Example 21 with Product
use of cbit.vcell.model.Product in project vcell by virtualcell.
the class ReactionCartoonFull method refreshAll.
@Override
protected void refreshAll(boolean reallocateShapes) {
try {
if (getModel() == null || getStructureSuite() == null) {
return;
}
System.out.println("ReactionCartoonFull, RefreshAll()");
for (Structure structure : structureSuite.getStructures()) {
Diagram diagram = getModel().getDiagram(structure);
if (diagram != null) {
// Maintain consistency between rule participant nodes, signatures and
// species pattern when a molecule is being modified.
rebindAll(diagram);
}
}
// calculate species context weight (number of reactions for which it's a participant)
Map<SpeciesContext, Integer> scWeightMap = new HashMap<>();
// all the species contexts that are catalysts
Set<SpeciesContext> scCatalystSet = new HashSet<>();
// calculate species context length (number of species patterns it contains, 1 if has no species patterns)
for (ReactionStep rs : getModel().getReactionSteps()) {
ReactionParticipant[] rpList = rs.getReactionParticipants();
for (int i = 0; i < rpList.length; i++) {
ReactionParticipant rp = rpList[i];
SpeciesContext sc = rp.getSpeciesContext();
// int increment = rp.getStoichiometry();
int increment = 1;
if (rp instanceof Catalyst) {
scCatalystSet.add(sc);
}
if (scWeightMap.containsKey(sc)) {
int weight = scWeightMap.get(sc);
weight += increment;
scWeightMap.put(sc, weight);
} else {
scWeightMap.put(sc, increment);
}
}
}
Set<Shape> unwantedShapes = new HashSet<Shape>();
Set<RuleParticipantSignature> unwantedSignatures = new HashSet<RuleParticipantSignature>();
unwantedShapes.addAll(getShapes());
unwantedSignatures.addAll(ruleParticipantSignatures);
ContainerContainerShape containerShape = (ContainerContainerShape) getShapeFromModelObject(getModel());
List<ReactionContainerShape> reactionContainerShapeList = new ArrayList<ReactionContainerShape>();
List<Structure> structureList = new ArrayList<Structure>(getStructureSuite().getStructures());
// create all ReactionContainerShapes (one for each Structure)
for (Structure structure : structureList) {
if (structure instanceof Membrane) {
Membrane membrane = (Membrane) structure;
ReactionContainerShape membraneShape = (ReactionContainerShape) getShapeFromModelObject(membrane);
if (membraneShape == null) {
membraneShape = new ReactionContainerShape(membrane, structureSuite, this);
addShape(membraneShape);
membrane.getMembraneVoltage().removePropertyChangeListener(this);
membrane.getMembraneVoltage().addPropertyChangeListener(this);
} else {
membraneShape.setStructureSuite(structureSuite);
}
membrane.removePropertyChangeListener(this);
membrane.addPropertyChangeListener(this);
membraneShape.refreshLabel();
unwantedShapes.remove(membraneShape);
reactionContainerShapeList.add(membraneShape);
} else if (structure instanceof Feature) {
Feature feature = (Feature) structure;
ReactionContainerShape featureShape = (ReactionContainerShape) getShapeFromModelObject(feature);
if (featureShape == null) {
featureShape = new ReactionContainerShape(feature, structureSuite, this);
addShape(featureShape);
} else {
featureShape.setStructureSuite(structureSuite);
}
feature.removePropertyChangeListener(this);
feature.addPropertyChangeListener(this);
featureShape.refreshLabel();
unwantedShapes.remove(featureShape);
reactionContainerShapeList.add(featureShape);
}
}
if (containerShape == null) {
containerShape = new ContainerContainerShape(this, getModel(), reactionContainerShapeList);
addShape(containerShape);
} else {
containerShape.setReactionContainerShapeList(reactionContainerShapeList);
}
containerShape.refreshLabel();
unwantedShapes.remove(containerShape);
// add all species context shapes within the structures
for (Structure structure : getStructureSuite().getStructures()) {
ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
structure.removePropertyChangeListener(this);
structure.addPropertyChangeListener(this);
for (SpeciesContext structSpeciesContext : getModel().getSpeciesContexts(structure)) {
SpeciesContextShape ss = (SpeciesContextShape) getShapeFromModelObject(structSpeciesContext);
if (ss == null) {
ss = new SpeciesContextShape(structSpeciesContext, this);
ss.truncateLabelName(false);
structSpeciesContext.getSpecies().removePropertyChangeListener(this);
structSpeciesContext.getSpecies().addPropertyChangeListener(this);
reactionContainerShape.addChildShape(ss);
addShape(ss);
ss.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
if (speciesSizeOption == SpeciesSizeOptions.weight) {
// this number sets the diameter of the shape
Integer weight = scWeightMap.get(structSpeciesContext);
if (weight != null) {
// we cap the diameter of the shape to something reasonable
weight = Math.min(weight, 16);
}
ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, weight);
} else if (speciesSizeOption == SpeciesSizeOptions.length) {
Integer length = null;
if (structSpeciesContext.getSpeciesPattern() != null && !structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
length = structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().size() * 2;
length = Math.min(length, 16);
}
ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, length);
} else {
ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, null);
}
structSpeciesContext.removePropertyChangeListener(this);
structSpeciesContext.addPropertyChangeListener(this);
ss.refreshLabel();
unwantedShapes.remove(ss);
}
}
// add all reactionSteps that are in this structure (ReactionContainerShape), and draw the lines
getModel().removePropertyChangeListener(this);
getModel().addPropertyChangeListener(this);
//
for (ReactionRule rr : getModel().getRbmModelContainer().getReactionRuleList()) {
rr.removePropertyChangeListener(this);
rr.addPropertyChangeListener(this);
Structure structure = rr.getStructure();
if (getStructureSuite().areReactionsShownFor(structure)) {
ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
ReactionRuleFullDiagramShape rrShape = (ReactionRuleFullDiagramShape) getShapeFromModelObject(rr);
if (rrShape == null) {
rrShape = new ReactionRuleFullDiagramShape(rr, this);
addShape(rrShape);
rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
reactionContainerShape.addChildShape(rrShape);
rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
rrShape.refreshLabel();
unwantedShapes.remove(rrShape);
//
// add reaction participants as edges and SignatureShapes as needed
//
List<ReactionRuleParticipant> participants = rr.getReactionRuleParticipants();
List<RuleParticipantEdgeDiagramShape> ruleEdges = new ArrayList<>();
for (ReactionRuleParticipant participant : participants) {
participant.getSpeciesPattern().removePropertyChangeListener(this);
participant.getSpeciesPattern().addPropertyChangeListener(this);
Structure speciesStructure = participant.getStructure();
Structure reactionStructure = rr.getStructure();
if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
//
// find existing RuleParticipantSignatureShape in cartoon
//
RuleParticipantLongSignature ruleParticipantLongSignature = null;
for (RuleParticipantSignature signature : ruleParticipantSignatures) {
if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == participant.getStructure() && signature.compareByCriteria(participant.getSpeciesPattern(), GroupingCriteria.full)) {
ruleParticipantLongSignature = (RuleParticipantLongSignature) signature;
break;
}
}
for (RuleParticipantSignature signature : ruleParticipantSignatures) {
if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == participant.getStructure()) {
System.out.println("ReactionCartoonFull, refreshAll(), RuleParticipantShortSignature");
}
}
//
// if didn't find signature in cartoons list of signatures, then create one (and create a shape for it).
