diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
index 3917a84ce5cc673ab1c41937b2a3b91e8a19b746..9f6fad6b9175a2d68ac0993d383d7733c9d92188 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
@@ -1,6 +1,8 @@
package lcsb.mapviewer.commands;
+import java.util.Collection;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Map;
import org.apache.log4j.Logger;
@@ -11,6 +13,11 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
import lcsb.mapviewer.model.map.layout.Layout;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
@@ -32,356 +39,390 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class CopyCommand extends NewModelCommand {
- /**
- * Defaul class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(CopyCommand.class);
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link #model}
- */
- public CopyCommand(Model model) {
- super(model);
- }
-
- /**
- * Executed the operation.
- *
- * @return copy of the model
- */
- public Model execute() {
- Map<Model, Model> copies = new HashMap<>();
-
- Model model = getModel();
-
- if (model.getModelData().getParentModels().size() > 0) {
- ModelSubmodelConnection parent = null;
- for (SubmodelConnection connection : model.getModelData().getParentModels()) {
- if (connection instanceof ModelSubmodelConnection) {
- if (parent != null) {
- throw new InvalidArgumentException("It looks like the model is a submodel, but has more than one parent...");
- } else {
- parent = (ModelSubmodelConnection) connection;
- }
- }
- }
- if (parent != null) {
- CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
- Model copy = copyParentCommand.execute();
- for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
- if (submodel.getName().equals(parent.getName())) {
- return submodel.getSubmodel().getModel();
- }
- }
- throw new InvalidStateException("Problem with copying submodel of a model");
- }
- }
-
- Model result = createNotNestedCopy(model);
-
- copies.put(model, result);
-
- for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
- Model submodel = submodelConnection.getSubmodel().getModel();
- Model submodelCopy = createNotNestedCopy(submodel);
- copies.put(submodel, submodelCopy);
- }
- for (Model modelCopy : copies.values()) {
- try {
- assignModelCopies(modelCopy, copies);
- } catch (InvalidModelException e) {
- throw new InvalidArgumentException(e);
- }
- }
- return result;
-
- }
-
- /**
- * Assign information about submodel to the copied links.
- *
- * @param modelCopy
- * copy of a model where substitution should be made
- * @param copies
- * map with map copies
- * @throws InvalidModelException
- * when there is inconsistency in data
- */
- private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
- for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
- // copy connection reference
- Model original = connection.getSubmodel().getModel();
- Model copy = copies.get(original);
- if (copy == null) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- connection.setSubmodel(copy);
-
- // copy connection parent reference
- if (connection.getParentModel() != null) {
- original = connection.getParentModel().getModel();
- if (original != null) {
- copy = copies.get(original);
- if (copy == null) {
- if (!copies.values().contains(original)) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- } else {
- connection.setParentModel(copy);
- }
- }
- }
- }
- for (Element alias : modelCopy.getElements()) {
- // if alias has connection to submodel
- if (alias.getSubmodel() != null) {
- ElementSubmodelConnection connection = alias.getSubmodel();
- // copy information about submodel
- Model original = connection.getSubmodel().getModel();
- Model copy = copies.get(original);
- if (copy == null) {
- throw new InvalidModelException("Original model contain reference to model that wasn't copied");
- }
- connection.setSubmodel(copy);
-
- // copy information about original alias
- if (connection.getFromElement() != null) {
- connection.setFromElement(modelCopy.getElementByElementId(connection.getFromElement().getElementId()));
- }
- // copy information about reference alias
- if (connection.getToElement() != null) {
- connection.setToElement(modelCopy.getElementByElementId(connection.getToElement().getElementId()));
- }
- }
- }
- }
-
- /**
- * Creates copy of the model without modifing information about submodels
- * (information about original submodels will be left in the copy).
- *
- * @param model
- * original model to copy
- * @return copy of the model
- */
- protected Model createNotNestedCopy(Model model) {
- Model result = new ModelFullIndexed(null);
-
- for (Element alias : model.getElements()) {
- if (alias instanceof Compartment) {
- Compartment copy = ((Compartment) alias).copy();
- copy.getElements().clear();
- copy.setCompartment(null);
- result.addElement(copy);
- }
-
- }
-
- for (Element alias : model.getElements()) {
- if (alias instanceof Species) {
- Species copy = ((Species) alias).copy();
- copy.setCompartment(null);
- result.addElement(copy);
-
- Compartment parentCompartment = alias.getCompartment();
-
- if (parentCompartment != null) {
- parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
- copy.setCompartment(parentCompartment);
- }
-
- } else if (alias instanceof Compartment) {
-
- Compartment parentCompartment = alias.getCompartment();
-
- if (parentCompartment != null) {
- Compartment copy = result.getElementByElementId(alias.getElementId());
- parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
- copy.setCompartment(parentCompartment);
- }
- } else {
- throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
- }
- }
-
- for (Layer layer : model.getLayers()) {
- result.addLayer(layer.copy());
- }
-
- for (Reaction reaction : model.getReactions()) {
- result.addReaction(createCopy(reaction));
- }
-
- assignSimpleDataToCopy(result, model);
- for (Layout layout : model.getLayouts()) {
- result.addLayout(layout.copy());
- }
- result.setProject(model.getProject());
-
- for (Element alias : result.getElements()) {
- updateAliasReferences(alias, result, model);
- }
- for (Reaction reaction : result.getReactions()) {
- updateReactionReferences(reaction, result);
- }
- for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
- result.addSubmodelConnection(connection.copy());
- }
- for (DataMiningSet dataMiningSet : model.getDataMiningSets()) {
- result.addDataMiningSet(new DataMiningSet(dataMiningSet));
- }
- return result;
- }
-
- /**
- * Copies simple information about model to the copy.
