.get(reaction)).equals(Color.WHITE)) {
- throw new InvalidColorSchemaException(eu.getElementTag(reaction) + "Reaction is colored by more than one rule.");
- }
- result.put(reaction, schema);
- }
- }
- }
- }
- return result;
- }
-
- @Override
- protected void undoImplementation() throws CommandExecutionException {
- throw new NotImplementedException();
-
- }
-
- @Override
- protected void redoImplementation() throws CommandExecutionException {
- throw new NotImplementedException();
- }
-
- /**
- * Colors parameter model using coloring for this command. This method is used
- * internally to color either top {@link Model} or one of it's sumbodels.
- *
- * @param result
- * model to color
- * @param top
- * is the model a top (parent) model
- * @throws InvalidColorSchemaException
- * thrown when set of {@link ColorSchema} is invalid
- */
- private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
-
- for (Element element : result.getElements()) {
- element.setColor(Color.WHITE);
- }
- for (Reaction reaction : result.getReactions()) {
- for (AbstractNode node : reaction.getNodes()) {
- node.getLine().setColor(Color.BLACK);
- }
- }
-
- for (ColorSchema schema : schemas) {
- for (Element element : result.getElements()) {
- if (match(element, schema)) {
- schema.setMatches(schema.getMatches() + 1);
- applyColor(element, schema);
- }
- }
- for (Reaction reaction : result.getReactions()) {
- if (match(reaction, schema)) {
- schema.setMatches(schema.getMatches() + 1);
- applyColor(reaction, schema);
- }
- }
- }
-
- if (top) {
- for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
- colorModel(connection.getSubmodel().getModel(), false);
- }
- }
-
- }
-
- @Override
- protected void executeImplementation() throws CommandExecutionException {
- try {
- colorModel(getModel(), true);
- } catch (InvalidColorSchemaException e) {
- throw new CommandExecutionException(e);
- }
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.ArrowTypeData;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.InvalidColorSchemaException;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.reaction.AbstractNode;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+/**
+ * This {@link ModelCommand} colors a model (nodes and reactions) according to
+ * set of {@link ColorSchema rules}.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class ColorModelCommand extends ModelCommand {
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private Logger logger = Logger.getLogger(ColorModelCommand.class);
+
+ /**
+ * Set of color schemas used in this command to color model.
+ */
+ private Collection<ColorSchema> schemas;
+
+ /**
+ * Object that helps to convert {@link ColorSchema} values into colors.
+ *
+ */
+ private ColorExtractor colorExtractor;
+
+ /**
+ * Util class for all {@link BioEntity} elements.
+ */
+ private ElementUtils eu = new ElementUtils();
+
+ /**
+ * Default constructor.
+ *
+ * @param colorExtractor
+ * object that helps to convert {@link ColorSchema} values into colors
+ * @param model
+ * original model
+ * @param schemas
+ * set of color schemas used in this command to color model.
+ */
+ public ColorModelCommand(Model model, Collection<ColorSchema> schemas, ColorExtractor colorExtractor) {
+ super(model);
+ this.schemas = schemas;
+ this.colorExtractor = colorExtractor;
+ }
+
+ /**
+ * Applies color schema into the reaction.
+ *
+ * @param reaction
+ * object to be colored
+ * @param schema
+ * color schema to be used
+ * @throws InvalidColorSchemaException
+ * thrown when {@link Reaction} was already colored by other schema
+ */
+ private void applyColor(Reaction reaction, ColorSchema schema) throws InvalidColorSchemaException {
+ if (!reaction.getReactants().get(0).getLine().getColor().equals(Color.BLACK)) {
+ throw new InvalidColorSchemaException(
+ "At least two rows try to set color to reaction: " + reaction.getIdReaction());
+ }
+
+ Color color = colorExtractor.getNormalizedColor(schema);
+ for (AbstractNode node : reaction.getNodes()) {
+ node.getLine().setColor(color);
+ if (schema.getLineWidth() != null) {
+ node.getLine().setWidth(schema.getLineWidth());
+ }
+ }
+ if (schema.getReverseReaction() != null && schema.getReverseReaction()) {
+ ArrowTypeData atdBegining = reaction.getReactants().get(0).getLine().getBeginAtd();
+ ArrowTypeData atdEnd = reaction.getProducts().get(0).getLine().getEndAtd();
+ for (Reactant reactant : reaction.getReactants()) {
+ reactant.getLine().setBeginAtd(atdEnd);
+ }
+ for (Product product : reaction.getProducts()) {
+ product.getLine().setEndAtd(atdBegining);
+ }
+ }
+ }
+
+ /**
+ * Checks if the coloring schema should be used for the reaction.