//
RuleParticipantSignatureFullDiagramShape signatureShape = null;
if (ruleParticipantLongSignature == null) {
ruleParticipantLongSignature = RuleParticipantLongSignature.fromReactionRuleParticipant(participant, this);
ruleParticipantSignatures.add(ruleParticipantLongSignature);
signatureShape = new RuleParticipantSignatureFullDiagramShape(ruleParticipantLongSignature, this);
addShape(signatureShape);
ReactionContainerShape participantContainerShape = (ReactionContainerShape) getShapeFromModelObject(participant.getStructure());
signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
participantContainerShape.addChildShape(signatureShape);
signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
} else {
signatureShape = (RuleParticipantSignatureFullDiagramShape) getShapeFromModelObject(ruleParticipantLongSignature);
}
unwantedShapes.remove(signatureShape);
unwantedSignatures.remove(ruleParticipantLongSignature);
signatureShape.refreshLabel();
signatureShape.setVisible(true);
//
// add edge for ReactionRuleParticipant if not already present.
//
RuleParticipantEdgeDiagramShape ruleParticipantShape = (RuleParticipantEdgeDiagramShape) getShapeFromModelObject(participant);
if (ruleParticipantShape == null || ruleParticipantShape.getRuleParticipantSignatureShape() != signatureShape) {
if (participant instanceof ReactantPattern && signatureShape.isVisible()) {
ruleParticipantShape = new ReactantPatternEdgeDiagramShape((ReactantPattern) participant, rrShape, signatureShape, this);
} else if (participant instanceof ProductPattern && signatureShape.isVisible()) {
ruleParticipantShape = new ProductPatternEdgeDiagramShape((ProductPattern) participant, rrShape, signatureShape, this);
} else {
throw new RuntimeException("unsupported ReactionRuleParticipant " + participant.getClass());
}
addShape(ruleParticipantShape);
}
if (!containerShape.getChildren().contains(ruleParticipantShape)) {
containerShape.addChildShape(ruleParticipantShape);
}
unwantedShapes.remove(ruleParticipantShape);
ruleParticipantShape.refreshLabel();
// all the edges for this rule
ruleEdges.add(ruleParticipantShape);
}
}
// a product edge (a closed loop) between the rule diagram shape and the signature diagram shape
for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
// reset them all
ours.setSibling(false);
}
for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
for (RuleParticipantEdgeDiagramShape theirs : ruleEdges) {
if (ours == theirs) {
// don't compare with self
continue;
}
if (ours.getRuleParticipantSignatureShape() == theirs.getRuleParticipantSignatureShape()) {
ours.setSibling(true);
theirs.setSibling(true);
}
}
}
}
}
ruleParticipantSignatures.removeAll(unwantedSignatures);
for (ReactionStep reactionStep : getModel().getReactionSteps()) {
reactionStep.removePropertyChangeListener(this);
reactionStep.addPropertyChangeListener(this);
Structure structure = reactionStep.getStructure();
if (getStructureSuite().areReactionsShownFor(structure)) {
ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
if (reactionContainerShape == null) {
System.out.println("Reaction container shape is null for structure " + structure + " for reaction step " + reactionStep);
}
ReactionStepShape reactionStepShape = (ReactionStepShape) getShapeFromModelObject(reactionStep);
if (reactionStepShape == null) {
if (reactionStep instanceof SimpleReaction) {
reactionStepShape = new SimpleReactionShape((SimpleReaction) reactionStep, this);
} else if (reactionStep instanceof FluxReaction) {
reactionStepShape = new FluxReactionShape((FluxReaction) reactionStep, this);
} else {
throw new RuntimeException("unknown type of ReactionStep '" + reactionStep.getClass().toString());
}
addShape(reactionStepShape);
reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
reactionContainerShape.addChildShape(reactionStepShape);
reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
reactionStepShape.refreshLabel();
unwantedShapes.remove(reactionStepShape);
// add reaction participants as edges
for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
participant.removePropertyChangeListener(this);
participant.addPropertyChangeListener(this);
Structure speciesStructure = participant.getStructure();
Structure reactionStructure = reactionStep.getStructure();
if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
SpeciesContext speciesContext = getModel().getSpeciesContext(participant.getSpecies(), speciesStructure);
// add speciesContextShapes that are not in this structure, but are referenced from the reactionParticipants
// these are only when reactionParticipants are from features that are outside of the membrane being displayed
SpeciesContextShape speciesContextShape = (SpeciesContextShape) getShapeFromModelObject(speciesContext);
if (speciesContextShape == null) {
speciesContextShape = new SpeciesContextShape(speciesContext, this);
speciesContextShape.truncateLabelName(false);
reactionContainerShape.addChildShape(speciesContextShape);
addShape(speciesContextShape);
speciesContextShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
speciesContextShape.refreshLabel();
unwantedShapes.remove(speciesContextShape);
ReactionParticipantShape reactionParticipantShape = (ReactionParticipantShape) getShapeFromModelObject(participant);
if (reactionParticipantShape == null) {
if (participant instanceof Reactant) {
reactionParticipantShape = new ReactantShape((Reactant) participant, reactionStepShape, speciesContextShape, this);
} else if (participant instanceof Product) {
reactionParticipantShape = new ProductShape((Product) participant, reactionStepShape, speciesContextShape, this);
} else if (participant instanceof Catalyst) {
reactionParticipantShape = new CatalystShape((Catalyst) participant, reactionStepShape, speciesContextShape, this);
} else {
throw new RuntimeException("unsupported ReactionParticipant " + participant.getClass());
}
addShape(reactionParticipantShape);
}
if (!containerShape.getChildren().contains(reactionParticipantShape)) {
containerShape.addChildShape(reactionParticipantShape);
}
unwantedShapes.remove(reactionParticipantShape);
reactionParticipantShape.refreshLabel();
}
}
}
}
for (Shape unwantedShape : unwantedShapes) {
removeShape(unwantedShape);
}
// update diagrams
for (Structure structure : structureSuite.getStructures()) {
Diagram diagram = getModel().getDiagram(structure);
if (diagram != null) {
applyDefaults(diagram);
}
}
fireGraphChanged(new GraphEvent(this));
} catch (Throwable e) {
handleException(e);
}
}
Also used :
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
Product(cbit.vcell.model.Product)
FluxReaction(cbit.vcell.model.FluxReaction)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Feature(cbit.vcell.model.Feature)
Reactant(cbit.vcell.model.Reactant)
HashSet(java.util.HashSet)
ReactionStep(cbit.vcell.model.ReactionStep)
ReactionRuleParticipant(cbit.vcell.model.ReactionRuleParticipant)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
Catalyst(cbit.vcell.model.Catalyst)
RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature)
Shape(cbit.gui.graph.Shape)
GraphEvent(cbit.gui.graph.GraphEvent)
RuleParticipantShortSignature(cbit.vcell.model.RuleParticipantShortSignature)
Membrane(cbit.vcell.model.Membrane)
Structure(cbit.vcell.model.Structure)
ReactantPattern(cbit.vcell.model.ReactantPattern)
RuleParticipantLongSignature(cbit.vcell.model.RuleParticipantLongSignature)
SimpleReaction(cbit.vcell.model.SimpleReaction)
ReactionRule(cbit.vcell.model.ReactionRule)
ProductPattern(cbit.vcell.model.ProductPattern)
Point(java.awt.Point)
Diagram(cbit.vcell.model.Diagram)
Example 22 with Product
use of cbit.vcell.model.Product in project vcell by virtualcell.
the class ReactionCartoonMolecule method refreshAll.