- *
- * @param copy
- * to this model data will be copied
- * @param original
- * original model
- */
- private void assignSimpleDataToCopy(Model copy, Model original) {
- copy.setName(original.getName());
-
- copy.setCreationDate(original.getCreationDate());
-
- copy.setWidth(original.getWidth());
- copy.setHeight(original.getHeight());
- copy.setNotes(original.getNotes());
- copy.setIdModel(original.getIdModel());
- copy.setZoomLevels(original.getZoomLevels());
- copy.setTileSize(original.getTileSize());
- }
-
- /**
- * Creates copy of the reaction that doesn't contain any references to the
- * original (so we have to substitute all references with the new ones...).
- *
- * @param reaction
- * original reaction
- * @return copy of the reaction
- */
- private Reaction createCopy(Reaction reaction) {
- Reaction copy = reaction.copy();
- reaction.getNodes().clear();
- for (AbstractNode node : copy.getNodes()) {
- reaction.addNode(node);
- }
- copy.getNodes().clear();
-
- for (AbstractNode node : reaction.getNodes()) {
- AbstractNode nodeCopy = node.copy();
- nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
- copy.addNode(nodeCopy);
- }
-
- for (int i = 0; i < copy.getOperators().size(); i++) {
- NodeOperator nodeCopy = copy.getOperators().get(i);
- NodeOperator nodeOriginal = reaction.getOperators().get(i);
- for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
- AbstractNode input = nodeCopy.getInputs().get(j);
- int index1 = reaction.getOperators().indexOf(input);
- int index2 = reaction.getNodes().indexOf(input);
- if (index1 >= 0) {
- nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
- copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
-
- reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
- } else if (index2 >= 0) {
- nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
- copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
-
- reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
- } else {
- throw new InvalidStateException("WTF");
- }
- }
-
- for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
- AbstractNode output = nodeCopy.getOutputs().get(j);
- int index1 = reaction.getOperators().indexOf(output);
- int index2 = reaction.getNodes().indexOf(output);
- if (index1 >= 0) {
- nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
- copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
-
- reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
- } else if (index2 >= 0) {
- nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
- copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
-
- reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
- } else {
- throw new InvalidStateException("WTF");
- }
- }
- }
-
- return copy;
- }
-
- /**
- * Updates references to elements and aliases in reaction to the objects taken
- * from model.
- *
- * @param reaction
- * references in this reaction will be updated
- * @param model
- * references from this model will be taken
- */
- private void updateReactionReferences(Reaction reaction, Model model) {
- reaction.setModel(model);
- for (ReactionNode rNode : reaction.getReactionNodes()) {
- rNode.setElement(model.getElementByElementId(rNode.getElement().getElementId()));
- }
-
- }
-
- /**
- * Updates information (like elements, parent aliases) in the alias with the
- * data from new model.
- *
- * @param alias
- * object to be updated
- * @param model
- * data from this model will be used for update
- * @param originalModel
- * original model from which alias copy was created
- */
- private void updateAliasReferences(Element alias, Model model, Model originalModel) {
- if (alias instanceof Compartment) {
- Compartment compartmentAlias = (Compartment) alias;
- Compartment original = originalModel.getElementByElementId(alias.getElementId());
- for (Element a : original.getElements()) {
- compartmentAlias.addElement(model.getElementByElementId(a.getElementId()));
- }
- }
-
- if (alias instanceof Complex) {
- Complex ca = (Complex) alias;
- for (int i = 0; i < ca.getElements().size(); i++) {
- Species newAlias = (Species) model.getElementByElementId(ca.getElements().get(i).getElementId());
- ca.getElements().set(i, newAlias);
- }
- }
- if (alias instanceof Species) {
- Species sa = (Species) alias;
-
- if (sa.getComplex() != null) {
- sa.setComplex((Complex) model.getElementByElementId(sa.getComplex().getElementId()));
- }
-
- }
-
- alias.setModel(model);
-
- if (alias.getCompartment() != null) {
- alias.setCompartment(model.getElementByElementId(alias.getCompartment().getElementId()));
- }
- }
+ /**
+ * Defaul class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(CopyCommand.class);
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link #model}
+ */
+ public CopyCommand(Model model) {
+ super(model);
+ }
+
+ /**
+ * Executed the operation.
+ *
+ * @return copy of the model
+ */
+ public Model execute() {
+ Map<Model, Model> copies = new HashMap<>();
+
+ Model model = getModel();
+
+ if (model.getModelData().getParentModels().size() > 0) {
+ ModelSubmodelConnection parent = null;
+ for (SubmodelConnection connection : model.getModelData().getParentModels()) {
+ if (connection instanceof ModelSubmodelConnection) {
+ if (parent != null) {
+ throw new InvalidArgumentException(
+ "It looks like the model is a submodel, but has more than one parent...");
+ } else {
+ parent = (ModelSubmodelConnection) connection;
+ }
+ }
+ }
+ if (parent != null) {
+ CopyCommand copyParentCommand = new CopyCommand(parent.getParentModel().getModel());
+ Model copy = copyParentCommand.execute();
+ for (ModelSubmodelConnection submodel : copy.getSubmodelConnections()) {
+ if (submodel.getName().equals(parent.getName())) {
+ return submodel.getSubmodel().getModel();
+ }
+ }
+ throw new InvalidStateException("Problem with copying submodel of a model");
+ }
+ }
+
+ Model result = createNotNestedCopy(model);
+
+ copies.put(model, result);
+
+ for (ModelSubmodelConnection submodelConnection : model.getSubmodelConnections()) {
+ Model submodel = submodelConnection.getSubmodel().getModel();
+ Model submodelCopy = createNotNestedCopy(submodel);
+ copies.put(submodel, submodelCopy);
+ }
+ for (Model modelCopy : copies.values()) {
+ try {
+ assignModelCopies(modelCopy, copies);
+ } catch (InvalidModelException e) {
+ throw new InvalidArgumentException(e);
+ }
+ }
+ return result;
+
+ }
+
+ /**
+ * Assign information about submodel to the copied links.