+ *
+ * @param reaction
+ * reaction to which coloring schema is checked
+ * @param schema
+ * coloring schema
+ * @return <code>true</code> if coloring schema should be used for
+ * {@link Reaction}, <code>false</code> otherwise
+ */
+ private boolean match(Reaction reaction, ColorSchema schema) {
+ if (schema.getName() != null) {
+ return false;
+ }
+
+ if (schema.getReactionIdentifier() != null
+ && schema.getReactionIdentifier().equalsIgnoreCase(reaction.getIdReaction())) {
+ return true;
+ }
+ if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
+ MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
+
+ if (reaction.getMiriamData().contains(md)) {
+ return true;
+ }
+ }
+ for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+ if (pair.getRight() != null && !pair.getRight().equals("")) {
+
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
+ if (reaction.getMiriamData().contains(md)) {
+ return true;
+ }
+ }
+ }
+
+ return false;
+ }
+
+ /**
+ * Applies color schema into the {@link Element}.
+ *
+ * @param element
+ * object to be colored
+ * @param schema
+ * color schema to be used
+ * @throws InvalidColorSchemaException
+ * thrown when alias was already colored by other schema
+ */
+ private void applyColor(Element element, ColorSchema schema) throws InvalidColorSchemaException {
+ if (element instanceof Species) {
+ if (!element.getColor().equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException("At least two rows try to set color to element: " + element.getName());
+ }
+ element.setColor(colorExtractor.getNormalizedColor(schema));
+ }
+ }
+
+ /**
+ * Checks if the coloring schema should be used for the {@link Element}.
+ *
+ * @param element
+ * {@link Element} for which coloring schema is checked
+ * @param schema
+ * coloring schema
+ * @return <code>true</code> if coloring schema should be used for
+ * {@link Element}, <code>false</code> otherwise
+ */
+ protected boolean match(Element element, ColorSchema schema) {
+ if (element instanceof Species) {
+ if (schema.getName() != null) {
+ if (!element.getName().equalsIgnoreCase(schema.getName())) {
+ return false;
+ }
+ }
+ if (schema.getTypes().size() > 0) {
+ boolean found = false;
+ for (Class<?> clazz : schema.getTypes()) {
+ if (clazz.isAssignableFrom(element.getClass())) {
+ found = true;
+ }
+ }
+
+ if (!found) {
+ return false;
+ }
+ }
+ if (schema.getGeneralIdentifier() != null && !schema.getGeneralIdentifier().equals("")) {
+ MiriamData md = MiriamType.getMiriamDataFromIdentifier(schema.getGeneralIdentifier());
+
+ if (!element.getMiriamData().contains(md)) {
+ return false;
+ }
+ }
+ for (Pair<MiriamType, String> pair : schema.getIdentifierColumns()) {
+ if (pair.getRight() != null && !pair.getRight().equals("")) {
+ MiriamData md = new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, pair.getLeft(), pair.getRight());
+ if (!element.getMiriamData().contains(md)) {
+ return false;
+ }
+ }
+ }
+
+ if (schema.getCompartments().size() > 0) {
+ boolean found = false;
+ for (Compartment compartment : element.getModelData().getModel().getCompartments()) {
+ for (String compartmentName : schema.getCompartments()) {
+ if (compartment.getName().equalsIgnoreCase(compartmentName)) {
+ if (compartment.cross(element)) {
+ found = true;
+ }
+ }
+ }
+ }
+ if (!found) {
+ return false;
+ }
+ }
+
+ // if we have reaction id to match then reject
+ if (schema.getReactionIdentifier() != null) {
+ return false;
+ }
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Checks which coloring schemas weren't used in the model coloring process.