@Override
protected void refreshAll(boolean reallocateShapes) {
try {
if (getModel() == null || getStructureSuite() == null) {
return;
}
System.out.println("ReactionCartoonMolecule, RefreshAll()");
for (Structure structure : structureSuite.getStructures()) {
Diagram diagram = getModel().getDiagram(structure);
if (diagram != null) {
// Maintain consistency between rule participant nodes, signatures and
// species pattern when a molecule is being modified.
rebindAll(diagram);
}
}
// calculate species context weight (number of reactions for which it's a participant)
Map<SpeciesContext, Integer> scWeightMap = new HashMap<>();
// all the species contexts that are catalysts
Set<SpeciesContext> scCatalystSet = new HashSet<>();
// calculate species context length (number of species patterns it contains, 1 if has no species patterns)
for (ReactionStep rs : getModel().getReactionSteps()) {
ReactionParticipant[] rpList = rs.getReactionParticipants();
for (int i = 0; i < rpList.length; i++) {
ReactionParticipant rp = rpList[i];
SpeciesContext sc = rp.getSpeciesContext();
int increment = 1;
if (rp instanceof Catalyst) {
scCatalystSet.add(sc);
}
if (scWeightMap.containsKey(sc)) {
int weight = scWeightMap.get(sc);
weight += increment;
scWeightMap.put(sc, weight);
} else {
scWeightMap.put(sc, increment);
}
}
}
Set<Shape> unwantedShapes = new HashSet<Shape>();
Set<RuleParticipantSignature> unwantedSignatures = new HashSet<RuleParticipantSignature>();
unwantedShapes.addAll(getShapes());
unwantedSignatures.addAll(ruleParticipantSignatures);
ContainerContainerShape containerShape = (ContainerContainerShape) getShapeFromModelObject(getModel());
List<ReactionContainerShape> reactionContainerShapeList = new ArrayList<ReactionContainerShape>();
List<Structure> structureList = new ArrayList<Structure>(getStructureSuite().getStructures());
// create all ReactionContainerShapes (one for each Structure)
for (Structure structure : structureList) {
if (structure instanceof Membrane) {
Membrane membrane = (Membrane) structure;
ReactionContainerShape membraneShape = (ReactionContainerShape) getShapeFromModelObject(membrane);
if (membraneShape == null) {
membraneShape = new ReactionContainerShape(membrane, structureSuite, this);
addShape(membraneShape);
membrane.getMembraneVoltage().removePropertyChangeListener(this);
membrane.getMembraneVoltage().addPropertyChangeListener(this);
} else {
membraneShape.setStructureSuite(structureSuite);
}
membrane.removePropertyChangeListener(this);
membrane.addPropertyChangeListener(this);
membraneShape.refreshLabel();
unwantedShapes.remove(membraneShape);
reactionContainerShapeList.add(membraneShape);
} else if (structure instanceof Feature) {
Feature feature = (Feature) structure;
ReactionContainerShape featureShape = (ReactionContainerShape) getShapeFromModelObject(feature);
if (featureShape == null) {
featureShape = new ReactionContainerShape(feature, structureSuite, this);
addShape(featureShape);
} else {
featureShape.setStructureSuite(structureSuite);
}
feature.removePropertyChangeListener(this);
feature.addPropertyChangeListener(this);
featureShape.refreshLabel();
unwantedShapes.remove(featureShape);
reactionContainerShapeList.add(featureShape);
}
}
if (containerShape == null) {
containerShape = new ContainerContainerShape(this, getModel(), reactionContainerShapeList);
addShape(containerShape);
} else {
containerShape.setReactionContainerShapeList(reactionContainerShapeList);
}
containerShape.refreshLabel();
unwantedShapes.remove(containerShape);
// add all species context shapes within the structures
for (Structure structure : getStructureSuite().getStructures()) {
ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
structure.removePropertyChangeListener(this);
structure.addPropertyChangeListener(this);
for (SpeciesContext structSpeciesContext : getModel().getSpeciesContexts(structure)) {
SpeciesContextShape ss = (SpeciesContextShape) getShapeFromModelObject(structSpeciesContext);
if (ss == null) {
ss = new SpeciesContextShape(structSpeciesContext, this);
ss.truncateLabelName(false);
structSpeciesContext.getSpecies().removePropertyChangeListener(this);
structSpeciesContext.getSpecies().addPropertyChangeListener(this);
reactionContainerShape.addChildShape(ss);
addShape(ss);
ss.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
if (speciesSizeOption == SpeciesSizeOptions.weight) {
// this number sets the diameter of the shape
Integer weight = scWeightMap.get(structSpeciesContext);
if (weight != null) {
// we cap the diameter of the shape to something reasonable
weight = Math.min(weight, 16);
}
ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, weight);
} else if (speciesSizeOption == SpeciesSizeOptions.length) {
Integer length = null;
if (structSpeciesContext.getSpeciesPattern() != null && !structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
length = structSpeciesContext.getSpeciesPattern().getMolecularTypePatterns().size() * 2;
length = Math.min(length, 16);
}
ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, length);
} else {
ss.setFilters(highlightCatalystOption ? scCatalystSet.contains(structSpeciesContext) : false, null);
}
structSpeciesContext.removePropertyChangeListener(this);
structSpeciesContext.addPropertyChangeListener(this);
ss.refreshLabel();
unwantedShapes.remove(ss);
}
}
// add all reactionSteps that are in this structure (ReactionContainerShape), and draw the lines
getModel().removePropertyChangeListener(this);
getModel().addPropertyChangeListener(this);
//
for (ReactionRule rr : getModel().getRbmModelContainer().getReactionRuleList()) {
rr.removePropertyChangeListener(this);
rr.addPropertyChangeListener(this);
Structure structure = rr.getStructure();
if (getStructureSuite().areReactionsShownFor(structure)) {
ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
ReactionRuleFullDiagramShape rrShape = (ReactionRuleFullDiagramShape) getShapeFromModelObject(rr);
if (rrShape == null) {
rrShape = new ReactionRuleFullDiagramShape(rr, this);
addShape(rrShape);
rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
reactionContainerShape.addChildShape(rrShape);
rrShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
rrShape.refreshLabel();
unwantedShapes.remove(rrShape);
//
// add reaction participants as edges and SignatureShapes as needed
//
List<ReactionRuleParticipant> participants = rr.getReactionRuleParticipants();
List<RuleParticipantEdgeDiagramShape> ruleEdges = new ArrayList<>();
for (ReactionRuleParticipant participant : participants) {
participant.getSpeciesPattern().removePropertyChangeListener(this);
participant.getSpeciesPattern().addPropertyChangeListener(this);
Structure speciesStructure = participant.getStructure();
Structure reactionStructure = rr.getStructure();
if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
//
// find existing RuleParticipantSignatureShape in cartoon
//
RuleParticipantShortSignature ruleParticipantShortSignature = null;
for (RuleParticipantSignature signature : ruleParticipantSignatures) {
if (signature instanceof RuleParticipantLongSignature && signature.getStructure() == participant.getStructure()) {
System.out.println("ReactionCartoonMolecule, refreshAll(), RuleParticipantLongSignature");
break;
}
}
for (RuleParticipantSignature signature : ruleParticipantSignatures) {
if (signature instanceof RuleParticipantShortSignature && signature.getStructure() == participant.getStructure() && signature.compareByCriteria(participant.getSpeciesPattern(), GroupingCriteria.molecule)) {
ruleParticipantShortSignature = (RuleParticipantShortSignature) signature;
break;
}
}
//
// if didn't find signature in cartoons list of signatures, then create one (and create a shape for it).