+ *
+ * @param modelCopy
+ * copy of a model where substitution should be made
+ * @param copies
+ * map with map copies
+ * @throws InvalidModelException
+ * when there is inconsistency in data
+ */
+ private void assignModelCopies(Model modelCopy, Map<Model, Model> copies) throws InvalidModelException {
+ for (ModelSubmodelConnection connection : modelCopy.getSubmodelConnections()) {
+ // copy connection reference
+ Model original = connection.getSubmodel().getModel();
+ Model copy = copies.get(original);
+ if (copy == null) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ connection.setSubmodel(copy);
+
+ // copy connection parent reference
+ if (connection.getParentModel() != null) {
+ original = connection.getParentModel().getModel();
+ if (original != null) {
+ copy = copies.get(original);
+ if (copy == null) {
+ if (!copies.values().contains(original)) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ } else {
+ connection.setParentModel(copy);
+ }
+ }
+ }
+ }
+ for (Element alias : modelCopy.getElements()) {
+ // if alias has connection to submodel
+ if (alias.getSubmodel() != null) {
+ ElementSubmodelConnection connection = alias.getSubmodel();
+ // copy information about submodel
+ Model original = connection.getSubmodel().getModel();
+ Model copy = copies.get(original);
+ if (copy == null) {
+ throw new InvalidModelException("Original model contain reference to model that wasn't copied");
+ }
+ connection.setSubmodel(copy);
+
+ // copy information about original alias
+ if (connection.getFromElement() != null) {
+ connection.setFromElement(modelCopy.getElementByElementId(connection.getFromElement().getElementId()));
+ }
+ // copy information about reference alias
+ if (connection.getToElement() != null) {
+ connection.setToElement(modelCopy.getElementByElementId(connection.getToElement().getElementId()));
+ }
+ }
+ }
+ }
+
+ /**
+ * Creates copy of the model without modifying information about submodels
+ * (information about original submodels will be left in the copy).
+ *
+ * @param model
+ * original model to copy
+ * @return copy of the model
+ */
+ protected Model createNotNestedCopy(Model model) {
+ Model result = new ModelFullIndexed(null);
+
+ for (SbmlUnit unit : model.getUnits()) {
+ result.addUnit(unit.copy());
+ }
+
+ for (SbmlFunction function : model.getFunctions()) {
+ result.addFunction(function.copy());
+ }
+
+ for (SbmlParameter parameter : model.getParameters()) {
+ result.addParameter(parameter.copy());
+ }
+
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Compartment) {
+ Compartment copy = ((Compartment) alias).copy();
+ copy.getElements().clear();
+ copy.setCompartment(null);
+ result.addElement(copy);
+ }
+
+ }
+
+ for (Element alias : model.getElements()) {
+ if (alias instanceof Species) {
+ Species copy = ((Species) alias).copy();
+ copy.setCompartment(null);
+ result.addElement(copy);
+
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
+ }
+
+ } else if (alias instanceof Compartment) {
+
+ Compartment parentCompartment = alias.getCompartment();
+
+ if (parentCompartment != null) {
+ Compartment copy = result.getElementByElementId(alias.getElementId());
+ parentCompartment = result.getElementByElementId(parentCompartment.getElementId());
+ copy.setCompartment(parentCompartment);
+ }
+ } else {
+ throw new InvalidClassException("Don't know what to do with: " + alias.getClass());
+ }
+ }
+
+ for (Layer layer : model.getLayers()) {
+ result.addLayer(layer.copy());
+ }
+
+ for (Reaction reaction : model.getReactions()) {
+ result.addReaction(createCopy(reaction));
+ }
+
+ assignSimpleDataToCopy(result, model);
+ for (Layout layout : model.getLayouts()) {
+ result.addLayout(layout.copy());
+ }
+ result.setProject(model.getProject());
+
+ for (Element element : result.getElements()) {
+ updateElementReferences(element, result, model);
+ }
+ for (Reaction reaction : result.getReactions()) {
+ updateReactionReferences(reaction, result);
+ }
+ for (ModelSubmodelConnection connection : model.getSubmodelConnections()) {
+ result.addSubmodelConnection(connection.copy());
+ }
+ for (DataMiningSet dataMiningSet : model.getDataMiningSets()) {
+ result.addDataMiningSet(new DataMiningSet(dataMiningSet));
+ }
+ return result;
+ }
+
+ /**
+ * Copies simple information about model to the copy.
+ *
+ * @param copy
+ * to this model data will be copied
+ * @param original
+ * original model
+ */
+ private void assignSimpleDataToCopy(Model copy, Model original) {
+ copy.setName(original.getName());
+
+ copy.setCreationDate(original.getCreationDate());
+
+ copy.setWidth(original.getWidth());
+ copy.setHeight(original.getHeight());
+ copy.setNotes(original.getNotes());
+ copy.setIdModel(original.getIdModel());
+ copy.setZoomLevels(original.getZoomLevels());
+ copy.setTileSize(original.getTileSize());
+ }
+
+ /**
+ * Creates copy of the reaction that doesn't contain any references to the
+ * original (so we have to substitute all references with the new ones...).