+ *
+ * @return list of schemas that weren't used during coloring
+ */
+ public Collection<ColorSchema> getMissingSchema() {
+ List<ColorSchema> result = new ArrayList<ColorSchema>();
+ for (ColorSchema schema : schemas) {
+ boolean found = false;
+ for (Element element : getModel().getElements()) {
+ if (match(element, schema)) {
+ found = true;
+ }
+ }
+ for (Reaction reaction : getModel().getReactions()) {
+ if (match(reaction, schema)) {
+ found = true;
+ }
+ }
+ if (!found) {
+ result.add(schema);
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns list of elements ({@link Reaction reactions} and {@link Element
+ * elements}) that are modified by the coloring command.
+ *
+ * @return {@link Map}, where key corresponds to modified {@link Reaction} or
+ * {@link Element} and value is a {@link ColorSchema} that should be
+ * used for coloring
+ * @throws InvalidColorSchemaException
+ * thrown when more than one {@link ColorSchema} match an element
+ */
+ public Map<Object, ColorSchema> getModifiedElements() throws InvalidColorSchemaException {
+ Map<Object, ColorSchema> result = new HashMap<>();
+
+ List<Model> models = new ArrayList<>();
+ models.add(getModel());
+ models.addAll(getModel().getSubmodels());
+ for (Model model2 : models) {
+ for (ColorSchema schema : schemas) {
+ for (Element element : model2.getElements()) {
+ if (match(element, schema)) {
+ if (result.get(element) != null
+ && !colorExtractor.getNormalizedColor(result.get(element)).equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException(
+ eu.getElementTag(element) + "Element is colored by more than one rule.");
+ }
+ result.put(element, schema);
+ }
+ }
+ for (Reaction reaction : model2.getReactions()) {
+ if (match(reaction, schema)) {
+ if (result.get(reaction) != null
+ && !colorExtractor.getNormalizedColor(result.get(reaction)).equals(Color.WHITE)) {
+ throw new InvalidColorSchemaException(
+ eu.getElementTag(reaction) + "Reaction is colored by more than one rule.");
+ }
+ result.put(reaction, schema);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ @Override
+ protected void undoImplementation() throws CommandExecutionException {
+ throw new NotImplementedException();
+
+ }
+
+ @Override
+ protected void redoImplementation() throws CommandExecutionException {
+ throw new NotImplementedException();
+ }
+
+ /**
+ * Colors parameter model using coloring for this command. This method is used
+ * internally to color either top {@link Model} or one of it's sumbodels.
+ *
+ * @param result
+ * model to color
+ * @param top
+ * is the model a top (parent) model
+ * @throws InvalidColorSchemaException
+ * thrown when set of {@link ColorSchema} is invalid
+ */
+ private void colorModel(Model result, boolean top) throws InvalidColorSchemaException {
+
+ for (Element element : result.getElements()) {
+ element.setColor(Color.WHITE);
+ }
+ for (Reaction reaction : result.getReactions()) {
+ for (AbstractNode node : reaction.getNodes()) {
+ node.getLine().setColor(Color.BLACK);
+ }
+ }
+
+ for (ColorSchema schema : schemas) {
+ for (Element element : result.getElements()) {
+ if (match(element, schema)) {
+ schema.setMatches(schema.getMatches() + 1);
+ applyColor(element, schema);
+ }
+ }
+ for (Reaction reaction : result.getReactions()) {
+ if (match(reaction, schema)) {
+ schema.setMatches(schema.getMatches() + 1);
+ applyColor(reaction, schema);
+ }
+ }
+ }
+
+ if (top) {
+ for (ModelSubmodelConnection connection : result.getSubmodelConnections()) {
+ colorModel(connection.getSubmodel().getModel(), false);
+ }
+ }
+
+ }
+
+ @Override
+ protected void executeImplementation() throws CommandExecutionException {
+ try {
+ colorModel(getModel(), true);
+ } catch (InvalidColorSchemaException e) {
+ throw new CommandExecutionException(e);
+ }
+ }
+
+}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
index 8bc1cd05cb..6514aa1dc9 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/ColorModelCommandTest.java
@@ -1,338 +1,365 @@
-package lcsb.mapviewer.commands;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.ColorSchema;
-import lcsb.mapviewer.model.map.layout.GenericColorSchema;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelComparator;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
-import lcsb.mapviewer.model.map.model.SubmodelType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.GenericProtein;
-
-public class ColorModelCommandTest extends CommandTestFunctions {
- Logger logger = Logger.getLogger(ColorModelCommandTest.class);
-
- ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- /**
- * Test if all elements were copied - if not hibernate will complain
- *
- * @throws Exception
- *
- */
- @Test
- public void testColorFullModel() throws Exception {
- ModelComparator comparator = new ModelComparator();