//
RuleParticipantSignatureShortDiagramShape signatureShape = null;
if (ruleParticipantShortSignature == null) {
ruleParticipantShortSignature = RuleParticipantShortSignature.fromReactionRuleParticipant(participant, this);
ruleParticipantSignatures.add(ruleParticipantShortSignature);
signatureShape = new RuleParticipantSignatureShortDiagramShape(ruleParticipantShortSignature, this);
addShape(signatureShape);
ReactionContainerShape participantContainerShape = (ReactionContainerShape) getShapeFromModelObject(participant.getStructure());
signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
participantContainerShape.addChildShape(signatureShape);
signatureShape.getSpaceManager().setRelPos(participantContainerShape.getRandomPosition());
} else {
signatureShape = (RuleParticipantSignatureShortDiagramShape) getShapeFromModelObject(ruleParticipantShortSignature);
}
unwantedShapes.remove(signatureShape);
unwantedSignatures.remove(ruleParticipantShortSignature);
signatureShape.refreshLabel();
signatureShape.setVisible(true);
//
// add edge for ReactionRuleParticipant if not already present.
//
RuleParticipantEdgeDiagramShape ruleParticipantShape = (RuleParticipantEdgeDiagramShape) getShapeFromModelObject(participant);
if (ruleParticipantShape == null || ruleParticipantShape.getRuleParticipantSignatureShape() != signatureShape) {
if (participant instanceof ReactantPattern && signatureShape.isVisible()) {
ruleParticipantShape = new ReactantPatternEdgeDiagramShape((ReactantPattern) participant, rrShape, signatureShape, this);
} else if (participant instanceof ProductPattern && signatureShape.isVisible()) {
ruleParticipantShape = new ProductPatternEdgeDiagramShape((ProductPattern) participant, rrShape, signatureShape, this);
} else {
throw new RuntimeException("unsupported ReactionRuleParticipant " + participant.getClass());
}
addShape(ruleParticipantShape);
}
if (!containerShape.getChildren().contains(ruleParticipantShape)) {
containerShape.addChildShape(ruleParticipantShape);
}
unwantedShapes.remove(ruleParticipantShape);
ruleParticipantShape.refreshLabel();
// all the edges for this rule
ruleEdges.add(ruleParticipantShape);
}
}
// a product edge (a closed loop) between the rule diagram shape and the signature diagram shape
for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
// reset them all
ours.setSibling(false);
}
for (RuleParticipantEdgeDiagramShape ours : ruleEdges) {
for (RuleParticipantEdgeDiagramShape theirs : ruleEdges) {
if (ours == theirs) {
// don't compare with self
continue;
}
if (ours.getRuleParticipantSignatureShape() == theirs.getRuleParticipantSignatureShape()) {
ours.setSibling(true);
theirs.setSibling(true);
}
}
}
}
}
ruleParticipantSignatures.removeAll(unwantedSignatures);
for (ReactionStep reactionStep : getModel().getReactionSteps()) {
reactionStep.removePropertyChangeListener(this);
reactionStep.addPropertyChangeListener(this);
Structure structure = reactionStep.getStructure();
if (getStructureSuite().areReactionsShownFor(structure)) {
ReactionContainerShape reactionContainerShape = (ReactionContainerShape) getShapeFromModelObject(structure);
if (reactionContainerShape == null) {
System.out.println("Reaction container shape is null for structure " + structure + " for reaction step " + reactionStep);
}
ReactionStepShape reactionStepShape = (ReactionStepShape) getShapeFromModelObject(reactionStep);
if (reactionStepShape == null) {
if (reactionStep instanceof SimpleReaction) {
reactionStepShape = new SimpleReactionShape((SimpleReaction) reactionStep, this);
} else if (reactionStep instanceof FluxReaction) {
reactionStepShape = new FluxReactionShape((FluxReaction) reactionStep, this);
} else {
throw new RuntimeException("unknown type of ReactionStep '" + reactionStep.getClass().toString());
}
addShape(reactionStepShape);
reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
reactionContainerShape.addChildShape(reactionStepShape);
reactionStepShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
reactionStepShape.refreshLabel();
unwantedShapes.remove(reactionStepShape);
// add reaction participants as edges
for (ReactionParticipant participant : reactionStep.getReactionParticipants()) {
participant.removePropertyChangeListener(this);
participant.addPropertyChangeListener(this);
Structure speciesStructure = participant.getStructure();
Structure reactionStructure = reactionStep.getStructure();
if (getStructureSuite().getStructures().contains(speciesStructure) && getStructureSuite().areReactionsShownFor(reactionStructure)) {
SpeciesContext speciesContext = getModel().getSpeciesContext(participant.getSpecies(), speciesStructure);
// add speciesContextShapes that are not in this structure, but are referenced from the reactionParticipants
// these are only when reactionParticipants are from features that are outside of the membrane being displayed
SpeciesContextShape speciesContextShape = (SpeciesContextShape) getShapeFromModelObject(speciesContext);
if (speciesContextShape == null) {
speciesContextShape = new SpeciesContextShape(speciesContext, this);
speciesContextShape.truncateLabelName(false);
reactionContainerShape.addChildShape(speciesContextShape);
addShape(speciesContextShape);
speciesContextShape.getSpaceManager().setRelPos(reactionContainerShape.getRandomPosition());
}
speciesContextShape.refreshLabel();
unwantedShapes.remove(speciesContextShape);
ReactionParticipantShape reactionParticipantShape = (ReactionParticipantShape) getShapeFromModelObject(participant);
if (reactionParticipantShape == null) {
if (participant instanceof Reactant) {
reactionParticipantShape = new ReactantShape((Reactant) participant, reactionStepShape, speciesContextShape, this);
} else if (participant instanceof Product) {
reactionParticipantShape = new ProductShape((Product) participant, reactionStepShape, speciesContextShape, this);
} else if (participant instanceof Catalyst) {
reactionParticipantShape = new CatalystShape((Catalyst) participant, reactionStepShape, speciesContextShape, this);
} else {
throw new RuntimeException("unsupported ReactionParticipant " + participant.getClass());
}
addShape(reactionParticipantShape);
}
if (!containerShape.getChildren().contains(reactionParticipantShape)) {
containerShape.addChildShape(reactionParticipantShape);
}
unwantedShapes.remove(reactionParticipantShape);
reactionParticipantShape.refreshLabel();
}
}
}
}
for (Shape unwantedShape : unwantedShapes) {
removeShape(unwantedShape);
}
// update diagrams
for (Structure structure : structureSuite.getStructures()) {
Diagram diagram = getModel().getDiagram(structure);
if (diagram != null) {
applyDefaults(diagram);
}
}
fireGraphChanged(new GraphEvent(this));
} catch (Throwable e) {
handleException(e);
}
}
Also used :
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
Product(cbit.vcell.model.Product)
FluxReaction(cbit.vcell.model.FluxReaction)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Feature(cbit.vcell.model.Feature)
Reactant(cbit.vcell.model.Reactant)
HashSet(java.util.HashSet)
ReactionStep(cbit.vcell.model.ReactionStep)
ReactionRuleParticipant(cbit.vcell.model.ReactionRuleParticipant)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
Catalyst(cbit.vcell.model.Catalyst)
RuleParticipantSignature(cbit.vcell.model.RuleParticipantSignature)
Shape(cbit.gui.graph.Shape)
GraphEvent(cbit.gui.graph.GraphEvent)
RuleParticipantShortSignature(cbit.vcell.model.RuleParticipantShortSignature)
Membrane(cbit.vcell.model.Membrane)
Structure(cbit.vcell.model.Structure)
ReactantPattern(cbit.vcell.model.ReactantPattern)
RuleParticipantLongSignature(cbit.vcell.model.RuleParticipantLongSignature)
SimpleReaction(cbit.vcell.model.SimpleReaction)
ReactionRule(cbit.vcell.model.ReactionRule)
ProductPattern(cbit.vcell.model.ProductPattern)
Point(java.awt.Point)
Diagram(cbit.vcell.model.Diagram)
Example 23 with Product
use of cbit.vcell.model.Product in project vcell by virtualcell.