+ *
+ * @param reaction
+ * original reaction
+ * @return copy of the reaction
+ */
+ private Reaction createCopy(Reaction reaction) {
+ Reaction copy = reaction.copy();
+ reaction.getNodes().clear();
+ for (AbstractNode node : copy.getNodes()) {
+ reaction.addNode(node);
+ }
+ copy.getNodes().clear();
+
+ for (AbstractNode node : reaction.getNodes()) {
+ AbstractNode nodeCopy = node.copy();
+ nodeCopy.setLine(new PolylineData(nodeCopy.getLine()));
+ copy.addNode(nodeCopy);
+ }
+
+ for (int i = 0; i < copy.getOperators().size(); i++) {
+ NodeOperator nodeCopy = copy.getOperators().get(i);
+ NodeOperator nodeOriginal = reaction.getOperators().get(i);
+ for (int j = 0; j < nodeCopy.getInputs().size(); j++) {
+ AbstractNode input = nodeCopy.getInputs().get(j);
+ int index1 = reaction.getOperators().indexOf(input);
+ int index2 = reaction.getNodes().indexOf(input);
+ if (index1 >= 0) {
+ nodeCopy.getInputs().set(j, copy.getOperators().get(index1));
+ copy.getOperators().get(index1).setNodeOperatorForInput(nodeCopy);
+
+ reaction.getOperators().get(index1).setNodeOperatorForInput(nodeOriginal);
+ } else if (index2 >= 0) {
+ nodeCopy.getInputs().set(j, copy.getNodes().get(index2));
+ copy.getNodes().get(index2).setNodeOperatorForInput(nodeCopy);
+
+ reaction.getNodes().get(index2).setNodeOperatorForInput(nodeOriginal);
+ } else {
+ throw new InvalidStateException("WTF");
+ }
+ }
+
+ for (int j = 0; j < nodeCopy.getOutputs().size(); j++) {
+ AbstractNode output = nodeCopy.getOutputs().get(j);
+ int index1 = reaction.getOperators().indexOf(output);
+ int index2 = reaction.getNodes().indexOf(output);
+ if (index1 >= 0) {
+ nodeCopy.getOutputs().set(j, copy.getOperators().get(index1));
+ copy.getOperators().get(index1).setNodeOperatorForOutput(nodeCopy);
+
+ reaction.getOperators().get(index1).setNodeOperatorForOutput(nodeOriginal);
+ } else if (index2 >= 0) {
+ nodeCopy.getOutputs().set(j, copy.getNodes().get(index2));
+ copy.getNodes().get(index2).setNodeOperatorForOutput(nodeCopy);
+
+ reaction.getNodes().get(index2).setNodeOperatorForOutput(nodeOriginal);
+ } else {
+ throw new InvalidStateException("WTF");
+ }
+ }
+ }
+
+ return copy;
+ }
+
+ /**
+ * Updates references to elements and aliases in reaction to the objects taken
+ * from model.
+ *
+ * @param reaction
+ * references in this reaction will be updated
+ * @param model
+ * references from this model will be taken
+ */
+ private void updateReactionReferences(Reaction reaction, Model model) {
+ reaction.setModel(model);
+ for (ReactionNode rNode : reaction.getReactionNodes()) {
+ rNode.setElement(model.getElementByElementId(rNode.getElement().getElementId()));
+ }
+ SbmlKinetics kinetics = reaction.getKinetics();
+ if (kinetics != null) {
+ Collection<SbmlArgument> arguments = new HashSet<>();
+ for (SbmlArgument argument : kinetics.getArguments()) {
+ if (argument instanceof Element) {
+ arguments.add(model.getElementByElementId(argument.getElementId()));
+ } else if (argument instanceof SbmlParameter) {
+ if (model.getParameterById(argument.getElementId()) != null) {
+ arguments.add(model.getParameterById(argument.getElementId()));
+ } else {
+ arguments.add(argument);
+ }
+ } else if (argument instanceof SbmlFunction) {
+ arguments.add(model.getFunctionById(argument.getElementId()));
+ } else {
+ throw new InvalidStateException("Don't know what to do with class: " + argument.getClass());
+ }
+ }
+ kinetics.removeArguments(kinetics.getArguments());
+ kinetics.addArguments(arguments);
+ }
+
+ }
+
+ /**
+ * Updates information (like elements, parent aliases) in the alias with the
+ * data from new model.