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model model2 = getModelForFile("testFiles/sample.xml", false);
- Model coloredModel = new CopyCommand(model).execute();
-
- List<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setName("CNC");
- schema.setValue(-1.0);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas, colorExtractor);
-
- assertFalse(Color.RED.equals(coloredModel.getElementByElementId("sa14").getColor()));
-
- factory.execute();
-
- assertEquals(0, comparator.compare(model, model2));
-
- assertFalse(comparator.compare(model, coloredModel) == 0);
-
- assertEquals(Color.RED, coloredModel.getElementByElementId("sa14").getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoring2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/coloring_model.xml", true);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setGeneralIdentifier("HGNC:11138");
- schema.setValue(1.0);
- schemas.add(schema);
- schema = new GenericColorSchema();
- schema.setGeneralIdentifier("CHEBI:CHEBI:15377");
- schema.setValue(1.0);
- schemas.add(schema);
- schema = new GenericColorSchema();
- schema.setGeneralIdentifier("CHEBI:CHEBI:15376");
- schema.setValue(1.0);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- Collection<ColorSchema> missing = factory.getMissingSchema();
-
- assertEquals(1, missing.size());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring1() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re4 = model.getReactionByReactionId("re4");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
-
- factory.execute();
- re4 = model.getReactionByReactionId("re4");
-
- assertEquals(Color.BLACK, re4.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re1 = model.getReactionByReactionId("re1");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
- schema.setColor(Color.RED);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
-
- factory.execute();
- re1 = model.getReactionByReactionId("re1");
-
- assertEquals(Color.RED, re1.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring3() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re2 = model.getReactionByReactionId("re2");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re2");
- schema.setValue(-1.0);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
- assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
-
- factory.execute();
- re2 = model.getReactionByReactionId("re2");
-
- assertEquals(Color.RED, re2.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testReactionColoring4() throws Exception {
- try {
- Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
- Reaction re3 = model.getReactionByReactionId("re3");
- Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
- ColorSchema schema = new GenericColorSchema();
- Pair<MiriamType, String> pair = new Pair<MiriamType, String>(MiriamType.PUBMED, "12345");
- List<Pair<MiriamType, String>> identifiers = new ArrayList<Pair<MiriamType, String>>();
- identifiers.add(pair);
-
- schema.setIdentifierColumns(identifiers);
- schema.setValue(-1.0);
- schemas.add(schema);
-
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
-
- assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
-
- factory.execute();
- re3 = model.getReactionByReactionId("re3");
-
- assertEquals(Color.RED, re3.getNodes().get(0).getLine().getColor());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoringComplexModel() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model model2 = getModelForFile("testFiles/sample.xml", false);
-
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "BLA"));
-
- Collection<ColorSchema> schemas = new ArrayList<>();
- Model coloredModel = new CopyCommand(model).execute();
- new ColorModelCommand(coloredModel, schemas, colorExtractor).execute();
-
- Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
- Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
-
- assertFalse(coloredModel2.getElementByElementId("sa2").getColor().equals(model2.getElementByElementId("sa2").getColor()));
- assertFalse(coloredModel3.getElementByElementId("sa2").getColor().equals(model2.getElementByElementId("sa2").getColor()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoredAliases() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setName("CNC");
- schema.setColor(Color.BLUE);
- schemas.add(schema);
- schema = new GenericColorSchema();
- schema.setName("BDH1");
- schema.setColor(Color.BLUE);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
-
- Map<Object, ColorSchema> map = factory.getModifiedElements();
- assertEquals(2, map.size());
- for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
- assertTrue(entry.getKey() instanceof Element);
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoredReactions() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
- schema.setLineWidth(3.0);
- schema.setColor(Color.BLUE);
- schema.setName("");