the class BioModelEditorModelPanel method initialize.
private void initialize() {
newButton = new JButton("New");
newButton2 = new JButton("New Rule");
newMemButton = new JButton("New Membrane");
deleteButton = new JButton("Delete");
duplicateButton = new JButton("Duplicate");
pathwayButton = new JButton("Pathway Links", new DownArrowIcon());
pathwayButton.setHorizontalTextPosition(SwingConstants.LEFT);
textFieldSearch = new JTextField();
textFieldSearch.putClientProperty("JTextField.variant", "search");
structuresTable = new EditorScrollTable();
reactionsTable = new EditorScrollTable();
speciesTable = new EditorScrollTable();
molecularTypeTable = new EditorScrollTable();
observablesTable = new EditorScrollTable();
structureTableModel = new BioModelEditorStructureTableModel(structuresTable);
reactionTableModel = new BioModelEditorReactionTableModel(reactionsTable);
speciesTableModel = new BioModelEditorSpeciesTableModel(speciesTable);
molecularTypeTableModel = new MolecularTypeTableModel(molecularTypeTable);
observableTableModel = new ObservableTableModel(observablesTable);
structuresTable.setModel(structureTableModel);
reactionsTable.setModel(reactionTableModel);
speciesTable.setModel(speciesTableModel);
molecularTypeTable.setModel(molecularTypeTableModel);
observablesTable.setModel(observableTableModel);
reactionCartoonEditorPanel = new ReactionCartoonEditorPanel();
reactionCartoonEditorPanel.addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonFull().addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonMolecule().addPropertyChangeListener(eventHandler);
reactionCartoonEditorPanel.getReactionCartoonRule().addPropertyChangeListener(eventHandler);
// cartoonEditorPanel = new CartoonEditorPanelFixed();
// cartoonEditorPanel.getStructureCartoon().addPropertyChangeListener(eventHandler);
/* button panel */
buttonPanel = new JPanel();
buttonPanel.setLayout(new GridBagLayout());
GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newButton2, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 0;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(newMemButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 3;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(duplicateButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 4;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(deleteButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 5;
gbc.insets = new Insets(4, 4, 4, 4);
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
buttonPanel.add(pathwayButton, gbc);
gbc = new GridBagConstraints();
gbc.gridx = 6;
gbc.gridy = 0;
gbc.weightx = 0.5;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(Box.createRigidArea(new Dimension(5, 5)), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 7;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.LINE_END;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(new JLabel("Search "), gbc);
gbc = new GridBagConstraints();
gbc.gridx = 8;
gbc.gridy = 0;
gbc.weightx = 1.5;
gbc.anchor = GridBagConstraints.LINE_START;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(4, 4, 4, 4);
buttonPanel.add(textFieldSearch, gbc);
/* button panel */
tabbedPane = new JTabbedPaneEnhanced();
tabbedPane.setTabLayoutPolicy(JTabbedPane.SCROLL_TAB_LAYOUT);
modelPanelTabs[ModelPanelTabID.reaction_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_diagram, reactionCartoonEditorPanel, VCellIcons.diagramIcon);
// modelPanelTabs[ModelPanelTabID.structure_diagram.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_diagram, cartoonEditorPanel, VCellIcons.structureIcon);
modelPanelTabs[ModelPanelTabID.reaction_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.reaction_table, reactionsTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.structure_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.structure_table, structuresTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.species_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_table, speciesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.species_definitions_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.species_definitions_table, molecularTypeTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
modelPanelTabs[ModelPanelTabID.observables_table.ordinal()] = new ModelPanelTab(ModelPanelTabID.observables_table, observablesTable.getEnclosingScrollPane(), VCellIcons.tableIcon);
tabbedPane.addChangeListener(eventHandler);
tabbedPane.addMouseListener(eventHandler);
for (ModelPanelTab tab : modelPanelTabs) {
tab.getComponent().setBorder(GuiConstants.TAB_PANEL_BORDER);
tabbedPane.addTab(tab.getName(), tab.getIcon(), tab.getComponent());
}
// tabbedPane.addChangeListener(changeListener);
setLayout(new BorderLayout());
add(tabbedPane, BorderLayout.CENTER);
add(buttonPanel, BorderLayout.SOUTH);
newButton.addActionListener(eventHandler);
newButton2.addActionListener(eventHandler);
newMemButton.addActionListener(eventHandler);
duplicateButton.addActionListener(eventHandler);
duplicateButton.setEnabled(false);
deleteButton.addActionListener(eventHandler);
deleteButton.setEnabled(false);
pathwayButton.addActionListener(eventHandler);
pathwayButton.setEnabled(false);
textFieldSearch.addActionListener(eventHandler);
textFieldSearch.getDocument().addDocumentListener(eventHandler);
structuresTable.getSelectionModel().addListSelectionListener(eventHandler);
reactionsTable.getSelectionModel().addListSelectionListener(eventHandler);
speciesTable.getSelectionModel().addListSelectionListener(eventHandler);
molecularTypeTable.getSelectionModel().addListSelectionListener(eventHandler);
observablesTable.getSelectionModel().addListSelectionListener(eventHandler);
DefaultScrollTableCellRenderer tableRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (value instanceof Structure) {
setText(((Structure) value).getName());
} else if (value instanceof Kinetics) {
setText(((Kinetics) value).getKineticsDescription().getDescription());
} else if (value instanceof RbmKineticLaw) {
setText(((RbmKineticLaw) value).getRateLawType().name());
}
return this;
}
};
RbmTableRenderer rbmTableRenderer = new RbmTableRenderer();
structuresTable.setDefaultRenderer(Structure.class, tableRenderer);
speciesTable.setDefaultRenderer(Structure.class, tableRenderer);
reactionsTable.setDefaultRenderer(Structure.class, tableRenderer);
reactionsTable.setDefaultRenderer(Kinetics.class, tableRenderer);
reactionsTable.setDefaultRenderer(RbmKineticLaw.class, tableRenderer);
reactionsTable.setDefaultRenderer(ModelProcessDynamics.class, tableRenderer);
DefaultScrollTableCellRenderer tableCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
BioModelEntityObject bioModelEntityObject = null;
if (table.getModel() instanceof VCellSortTableModel<?>) {
if (table.getModel() == reactionTableModel && reactionTableModel.getValueAt(row) instanceof BioModelEntityObject) {
bioModelEntityObject = (BioModelEntityObject) reactionTableModel.getValueAt(row);
} else if (table.getModel() == speciesTableModel) {
bioModelEntityObject = speciesTableModel.getValueAt(row);
} else if (table.getModel() == molecularTypeTableModel) {
bioModelEntityObject = molecularTypeTableModel.getValueAt(row);
}
if (bioModelEntityObject != null) {
Set<RelationshipObject> relationshipSet = bioModel.getRelationshipModel().getRelationshipObjects(bioModelEntityObject);
if (relationshipSet.size() > 0) {
StringBuilder tooltip = new StringBuilder("<html>Links to Pathway objects:<br>");
for (RelationshipObject ro : relationshipSet) {