+ *
+ * @param element
+ * object to be updated
+ * @param model
+ * data from this model will be used for update
+ * @param originalModel
+ * original model from which alias copy was created
+ */
+ private void updateElementReferences(Element element, Model model, Model originalModel) {
+ if (element instanceof Compartment) {
+ Compartment compartment = (Compartment) element;
+ Compartment original = originalModel.getElementByElementId(element.getElementId());
+ for (Element child : original.getElements()) {
+ compartment.addElement(model.getElementByElementId(child.getElementId()));
+ }
+ }
+
+ if (element instanceof Complex) {
+ Complex complex = (Complex) element;
+ for (int i = 0; i < complex.getElements().size(); i++) {
+ Species newElement = model.getElementByElementId(complex.getElements().get(i).getElementId());
+ complex.getElements().set(i, newElement);
+ }
+ }
+ if (element instanceof Species) {
+ Species species = (Species) element;
+
+ if (species.getComplex() != null) {
+ species.setComplex((Complex) model.getElementByElementId(species.getComplex().getElementId()));
+ }
+
+ }
+
+ element.setModel(model);
+
+ if (element.getCompartment() != null) {
+ element.setCompartment(model.getElementByElementId(element.getCompartment().getElementId()));
+ }
+ }
}
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 9421f1661d7e59624d1463fedc2e3765dc8285f6..d942482d7b7e014eb922b4eac6e3fadd33b518be 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -21,6 +21,8 @@ import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
@@ -38,317 +40,350 @@ import lcsb.mapviewer.model.map.species.GenericProtein;
public class CopyCommandTest extends CommandTestFunctions {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCopyModel() {
- try {
- Model model = getModelForFile("testFiles/sample.xml", false);
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- fail("exception occurred");
- }
- }
-
- @Test
- public void testCopyCustomModel() {
- try {
- Model model = new ModelFullIndexed(null);
-
- GenericProtein protein = new GenericProtein("A");
- protein.setNotes(null);
-
- model.addElement(protein);
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- fail("exception occurred");
- }
- }
-
- @Test
- public void testCopyCustomModel2() {
- try {
- Model model = new ModelFullIndexed(null);
-
- Complex complexAlias = new Complex("id2");
- GenericProtein protein = new GenericProtein("A");
- protein.setNotes(null);
- complexAlias.addSpecies(protein);
- model.addElement(protein);
- model.addElement(complexAlias);
-
- GenericProtein alias = new GenericProtein("B");
- alias.setNotes(null);
-
- complexAlias.addSpecies(alias);
- model.addElement(alias);
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModel3() throws Exception {
- try {
- Model model = getModelForFile("testFiles/complex_with_state.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModel4() throws Exception {
- try {
- Model model = getModelForFile("testFiles/problematic_description.xml", true);
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithArtifitialAliases() throws Exception {
- try {
- Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
- new CreateHierarchyCommand(model, 2, 2).execute();
-
- Model copy = new CopyCommand(model).execute();
-
- CellDesignerXmlParser parser = new CellDesignerXmlParser();
- String xml = parser.toXml(copy);
-
- InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
- Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
- ModelComparator comparator = new ModelComparator();
-
- new CreateHierarchyCommand(copy2, 2, 2).execute();
-
- // check if after conversion to xml everything works
- assertEquals(0, comparator.compare(copy, copy2));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodels() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopySubmodel() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
-
- Model model3 = getModel();
- model3.setNotes("ASDSA");
- model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
- Element alias = model2.getElementByElementId("a_id");
- alias.setSubmodel(new ElementSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
- Model copy = new CopyCommand(model2).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model2, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodels2() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA2");
-
- model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- model.getElementByElementId("a_id").setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithName() throws Exception {
- try {
- Model model = getModel();
- model.setName("ASDSA2");
-
- Model copy = new CopyCommand(model).execute();
-
- ModelComparator comparator = new ModelComparator();
-
- assertEquals(0, comparator.compare(model, copy));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCopyModelWithSubmodelsThrowException() throws Exception {
- try {
- Model model = getModel();
- Model model2 = getModel();
- model2.setNotes("ASDSA2");
-
- model.getElementByElementId("a_id").setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
- try {
- new CopyCommand(model).execute();
- fail("Exception expected");
- } catch (InvalidArgumentException e) {
- }
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model getModel() {
- Model model = new ModelFullIndexed(null);
- model.setNotes("Some description");
-
- GenericProtein alias = new GenericProtein("a_id");
- alias.setName("ad");
- model.addElement(alias);
-
- Layer layer = new Layer();
- layer.setName("layer name");
- model.addLayer(layer);
-
- model.addReaction(new Reaction());
- return model;
- }
-
- @Test
- public void testCopyModelReaction() throws Exception {
- try {
- Model model = new ModelFullIndexed(null);
-
- Compartment c1 = new SquareCompartment("c1");
- Compartment c2 = new SquareCompartment("c2");
- c1.setVisibilityLevel("2");
- c2.setVisibilityLevel("3");
-
- model.addElement(c1);
- model.addElement(c2);
-
- GenericProtein s1 = new GenericProtein("s1");
- s1.setCompartment(c1);
- model.addElement(s1);
-
- GenericProtein s2 = new GenericProtein("s2");
- s2.setCompartment(c2);
- model.addElement(s2);
-
- StateTransitionReaction reaction = new StateTransitionReaction();
- Reactant reactant = new Reactant(s1);
- reactant.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10)));
- reaction.addReactant(reactant);