- schema.setReverseReaction(true);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
-
- Map<Object, ColorSchema> map = factory.getModifiedElements();
- assertEquals(0, map.size());
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testColoredReactions2() throws Exception {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Collection<ColorSchema> schemas = new ArrayList<>();
- ColorSchema schema = new GenericColorSchema();
- schema.setReactionIdentifier("re1");
- schema.setLineWidth(3.0);
- schema.setColor(Color.BLUE);
- schema.setName(null);
- schema.setReverseReaction(true);
- schemas.add(schema);
- ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
-
- Map<Object, ColorSchema> map = factory.getModifiedElements();
- assertEquals(1, map.size());
- for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
- assertTrue(entry.getKey() instanceof Reaction);
- assertEquals("re1", ((Reaction) entry.getKey()).getIdReaction());
- assertEquals(entry.getValue(), schema);
- }
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testAliasMatchWithReactionId() throws Exception {
- try {
- GenericColorSchema colorSchema = new GenericColorSchema();
- colorSchema.setName(null);
- colorSchema.setReactionIdentifier("1");
-
- GenericProtein alias = new GenericProtein("id");
- alias.setName("test");
-
- List<ColorSchema> schemas = new ArrayList<>();
- schemas.add(colorSchema);
-
- ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
-
- assertFalse(factory.match(alias, colorSchema));
-
- colorSchema.setReactionIdentifier(null);
- assertTrue(factory.match(alias, colorSchema));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
-
- }
-
-}
+package lcsb.mapviewer.commands;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.ColorSchema;
+import lcsb.mapviewer.model.map.layout.GenericColorSchema;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
+import lcsb.mapviewer.model.map.model.SubmodelType;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.map.species.GenericProtein;
+import lcsb.mapviewer.model.map.species.Protein;
+
+public class ColorModelCommandTest extends CommandTestFunctions {
+ Logger logger = Logger.getLogger(ColorModelCommandTest.class);
+
+ ColorExtractor colorExtractor = new ColorExtractor(Color.RED, Color.GREEN, Color.BLUE);
+
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ /**
+ * Test if all elements were copied - if not hibernate will complain
+ *
+ * @throws Exception
+ *
+ */
+ @Test
+ public void testColorFullModel() throws Exception {
+ ModelComparator comparator = new ModelComparator();
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Model model2 = getModelForFile("testFiles/sample.xml", false);
+ Model coloredModel = new CopyCommand(model).execute();
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setName("CNC");
+ schema.setValue(-1.0);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(coloredModel, schemas, colorExtractor);
+
+ assertFalse(Color.RED.equals(coloredModel.getElementByElementId("sa14").getColor()));
+
+ factory.execute();
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ assertFalse(comparator.compare(model, coloredModel) == 0);
+
+ assertEquals(Color.RED, coloredModel.getElementByElementId("sa14").getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoring2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/coloring_model.xml", true);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setGeneralIdentifier("HGNC:11138");
+ schema.setValue(1.0);
+ schemas.add(schema);
+ schema = new GenericColorSchema();
+ schema.setGeneralIdentifier("CHEBI:CHEBI:15377");
+ schema.setValue(1.0);
+ schemas.add(schema);
+ schema = new GenericColorSchema();
+ schema.setGeneralIdentifier("CHEBI:CHEBI:15376");
+ schema.setValue(1.0);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ Collection<ColorSchema> missing = factory.getMissingSchema();
+
+ assertEquals(1, missing.size());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring1() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re4 = model.getReactionByReactionId("re4");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ assertFalse(Color.BLACK.equals(re4.getNodes().get(0).getLine().getColor()));
+
+ factory.execute();
+ re4 = model.getReactionByReactionId("re4");
+
+ assertEquals(Color.BLACK, re4.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re1 = model.getReactionByReactionId("re1");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re1");
+ schema.setColor(Color.RED);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ assertEquals(Color.BLACK, re1.getNodes().get(0).getLine().getColor());
+
+ factory.execute();
+ re1 = model.getReactionByReactionId("re1");
+
+ assertEquals(Color.RED, re1.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring3() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re2 = model.getReactionByReactionId("re2");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re2");