tooltip.append("<li>" + ro.getBioPaxObject() + "</li>");
}
if (!isSelected) {
setForeground(Color.blue);
}
String finalName = null;
BioPaxObject bioPaxObject = relationshipSet.iterator().next().getBioPaxObject();
if (bioPaxObject instanceof EntityImpl && ((EntityImpl) bioPaxObject).getName() != null && ((EntityImpl) bioPaxObject).getName().size() > 0) {
finalName = ((EntityImpl) bioPaxObject).getName().get(0);
} else if (bioPaxObject instanceof Conversion) {
Conversion mp = (Conversion) bioPaxObject;
finalName = "[" + bioPaxObject.getIDShort() + "]";
} else {
finalName = bioModelEntityObject.getName();
}
final int LIMIT = 40;
final String DOTS = "...";
if (finalName != null && finalName.length() > LIMIT) {
finalName = finalName.substring(0, LIMIT - DOTS.length() - 1) + DOTS;
}
setText("<html><u>" + finalName + "</u></html>");
setToolTipText(tooltip.toString());
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmReactionExpressionCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
String text = "<html>";
text += "Reaction Rule";
text += "</html>";
setText(text);
} else {
// plain reaction, check if reactants have species pattern
ReactionStep rs = (ReactionStep) selectedObject;
String text = "<html>";
for (int i = 0; i < rs.getNumReactants(); i++) {
Reactant p = rs.getReactant(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
// text += "<b>" + p.getName() + "</b>";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumReactants() - 1) {
text += " + ";
}
}
text += " -> ";
for (int i = 0; i < rs.getNumProducts(); i++) {
Product p = rs.getProduct(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
// text += "<b>" + p.getName() + "</b>";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumProducts() - 1) {
text += " + ";
}
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmReactionDefinitionCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule && value instanceof ModelProcessEquation) {
ReactionRule rr = (ReactionRule) selectedObject;
String text = "<html>";
for (int i = 0; i < rr.getReactantPatterns().size(); i++) {
ReactantPattern rp = rr.getReactantPattern(i);
if (rp.getStructure() != null && !rp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
text += "@" + rp.getStructure().getName() + ":";
}
text += RbmUtils.toBnglString(rp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
// text += RbmTableRenderer.toHtml(rp.getSpeciesPattern(), isSelected);
if (i < rr.getReactantPatterns().size() - 1) {
text += "+";
}
}
if (rr.isReversible()) {
// <-> <->
text += " <-> ";
} else {
text += " -> ";
}
for (int i = 0; i < rr.getProductPatterns().size(); i++) {
ProductPattern pp = rr.getProductPattern(i);
if (pp.getStructure() != null && !pp.getSpeciesPattern().getMolecularTypePatterns().isEmpty()) {
text += "@" + pp.getStructure().getName() + ":";
}
text += RbmUtils.toBnglString(pp.getSpeciesPattern(), null, CompartmentMode.hide, 0);
if (i < rr.getProductPatterns().size() - 1) {
text += "+";
}
}
text += "</html>";
setText(text);
} else {
// plain reaction, check if reactants have species pattern
ReactionStep rs = (ReactionStep) selectedObject;
String text = "<html>";
for (int i = 0; i < rs.getNumReactants(); i++) {
Reactant p = rs.getReactant(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumReactants() - 1) {
text += " + ";
}
}
if (rs.isReversible()) {
// <-> <->
text += " <-> ";
} else {
text += " -> ";
}
for (int i = 0; i < rs.getNumProducts(); i++) {
Product p = rs.getProduct(i);
if (p.getSpeciesContext().hasSpeciesPattern()) {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
} else {
text += p.getStoichiometry() > 1 ? (p.getStoichiometry() + "") : "";
text += p.getName();
}
if (i < rs.getNumProducts() - 1) {
text += " + ";
}
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmObservablePatternCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == observableTableModel) {
selectedObject = observableTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof RbmObservable && value instanceof String) {
RbmObservable o = (RbmObservable) selectedObject;
String text = "<html>";
for (int i = 0; i < o.getSpeciesPatternList().size(); i++) {
SpeciesPattern sp = o.getSpeciesPattern(i);
text += RbmTableRenderer.toHtml(sp, isSelected);
if (i < o.getSpeciesPatternList().size() - 1) {
text += " ";
}
}
text = RbmUtils.appendSequence(text, o);
text += "</html>";
setText(text);
}
}
}
return this;
}
};
DefaultScrollTableCellRenderer rbmSpeciesNameCellRenderer = new DefaultScrollTableCellRenderer() {
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == speciesTableModel) {
selectedObject = speciesTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof SpeciesContext) {
SpeciesContext sc = (SpeciesContext) selectedObject;
String text = "<html>";
if (sc.hasSpeciesPattern()) {
text += "<b>" + sc.getName() + "</b>";
} else {
text += sc.getName();
}
text += "</html>";
setText(text);
}
}
}
return this;
}
};
//
// this renderer only paints the molecular type small shape in the MolecularType Table
//
DefaultScrollTableCellRenderer rbmMolecularTypeShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
MolecularTypeSmallShape stls = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == molecularTypeTableModel) {
selectedObject = molecularTypeTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof MolecularType) {
MolecularType mt = (MolecularType) selectedObject;
Graphics cellContext = table.getGraphics();
if (mt != null) {
stls = new MolecularTypeSmallShape(4, 3, mt, null, cellContext, mt, null, issueManager);
}
}
} else {
stls = null;
}
}
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (stls != null) {
stls.paintSelf(g);
}
}
};
// painting of species patterns small shapes inside the species context table
DefaultScrollTableCellRenderer rbmSpeciesShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
SpeciesPatternSmallShape spss = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == speciesTableModel) {
selectedObject = speciesTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof SpeciesContext) {
SpeciesContext sc = (SpeciesContext) selectedObject;
// sp may be null for "plain" species contexts
SpeciesPattern sp = sc.getSpeciesPattern();
Graphics panelContext = table.getGraphics();
spss = new SpeciesPatternSmallShape(4, 2, sp, panelContext, sc, isSelected, issueManager);
}
} else {
spss = null;
}
}
setText("");
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
if (spss != null) {
spss.paintSelf(g);
}
}
};
// ---------------------------------------------------------------------------------------------------------------------------------
DefaultScrollTableCellRenderer rbmReactionShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();
SpeciesPatternSmallShape spss = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == reactionTableModel) {
selectedObject = reactionTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof ReactionRule) {
ReactionRule rr = (ReactionRule) selectedObject;
Graphics panelContext = table.getGraphics();
spssList.clear();
List<ReactantPattern> rpList = rr.getReactantPatterns();
int xPos = 4;
for (int i = 0; i < rpList.size(); i++) {
SpeciesPattern sp = rr.getReactantPattern(i).getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
if (i < rpList.size() - 1) {
spss.addEndText("+");
} else {
if (rr.isReversible()) {
spss.addEndText("<->");
xPos += 7;
} else {
spss.addEndText("->");
}
}
xPos += spss.getWidth() + 15;
spssList.add(spss);
}
List<ProductPattern> ppList = rr.getProductPatterns();
xPos += 7;
for (int i = 0; i < ppList.size(); i++) {