- Product product = new Product(s2);
- product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(120, 10)));
- reaction.addProduct(product);
- reaction.setVisibilityLevel("4");
-
- model.addReaction(reaction);
-
- assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
- assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
-
- Model model2 = new CopyCommand(model).execute();
- Reaction reaction2 = model2.getReactions().iterator().next();
-
- assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
- assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
-
- assertFalse(s1.equals(reaction2.getReactants().get(0).getElement()));
- assertFalse(s2.equals(reaction2.getProducts().get(0).getElement()));
-
- assertNotNull(reaction2.getReactants().get(0).getElement().getCompartment());
- assertNotNull(reaction2.getProducts().get(0).getElement().getCompartment());
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ @Before
+ public void setUp() throws Exception {
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testCopyModel() {
+ try {
+ Model model = getModelForFile("testFiles/sample.xml", false);
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("exception occurred");
+ }
+ }
+
+ @Test
+ public void testCopyModelWithKinetics() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/kinetics_with_compartment.xml", false);
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ for (Reaction reaction : copy.getReactions()) {
+ if (reaction.getKinetics() != null) {
+ for (Element element : reaction.getKinetics().getElements()) {
+ assertTrue("Element in the copy doesn't belong to copy", copy.getElements().contains(element));
+ }
+ for (SbmlFunction function : reaction.getKinetics().getFunctions()) {
+ assertTrue("Function in the copy doesn't belong to copy", copy.getFunctions().contains(function));
+ }
+ for (SbmlParameter parameter : reaction.getKinetics().getParameters()) {
+ if (parameter.getParameterId().equals("k2")) {
+ assertTrue("Global parameter in the function copy doesn't belong to copy",
+ copy.getParameters().contains(parameter));
+ }
+ }
+ }
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyCustomModel() {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ GenericProtein protein = new GenericProtein("A");
+ protein.setNotes(null);
+
+ model.addElement(protein);
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ fail("exception occurred");
+ }
+ }
+
+ @Test
+ public void testCopyCustomModel2() {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Complex complexAlias = new Complex("id2");
+ GenericProtein protein = new GenericProtein("A");
+ protein.setNotes(null);
+ complexAlias.addSpecies(protein);
+ model.addElement(protein);
+ model.addElement(complexAlias);
+
+ GenericProtein alias = new GenericProtein("B");
+ alias.setNotes(null);
+
+ complexAlias.addSpecies(alias);
+ model.addElement(alias);
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModel3() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/complex_with_state.xml", true);
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModel4() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/problematic_description.xml", true);
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithArtifitialAliases() throws Exception {
+ try {
+ Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
+ new CreateHierarchyCommand(model, 2, 2).execute();
+
+ Model copy = new CopyCommand(model).execute();
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xml = parser.toXml(copy);
+
+ InputStream stream = new ByteArrayInputStream(xml.getBytes(StandardCharsets.UTF_8));
+ Model copy2 = parser.createModel(new ConverterParams().inputStream(stream).sizeAutoAdjust(false));
+ ModelComparator comparator = new ModelComparator();
+
+ new CreateHierarchyCommand(copy2, 2, 2).execute();
+
+ // check if after conversion to xml everything works
+ assertEquals(0, comparator.compare(copy, copy2));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodels() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopySubmodel() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS, "name a"));
+
+ Model model3 = getModel();
+ model3.setNotes("ASDSA");
+ model.addSubmodelConnection(new ModelSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name b"));
+ Element alias = model2.getElementByElementId("a_id");
+ alias.setSubmodel(new ElementSubmodelConnection(model3, SubmodelType.DOWNSTREAM_TARGETS, "name c"));
+ Model copy = new CopyCommand(model2).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model2, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodels2() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA2");
+
+ model.addSubmodelConnection(new ModelSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ model.getElementByElementId("a_id")
+ .setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithName() throws Exception {
+ try {
+ Model model = getModel();
+ model.setName("ASDSA2");
+
+ Model copy = new CopyCommand(model).execute();
+
+ ModelComparator comparator = new ModelComparator();
+
+ assertEquals(0, comparator.compare(model, copy));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCopyModelWithSubmodelsThrowException() throws Exception {
+ try {
+ Model model = getModel();
+ Model model2 = getModel();
+ model2.setNotes("ASDSA2");
+
+ model.getElementByElementId("a_id")
+ .setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
+ try {
+ new CopyCommand(model).execute();
+ fail("Exception expected");
+ } catch (InvalidArgumentException e) {
+ }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model getModel() {
+ Model model = new ModelFullIndexed(null);
+ model.setNotes("Some description");
+
+ GenericProtein alias = new GenericProtein("a_id");
+ alias.setName("ad");
+ model.addElement(alias);
+
+ Layer layer = new Layer();
+ layer.setName("layer name");
+ model.addLayer(layer);
+
+ model.addReaction(new Reaction());
+ return model;
+ }
+
+ @Test
+ public void testCopyModelReaction() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+
+ Compartment c1 = new SquareCompartment("c1");
+ Compartment c2 = new SquareCompartment("c2");
+ c1.setVisibilityLevel("2");
+ c2.setVisibilityLevel("3");
+
+ model.addElement(c1);
+ model.addElement(c2);
+
+ GenericProtein s1 = new GenericProtein("s1");
+ s1.setCompartment(c1);
+ model.addElement(s1);
+