+ schema.setValue(-1.0);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+ assertEquals(Color.BLACK, re2.getNodes().get(0).getLine().getColor());
+
+ factory.execute();
+ re2 = model.getReactionByReactionId("re2");
+
+ assertEquals(Color.RED, re2.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testReactionColoring4() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/reactions_to_color.xml", false);
+ Reaction re3 = model.getReactionByReactionId("re3");
+ Collection<ColorSchema> schemas = new ArrayList<ColorSchema>();
+ ColorSchema schema = new GenericColorSchema();
+ Pair<MiriamType, String> pair = new Pair<MiriamType, String>(MiriamType.PUBMED, "12345");
+ List<Pair<MiriamType, String>> identifiers = new ArrayList<Pair<MiriamType, String>>();
+ identifiers.add(pair);
+
+ schema.setIdentifierColumns(identifiers);
+ schema.setValue(-1.0);
+ schemas.add(schema);
+
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+
+ assertEquals(Color.BLACK, re3.getNodes().get(0).getLine().getColor());
+
+ factory.execute();
+ re3 = model.getReactionByReactionId("re3");
+
+ assertEquals(Color.RED, re3.getNodes().get(0).getLine().getColor());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoringComplexModel() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Model model2 = getModelForFile("testFiles/sample.xml", false);
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.UNKNOWN, "BLA"));
+
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ Model coloredModel = new CopyCommand(model).execute();
+ new ColorModelCommand(coloredModel, schemas, colorExtractor).execute();
+
+ Model coloredModel2 = coloredModel.getSubmodelConnections().iterator().next().getSubmodel().getModel();
+ Model coloredModel3 = coloredModel.getSubmodelByConnectionName("BLA");
+
+ assertFalse(
+ coloredModel2.getElementByElementId("sa2").getColor().equals(model2.getElementByElementId("sa2").getColor()));
+ assertFalse(
+ coloredModel3.getElementByElementId("sa2").getColor().equals(model2.getElementByElementId("sa2").getColor()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoredAliases() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setName("CNC");
+ schema.setColor(Color.BLUE);
+ schemas.add(schema);
+ schema = new GenericColorSchema();
+ schema.setName("BDH1");
+ schema.setColor(Color.BLUE);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(2, map.size());
+ for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
+ assertTrue(entry.getKey() instanceof Element);
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoredReactions() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re1");
+ schema.setLineWidth(3.0);
+ schema.setColor(Color.BLUE);
+ schema.setName("");
+ schema.setReverseReaction(true);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(0, map.size());
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testColoredReactions2() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Collection<ColorSchema> schemas = new ArrayList<>();
+ ColorSchema schema = new GenericColorSchema();
+ schema.setReactionIdentifier("re1");
+ schema.setLineWidth(3.0);
+ schema.setColor(Color.BLUE);
+ schema.setName(null);
+ schema.setReverseReaction(true);
+ schemas.add(schema);
+ ColorModelCommand factory = new ColorModelCommand(model, schemas, colorExtractor);
+
+ Map<Object, ColorSchema> map = factory.getModifiedElements();
+ assertEquals(1, map.size());
+ for (Map.Entry<Object, ColorSchema> entry : map.entrySet()) {
+ assertTrue(entry.getKey() instanceof Reaction);
+ assertEquals("re1", ((Reaction) entry.getKey()).getIdReaction());
+ assertEquals(entry.getValue(), schema);
+ }
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testAliasMatchWithReactionId() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.setName(null);
+ colorSchema.setReactionIdentifier("1");
+
+ GenericProtein protein = new GenericProtein("id");
+ protein.setName("test");
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertFalse(factory.match(protein, colorSchema));
+
+ colorSchema.setReactionIdentifier(null);
+ assertTrue(factory.match(protein, colorSchema));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+ @Test
+ public void testSpeciesMatchWithProteinType() throws Exception {
+ try {
+ GenericColorSchema colorSchema = new GenericColorSchema();
+ colorSchema.setName("s1");
+ colorSchema.addType(Protein.class);
+
+ GenericProtein species = new GenericProtein("id");
+ species.setName("s1");
+
+ List<ColorSchema> schemas = new ArrayList<>();
+ schemas.add(colorSchema);
+
+ ColorModelCommand factory = new ColorModelCommand(new ModelFullIndexed(null), schemas, colorExtractor);
+
+ assertTrue(factory.match(species, colorSchema));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+
+ }
+
+}
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