SpeciesPattern sp = rr.getProductPattern(i).getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, null, panelContext, rr, isSelected, issueManager);
if (i < ppList.size() - 1) {
spss.addEndText("+");
}
xPos += spss.getWidth() + 15;
spssList.add(spss);
}
} else {
ReactionStep rs = (ReactionStep) selectedObject;
Graphics panelContext = table.getGraphics();
spssList.clear();
int xPos = 4;
int extraSpace = 0;
for (int i = 0; i < rs.getNumReactants(); i++) {
SpeciesPattern sp = rs.getReactant(i).getSpeciesContext().getSpeciesPattern();
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
if (i < rs.getNumReactants() - 1) {
spss.addEndText("+");
} else {
if (rs.isReversible()) {
spss.addEndText("<->");
extraSpace += 7;
} else {
spss.addEndText("->");
}
}
int offset = sp == null ? 17 : 15;
offset += extraSpace;
int w = spss.getWidth();
xPos += w + offset;
spssList.add(spss);
}
xPos += 8;
for (int i = 0; i < rs.getNumProducts(); i++) {
SpeciesPattern sp = rs.getProduct(i).getSpeciesContext().getSpeciesPattern();
if (i == 0 && rs.getNumReactants() == 0) {
xPos += 14;
}
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, rs, isSelected, issueManager);
if (i == 0 && rs.getNumReactants() == 0) {
spss.addStartText("->");
}
if (i < rs.getNumProducts() - 1) {
spss.addEndText("+");
}
int offset = sp == null ? 17 : 15;
int w = spss.getWidth();
xPos += w + offset;
spssList.add(spss);
}
}
} else {
spssList.clear();
}
}
setText("");
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
for (SpeciesPatternSmallShape spss : spssList) {
if (spss == null) {
continue;
}
spss.paintSelf(g);
}
}
};
// -------------------------------------------------------------------------------------------------------------------------------
DefaultScrollTableCellRenderer rbmObservableShapeDepictionCellRenderer = new DefaultScrollTableCellRenderer() {
List<SpeciesPatternSmallShape> spssList = new ArrayList<SpeciesPatternSmallShape>();
SpeciesPatternSmallShape spss = null;
@Override
public Component getTableCellRendererComponent(JTable table, Object value, boolean isSelected, boolean hasFocus, int row, int column) {
super.getTableCellRendererComponent(table, value, isSelected, hasFocus, row, column);
if (table.getModel() instanceof VCellSortTableModel<?>) {
Object selectedObject = null;
if (table.getModel() == observableTableModel) {
selectedObject = observableTableModel.getValueAt(row);
}
if (selectedObject != null) {
if (selectedObject instanceof RbmObservable) {
RbmObservable observable = (RbmObservable) selectedObject;
Graphics panelContext = table.getGraphics();
int xPos = 4;
spssList.clear();
for (int i = 0; i < observable.getSpeciesPatternList().size(); i++) {
SpeciesPattern sp = observable.getSpeciesPatternList().get(i);
spss = new SpeciesPatternSmallShape(xPos, 2, sp, panelContext, observable, isSelected, issueManager);
xPos += spss.getWidth() + 6;
spssList.add(spss);
}
}
} else {
spssList.clear();
}
}
setText("");
return this;
}
@Override
public void paintComponent(Graphics g) {
super.paintComponent(g);
for (SpeciesPatternSmallShape spss : spssList) {
if (spss == null) {
continue;
}
spss.paintSelf(g);
}
}
};
// TODO: here are the renderers associated with the columns
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_EQUATION).setCellRenderer(rbmReactionExpressionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEFINITION).setCellRenderer(rbmReactionDefinitionCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_NAME).setCellRenderer(rbmSpeciesNameCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_LINK).setCellRenderer(tableCellRenderer);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.link.ordinal()).setCellRenderer(tableCellRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.species_pattern.ordinal()).setCellRenderer(rbmObservablePatternCellRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.structure.ordinal()).setCellRenderer(tableRenderer);
// all "depictions" have their own renderer
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setCellRenderer(rbmMolecularTypeShapeDepictionCellRenderer);
molecularTypeTable.getColumnModel().getColumn(MolecularTypeTableModel.Column.depiction.ordinal()).setMaxWidth(180);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEPICTION).setCellRenderer(rbmSpeciesShapeDepictionCellRenderer);
speciesTable.getColumnModel().getColumn(BioModelEditorSpeciesTableModel.COLUMN_DEFINITION).setCellRenderer(rbmTableRenderer);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.depiction.ordinal()).setCellRenderer(rbmObservableShapeDepictionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setCellRenderer(rbmReactionShapeDepictionCellRenderer);
reactionsTable.getColumnModel().getColumn(BioModelEditorReactionTableModel.COLUMN_DEPICTION).setPreferredWidth(180);
observablesTable.getColumnModel().getColumn(ObservableTableModel.Column.type.ordinal()).setCellEditor(observableTableModel.getObservableTypeComboBoxEditor());
observableTableModel.updateObservableTypeComboBox();
reactionsTable.addMouseListener(eventHandler);
reactionsTable.addKeyListener(eventHandler);
speciesTable.addMouseListener(eventHandler);
speciesTable.addKeyListener(eventHandler);
molecularTypeTable.addMouseListener(eventHandler);
molecularTypeTable.addKeyListener(eventHandler);
observablesTable.addMouseListener(eventHandler);
observablesTable.addKeyListener(eventHandler);
structuresTable.addKeyListener(eventHandler);
}
Also used :
JPanel(javax.swing.JPanel)
GridBagConstraints(java.awt.GridBagConstraints)
Product(cbit.vcell.model.Product)
SpeciesContext(cbit.vcell.model.SpeciesContext)
RelationshipObject(org.vcell.relationship.RelationshipObject)
Reactant(cbit.vcell.model.Reactant)
JTabbedPaneEnhanced(org.vcell.util.gui.JTabbedPaneEnhanced)
BorderLayout(java.awt.BorderLayout)
ArrayList(java.util.ArrayList)
List(java.util.List)
JList(javax.swing.JList)
EntityImpl(org.vcell.pathway.EntityImpl)
RbmObservable(cbit.vcell.model.RbmObservable)
BioModelEntityObject(cbit.vcell.model.BioModelEntityObject)
Conversion(org.vcell.pathway.Conversion)
ReactionCartoonEditorPanel(cbit.vcell.graph.gui.ReactionCartoonEditorPanel)
MolecularType(org.vcell.model.rbm.MolecularType)
JTable(javax.swing.JTable)
ReactionStep(cbit.vcell.model.ReactionStep)
RelationshipObject(org.vcell.relationship.RelationshipObject)
BioModelEntityObject(cbit.vcell.model.BioModelEntityObject)
BioPaxObject(org.vcell.pathway.BioPaxObject)
EditorScrollTable(org.vcell.util.gui.EditorScrollTable)
Kinetics(cbit.vcell.model.Kinetics)
Insets(java.awt.Insets)
GridBagLayout(java.awt.GridBagLayout)
SpeciesPatternSmallShape(cbit.vcell.graph.SpeciesPatternSmallShape)
BioPaxObject(org.vcell.pathway.BioPaxObject)
JButton(javax.swing.JButton)
JTextField(javax.swing.JTextField)
SpeciesPattern(org.vcell.model.rbm.SpeciesPattern)
Structure(cbit.vcell.model.Structure)
ReactantPattern(cbit.vcell.model.ReactantPattern)
ReactionRule(cbit.vcell.model.ReactionRule)
ProductPattern(cbit.vcell.model.ProductPattern)
JLabel(javax.swing.JLabel)
Dimension(java.awt.Dimension)
RbmKineticLaw(cbit.vcell.model.RbmKineticLaw)
Graphics(java.awt.Graphics)
MolecularTypeSmallShape(cbit.vcell.graph.MolecularTypeSmallShape)
DownArrowIcon(org.vcell.util.gui.DownArrowIcon)
ModelProcessEquation(cbit.gui.ModelProcessEquation)
DefaultScrollTableCellRenderer(org.vcell.util.gui.DefaultScrollTableCellRenderer)
Example 24 with Product
use of cbit.vcell.model.Product in project vcell by virtualcell.
the class BNGOutputPanel method getCollapsedReactionSteps.