+ GenericProtein s2 = new GenericProtein("s2");
+ s2.setCompartment(c2);
+ model.addElement(s2);
+
+ StateTransitionReaction reaction = new StateTransitionReaction();
+ Reactant reactant = new Reactant(s1);
+ reactant.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(10, 10)));
+ reaction.addReactant(reactant);
+ Product product = new Product(s2);
+ product.setLine(new PolylineData(new Point2D.Double(10, 0), new Point2D.Double(120, 10)));
+ reaction.addProduct(product);
+ reaction.setVisibilityLevel("4");
+
+ model.addReaction(reaction);
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ Model model2 = new CopyCommand(model).execute();
+ Reaction reaction2 = model2.getReactions().iterator().next();
+
+ assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
+ assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+
+ assertFalse(s1.equals(reaction2.getReactants().get(0).getElement()));
+ assertFalse(s2.equals(reaction2.getProducts().get(0).getElement()));
+
+ assertNotNull(reaction2.getReactants().get(0).getElement().getCompartment());
+ assertNotNull(reaction2.getProducts().get(0).getElement().getCompartment());
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/model-command/testFiles/kinetics_with_compartment.xml b/model-command/testFiles/kinetics_with_compartment.xml
new file mode 100644
index 0000000000000000000000000000000000000000..209c35ca73ee4b52c9312283f5c62b0c30c9bbf6
--- /dev/null
+++ b/model-command/testFiles/kinetics_with_compartment.xml
@@ -0,0 +1,217 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>4.0</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="600" sizeY="400"/>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE</celldesigner:class>
+<celldesigner:bounds x="46.0" y="105.0" w="413.0" h="201.0"/>
+<celldesigner:namePoint x="244.0" y="270.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases>
+<celldesigner:speciesAlias id="sa1" species="s1" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="67.0" y="151.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="21.0" y="46.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+<celldesigner:speciesAlias id="sa2" species="s2" compartmentAlias="ca1">
+<celldesigner:activity>inactive</celldesigner:activity>
+<celldesigner:bounds x="296.0" y="174.0" w="80.0" h="40.0"/>
+<celldesigner:font size="12"/>
+<celldesigner:view state="usual"/>
+<celldesigner:usualView>
+<celldesigner:innerPosition x="250.0" y="69.0"/>
+<celldesigner:boxSize width="80.0" height="40.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="ffccffcc" scheme="Color"/>
+</celldesigner:usualView>
+<celldesigner:briefView>
+<celldesigner:innerPosition x="0.0" y="0.0"/>
+<celldesigner:boxSize width="80.0" height="60.0"/>
+<celldesigner:singleLine width="1.0"/>
+<celldesigner:paint color="3fff0000" scheme="Color"/>
+</celldesigner:briefView>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:speciesAlias>
+</celldesigner:listOfSpeciesAliases>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins>
+<celldesigner:protein id="pr1" name="s1" type="GENERIC"/>
+<celldesigner:protein id="pr2" name="s2" type="GENERIC"/>
+</celldesigner:listOfProteins>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfParameters>
+<parameter metaid="k2" id="k2" name="global param" value="0" units="substance"/>
+</listOfParameters>
+<listOfFunctionDefinitions>
+<functionDefinition metaid="fun" id="fun" name="Function name">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<lambda>
+<bvar>
+<ci> x </ci>
+</bvar>
+<bvar>
+<ci> y </ci>
+</bvar>
+<apply>
+<plus/>
+<ci> x </ci>
+<ci> y </ci>
+</apply>
+</lambda>
+</math>
+</functionDefinition>
+</listOfFunctionDefinitions>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00006" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00007" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00008" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment metaid="c1" id="c1" name="c1" size="1" units="volume" outside="default">
+<annotation>
+<celldesigner:extension>
+<celldesigner:name>c1</celldesigner:name>
+</celldesigner:extension>
+</annotation>
+</compartment>
+</listOfCompartments>
+<listOfSpecies>
+<species metaid="s1" id="s1" name="s1" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr1</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+<species metaid="s2" id="s2" name="s2" compartment="c1" initialAmount="0">
+<annotation>
+<celldesigner:extension>
+<celldesigner:positionToCompartment>inside</celldesigner:positionToCompartment>
+<celldesigner:speciesIdentity>
+<celldesigner:class>PROTEIN</celldesigner:class>
+<celldesigner:proteinReference>pr2</celldesigner:proteinReference>
+</celldesigner:speciesIdentity>
+</celldesigner:extension>
+</annotation>
+</species>
+</listOfSpecies>
+<listOfReactions>
+<reaction metaid="re1" id="re1" reversible="false" fast="false">
+<annotation>
+<celldesigner:extension>
+<celldesigner:reactionType>STATE_TRANSITION</celldesigner:reactionType>
+<celldesigner:baseReactants>
+<celldesigner:baseReactant species="s1" alias="sa1"/>
+</celldesigner:baseReactants>
+<celldesigner:baseProducts>
+<celldesigner:baseProduct species="s2" alias="sa2"/>
+</celldesigner:baseProducts>
+<celldesigner:connectScheme connectPolicy="direct" rectangleIndex="0">
+<celldesigner:listOfLineDirection>
+<celldesigner:lineDirection index="0" value="unknown"/>
+</celldesigner:listOfLineDirection>
+</celldesigner:connectScheme>
+<celldesigner:line width="1.0" color="ff000000"/>
+</celldesigner:extension>
+</annotation>
+<listOfReactants>
+<speciesReference metaid="CDMT00001" species="s1">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa1</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfReactants>
+<listOfProducts>
+<speciesReference metaid="CDMT00002" species="s2">
+<annotation>
+<celldesigner:extension>
+<celldesigner:alias>sa2</celldesigner:alias>
+</celldesigner:extension>
+</annotation>
+</speciesReference>
+</listOfProducts>
+<kineticLaw metaid="CDMT00003">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<apply>
+<divide/>
+<apply>
+<times/>
+<ci> c1 </ci>
+<apply>
+<plus/>
+<ci> s1 </ci>
+<ci> s2 </ci>
+<ci> fun </ci>
+<ci> k2 </ci>
+<ci> k1 </ci>
+</apply>
+</apply>
+<cn type="integer"> 2 </cn>
+</apply>
+</math>
+<listOfParameters>
+<parameter metaid="k1" id="k1" name="local param" value="0" units="substance"/>