private ReactionStep[] getCollapsedReactionSteps(ReactionStep[] reactionSteps) {
Vector<ReactionStep> collapsedRxnStepsVector = new Vector<ReactionStep>();
Vector<ReactionStep> rxnStepsVector = new Vector<ReactionStep>();
for (int i = 0; i < reactionSteps.length; i++) {
rxnStepsVector.addElement(reactionSteps[i]);
}
for (int i = 0; i < rxnStepsVector.size(); i++) {
ReactionStep fwdRStep = rxnStepsVector.elementAt(i);
// Get the reactionParticipants and the corresponding reactants and products in an array
ReactionParticipant[] rps = fwdRStep.getReactionParticipants();
Vector<SpeciesContext> fwdReactantsVector = new Vector<SpeciesContext>();
Vector<SpeciesContext> fwdProductsVector = new Vector<SpeciesContext>();
for (int j = 0; j < rps.length; j++) {
if (rps[j] instanceof Reactant) {
fwdReactantsVector.addElement(rps[j].getSpeciesContext());
} else if (rps[j] instanceof Product) {
fwdProductsVector.addElement(rps[j].getSpeciesContext());
}
}
SpeciesContext[] fwdReactants = (SpeciesContext[]) BeanUtils.getArray(fwdReactantsVector, SpeciesContext.class);
SpeciesContext[] fwdProducts = (SpeciesContext[]) BeanUtils.getArray(fwdProductsVector, SpeciesContext.class);
boolean bReverseReactionFound = false;
// Loop through all the reactions to find the corresponding reverse reaction
for (int ii = 0; ii < reactionSteps.length; ii++) {
ReactionStep revRStep = reactionSteps[ii];
// Get the reactionParticipants and the corresponding reactants and products in an array
ReactionParticipant[] revRps = revRStep.getReactionParticipants();
Vector<SpeciesContext> revReactantsVector = new Vector<SpeciesContext>();
Vector<SpeciesContext> revProductsVector = new Vector<SpeciesContext>();
for (int j = 0; j < revRps.length; j++) {
if (revRps[j] instanceof Reactant) {
revReactantsVector.addElement(revRps[j].getSpeciesContext());
} else if (revRps[j] instanceof Product) {
revProductsVector.addElement(revRps[j].getSpeciesContext());
}
}
SpeciesContext[] revReactants = (SpeciesContext[]) BeanUtils.getArray(revReactantsVector, SpeciesContext.class);
SpeciesContext[] revProducts = (SpeciesContext[]) BeanUtils.getArray(revProductsVector, SpeciesContext.class);
// Check if reactants of reaction in outer 'for' loop match products in inner 'for' loop and vice versa.
if (BeanUtils.arrayEquals(fwdReactants, revProducts) && BeanUtils.arrayEquals(fwdProducts, revReactants)) {
// Set the reverse kinetic rate expression for the reaction in outer loop with the forward rate from reactionStep in inner loop
// inner 'for' loop
MassActionKinetics revMAKinetics = (MassActionKinetics) revRStep.getKinetics();
// outer 'for' loop
MassActionKinetics fwdMAKinetics = (MassActionKinetics) fwdRStep.getKinetics();
try {
fwdMAKinetics.setParameterValue(fwdMAKinetics.getReverseRateParameter(), revMAKinetics.getForwardRateParameter().getExpression());
Kinetics.KineticsParameter param = revMAKinetics.getKineticsParameter(revMAKinetics.getForwardRateParameter().getExpression().infix());
fwdMAKinetics.setParameterValue(param, param.getExpression());
} catch (Exception e) {
e.printStackTrace(System.out);
throw new RuntimeException(e.getMessage());
}
// Add this to the collapsedRxnStepsVector
collapsedRxnStepsVector.addElement(fwdRStep);
rxnStepsVector.removeElement(revRStep);
bReverseReactionFound = true;
break;
}
}
// Add it as is to the 'collapsedRxnStepsVector'
if (!bReverseReactionFound) {
collapsedRxnStepsVector.addElement(fwdRStep);
}
}
// Convert the vector into an array of reactionSteps and return
ReactionStep[] collapsedRxnSteps = (ReactionStep[]) BeanUtils.getArray(collapsedRxnStepsVector, ReactionStep.class);
return collapsedRxnSteps;
}
Also used :
Product(cbit.vcell.model.Product)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Reactant(cbit.vcell.model.Reactant)
SbmlTransformException(cbit.vcell.xml.sbml_transform.SbmlTransformException)
IOException(java.io.IOException)
ReactionStep(cbit.vcell.model.ReactionStep)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
Kinetics(cbit.vcell.model.Kinetics)
MassActionKinetics(cbit.vcell.model.MassActionKinetics)
Vector(java.util.Vector)
ReactionParticipant(cbit.vcell.model.ReactionParticipant)
Example 25 with Product
use of cbit.vcell.model.Product in project vcell by virtualcell.
the class XmlReader method getProduct.
/**
* This method returns a Product object from a XML representation.
* Creation date: (5/4/2001 2:22:56 PM)
* @return cbit.vcell.model.Product
* @param param org.jdom.Element
* @exception cbit.vcell.xml.XmlParseException The exception description.
*/
private Product getProduct(Element param, ReactionStep reaction, Model model) throws XmlParseException {
// retrieve the key if there is one
KeyValue key = null;
String keystring = param.getAttributeValue(XMLTags.KeyValueAttrTag);
if (keystring != null && keystring.length() > 0 && this.readKeysFlag) {
key = new KeyValue(keystring);
}
String speccontref = unMangle(param.getAttributeValue(XMLTags.SpeciesContextRefAttrTag));
SpeciesContext speccont = model.getSpeciesContext(speccontref);
if (speccont == null) {
throw new XmlParseException("The reference to the SpecieContext " + speccontref + " for a Product could not be resolved!");
}
// Retrieve Stoichiometry
int stoch = 1;
org.jdom.Attribute tempAttrib = param.getAttribute(XMLTags.StoichiometryAttrTag);
if (tempAttrib != null) {
String temp = tempAttrib.getValue();
if (temp.length() > 0) {
stoch = Integer.parseInt(temp);
}
}
return new Product(key, reaction, speccont, stoch);
}
Also used :
KeyValue(org.vcell.util.document.KeyValue)
Product(cbit.vcell.model.Product)
Attribute(org.jdom.Attribute)
SpeciesContext(cbit.vcell.model.SpeciesContext)
Aggregations
Product (cbit.vcell.model.Product)31
Reactant (cbit.vcell.model.Reactant)30
ReactionParticipant (cbit.vcell.model.ReactionParticipant)26
ReactionStep (cbit.vcell.model.ReactionStep)22
SpeciesContext (cbit.vcell.model.SpeciesContext)19
SimpleReaction (cbit.vcell.model.SimpleReaction)12
ArrayList (java.util.ArrayList)12
Model (cbit.vcell.model.Model)11
Structure (cbit.vcell.model.Structure)11
Catalyst (cbit.vcell.model.Catalyst)10
FluxReaction (cbit.vcell.model.FluxReaction)10
Expression (cbit.vcell.parser.Expression)10
Kinetics (cbit.vcell.model.Kinetics)8
KineticsParameter (cbit.vcell.model.Kinetics.KineticsParameter)8
ReactionRule (cbit.vcell.model.ReactionRule)8
HashMap (java.util.HashMap)8
LumpedKinetics (cbit.vcell.model.LumpedKinetics)6
ModelParameter (cbit.vcell.model.Model.ModelParameter)5
ExpressionException (cbit.vcell.parser.ExpressionException)5
BioModel (cbit.vcell.biomodel.BioModel)4