+</listOfParameters>
+</kineticLaw>
+</reaction>
+</listOfReactions>
+</model>
+</sbml>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
index aa0a577447c7f3f667d16f957c19e0f09da0e124..8b7b1058ff6e3ce6893aaaceb3e59198457e7696 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
@@ -16,8 +16,6 @@ import javax.persistence.Id;
import javax.persistence.JoinColumn;
import javax.persistence.JoinTable;
import javax.persistence.ManyToMany;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToOne;
import javax.persistence.Table;
import javax.xml.bind.annotation.XmlRootElement;
@@ -25,7 +23,6 @@ import org.apache.log4j.Logger;
import org.hibernate.annotations.Cascade;
import org.hibernate.annotations.CascadeType;
-import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.species.Element;
/**
@@ -134,8 +131,8 @@ public class SbmlKinetics implements Serializable {
}
- public void addArguments(Set<SbmlArgument> elementsUsedInKinetics) {
- for (SbmlArgument argument : elementsUsedInKinetics) {
+ public void addArguments(Collection<SbmlArgument> arguments) {
+ for (SbmlArgument argument : arguments) {
addArgument(argument);
}
@@ -180,4 +177,29 @@ public class SbmlKinetics implements Serializable {
public void removeElement(Element elementToRemove) {
elements.remove(elementToRemove);
}
+
+ public void removeArguments(Collection<SbmlArgument> arguments) {
+ for (SbmlArgument sbmlArgument : arguments) {
+ removeArgument(sbmlArgument);
+ }
+ }
+
+ private void removeArgument(SbmlArgument argument) {
+ if (argument instanceof SbmlParameter) {
+ removeParameter((SbmlParameter) argument);
+ } else if (argument instanceof SbmlFunction) {
+ removeFunction((SbmlFunction) argument);
+ } else {
+ removeElement((Element) argument);
+ }
+ }
+
+ private void removeFunction(SbmlFunction function) {
+ functions.remove(function);
+ }
+
+ private void removeParameter(SbmlParameter parameter) {
+ parameters.remove(parameter);
+
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
index 3a0b60ad84756d1d3bac0ddca634192482a825b3..f1a1339c6a08ca74058334d81c3d5be9f5199349 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnit.java
@@ -76,6 +76,14 @@ public class SbmlUnit implements Serializable {
this.unitId = unitId;
}
+ public SbmlUnit(SbmlUnit sbmlUnit) {
+ this(sbmlUnit.getUnitId());
+ this.setName(sbmlUnit.getName());
+ for (SbmlUnitTypeFactor factor : sbmlUnit.getUnitTypeFactors()) {
+ this.addUnitTypeFactor(factor.copy());
+ }
+ }
+
public String getUnitId() {
return unitId;
}
@@ -109,4 +117,8 @@ public class SbmlUnit implements Serializable {
this.model = model;
}
+ public SbmlUnit copy() {
+ return new SbmlUnit(this);
+ }
+
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
index 0f4b585b9f78546434943fcc14032cdb3b553fd2..c76949b4914634ca8eb62cc53255061ad55dcf71 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitComparator.java
@@ -1,10 +1,13 @@
package lcsb.mapviewer.model.map.kinetics;
+import org.apache.log4j.Logger;
+
import lcsb.mapviewer.common.Comparator;
import lcsb.mapviewer.common.comparator.SetComparator;
import lcsb.mapviewer.common.comparator.StringComparator;
public class SbmlUnitComparator extends Comparator<SbmlUnit> {
+ Logger logger =Logger.getLogger(SbmlUnitComparator.class);
public SbmlUnitComparator() {
super(SbmlUnit.class);
@@ -16,22 +19,18 @@ public class SbmlUnitComparator extends Comparator<SbmlUnit> {
SetComparator<SbmlUnitTypeFactor> unitTypeFactorComparator = new SetComparator<>(
new SbmlUnitTypeFactorComparator());
if (stringComparator.compare(arg0.getUnitId(), arg1.getUnitId()) != 0) {
+ logger.debug("unitId different");
return stringComparator.compare(arg0.getUnitId(), arg1.getUnitId());
}
if (stringComparator.compare(arg0.getName(), arg1.getName()) != 0) {
+ logger.debug("name different");
return stringComparator.compare(arg0.getName(), arg1.getName());
}
if (unitTypeFactorComparator.compare(arg0.getUnitTypeFactors(), arg1.getUnitTypeFactors()) != 0) {
+ logger.debug("unit type factor different");
return unitTypeFactorComparator.compare(arg0.getUnitTypeFactors(), arg1.getUnitTypeFactors());
}
- //
- // if (stringListComparator.compare(arg0.getArguments(), arg1.getArguments()) !=
- // 0) {
- // return stringListComparator.compare(arg0.getArguments(),
- // arg1.getArguments());
- // }
-
return 0;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
index 1e4c15b550157b86fcdd11d3b29e6de03b17bc54..b718204ce9d1133caf73ad27591138cf98b91525 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTypeFactor.java
@@ -16,8 +16,6 @@ import javax.xml.bind.annotation.XmlRootElement;
import org.apache.log4j.Logger;
-import lcsb.mapviewer.model.map.model.ModelData;
-
/**
* Representation of a single SBML unit factor. For example unit for velocity is
* m/s. It means that we have two unit types here:
@@ -78,6 +76,10 @@ public class SbmlUnitTypeFactor implements Serializable {
this.multiplier = multiplier;
}
+ public SbmlUnitTypeFactor(SbmlUnitTypeFactor original) {
+ this(original.getUnitType(), original.getExponent(), original.getScale(), original.getMultiplier());
+ }
+
public SbmlUnitType getUnitType() {
return unitType;
}
@@ -118,4 +120,8 @@ public class SbmlUnitTypeFactor implements Serializable {
this.unit = unit;
}
+ public SbmlUnitTypeFactor copy() {
+ return new SbmlUnitTypeFactor(this);
+ }
+
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
index 3e1d4e4f8785f4ac012ae54f058805b6cde06777..05018314821db4dc3d189b56e0f3a5d4d2e2ec18 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/kinetics/SbmlUnitTest.java
@@ -5,6 +5,7 @@ import static org.junit.Assert.assertEquals;
import org.junit.Test;
public class SbmlUnitTest {
+ SbmlUnitComparator comparator = new SbmlUnitComparator();
@Test
public void testConstructor() {
@@ -15,12 +16,22 @@ public class SbmlUnitTest {
@Test
public void testSetName() {
- String name= "id";
+ String name = "id";
SbmlUnit unit = new SbmlUnit("");
unit.setName(name);
assertEquals(unit.getName(), name);
}
+ @Test
+ public void testCopy() {
+ SbmlUnit unit = new SbmlUnit("");
+ unit.setName("nam");
+ unit.addUnitTypeFactor(new SbmlUnitTypeFactor(SbmlUnitType.METRE, 2, 0, 1.0));
+
+ SbmlUnit copy = unit.copy();
+ assertEquals(0, comparator.compare(unit, copy));
+ }
+
@Test
public void testAddUnitTypeFactor() {
SbmlUnitTypeFactor factor = new SbmlUnitTypeFactor(SbmlUnitType.METRE, 2, 0, 1.0);