use of org.vcell.pathway.Complex in project vcell by virtualcell.
the class BioPaxObjectPropertiesPanel method refreshInterface.
protected void refreshInterface() {
if (bioPaxObject == null) {
// sanity check
return;
}
ArrayList<BioPaxObjectProperty> propertyList = new ArrayList<BioPaxObjectProperty>();
if (!(bioPaxObject instanceof SBEntity)) {
tableModel.setData(propertyList);
return;
}
SBEntity sbEntity = (SBEntity) bioPaxObject;
if (!(sbEntity instanceof Entity)) {
tableModel.setData(propertyList);
return;
}
Entity entity = (Entity) sbEntity;
// entity::type
propertyList.add(new BioPaxObjectProperty("Type", bioPaxObject.getTypeLabel()));
if (lookupContains(entity)) {
propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (looking...)"));
} else if (entity.getFormalNames() != null && entity.getFormalNames().size() != 0) {
propertyList.add(new BioPaxObjectProperty("Name", entity.getName().get(0) + " (" + entity.getFormalNames().get(0) + ")"));
} else if (entity.getName() != null && entity.getName().size() > 0) {
String displayName = entity.getName().get(0);
if (entity.getxRef() != null && entity.getxRef().size() > 0) {
displayName = displayName + " (double-click lookup)";
}
// entity::name
propertyList.add(new BioPaxObjectProperty("Name", displayName));
}
// entity::Link
for (RelationshipObject rObject : bioModel.getRelationshipModel().getRelationshipObjects(bioPaxObject)) {
BioModelEntityObject beObject = rObject.getBioModelEntityObject();
propertyList.add(new BioPaxObjectProperty("Linked physiology object", beObject.getName(), beObject));
}
if (entity instanceof PhysicalEntity) {
// ------------------------ PHYSICAL ENTITY -----------------------
PhysicalEntity physicalEntity = (PhysicalEntity) entity;
// physicalEntity::feature (***ignored***)
// physicalEntity::memberPhysicalEntity (***ignored***)
// physicalEntity::notFeature (***ignored***)
// TODO: extract the kinetic law, then the SBEntities, then the measurables, units, aso
boolean isReactionParticipant = BioPAXUtil.isReactionParticipant(physicalEntity, bioModel.getPathwayModel());
String role = "";
if (BioPAXUtil.isController(physicalEntity, bioModel.getPathwayModel())) {
role += "Controller";
if (isReactionParticipant) {
role += ", Participant";
}
} else if (isReactionParticipant) {
role += "Participant";
}
if (!role.isEmpty()) {
propertyList.add(new BioPaxObjectProperty("Role(s)", role));
}
if (!(physicalEntity instanceof SmallMolecule)) {
// physicalEntity::cellular location
CellularLocationVocabulary cellularLocation = physicalEntity.getCellularLocation();
if (cellularLocation != null && cellularLocation.getTerm() != null && cellularLocation.getTerm().size() > 0) {
propertyList.add(new BioPaxObjectProperty("Cellular Location", cellularLocation.getTerm().get(0), cellularLocation));
} else if (entity.getName() != null && entity.getName().size() > 1) {
String location = entity.getName().get(1);
if (location.contains("[") && location.contains("]")) {
location = location.substring(location.indexOf("[") + 1, location.indexOf("]"));
propertyList.add(new BioPaxObjectProperty("Cellular Location", location));
}
}
}
if (physicalEntity instanceof Complex) {
Complex complex = (Complex) physicalEntity;
// complex::components
for (PhysicalEntity pe : complex.getComponents()) {
propertyList.add(new BioPaxObjectProperty("Component", getEntityName(pe), pe));
}
} else if (physicalEntity instanceof Protein) {
// Protein protein = (Protein)entity;
// protein::entity reference (***ignored***)
} else if (physicalEntity instanceof SmallMolecule) {
SmallMolecule sm = (SmallMolecule) physicalEntity;
EntityReference er = sm.getEntityReference();
if (er != null && !er.getName().isEmpty() && er.getName().get(0) != null && !er.getName().get(0).isEmpty()) {
propertyList.add(new BioPaxObjectProperty("Entity Reference", er.getName().get(0)));
ArrayList<Xref> xrefList = er.getxRef();
for (Xref xref : xrefList) {
propertyList.add(new BioPaxObjectProperty(" Xref", xref.getDb() + ":" + xref.getId(), xref));
}
}
} else if (physicalEntity instanceof Dna) {
// dna::entityReference (***ignored***)
} else if (physicalEntity instanceof DnaRegion) {
// dnaRegion::entityReference (***ignored***)
} else if (physicalEntity instanceof Rna) {
// rna::entityReference (***ignored***)
} else if (physicalEntity instanceof RnaRegion) {
// rnaRegion::entityReference (***ignored***)
}
} else if (entity instanceof Interaction) {
// --------------------------- INTERACTION -------------------
Interaction interaction = (Interaction) entity;
// interaction::interactionType
for (InteractionVocabulary interactionVocabulary : interaction.getInteractionTypes()) {
if (interactionVocabulary.getTerm().size() > 0) {
propertyList.add(new BioPaxObjectProperty("Interaction Type", interactionVocabulary.getTerm().get(0), interactionVocabulary));
}
}
// interaction::participants
for (InteractionParticipant interactionParticipant : interaction.getParticipants()) {
PhysicalEntity physicalEntity = interactionParticipant.getPhysicalEntity();
String physicalEntityName = physicalEntity.getName().size() > 0 ? physicalEntity.getName().get(0) : physicalEntity.getIDShort();
String cellularLocation = "";
if (physicalEntity.getCellularLocation() != null) {
cellularLocation = physicalEntity.getCellularLocation().getTerm().size() > 0 ? " [" + physicalEntity.getCellularLocation().getTerm().get(0) + "]" : "";
}
propertyList.add(new BioPaxObjectProperty(interactionParticipant.getLevel3PropertyName(), physicalEntityName + cellularLocation, physicalEntity));
}
// get the controllers for interactions
// we always need this because there's no guarantee we'll have kinetic laws
// for instance pathway commons doesn't have quantitative information
Set<String> controllersNames = getControllersNames(interaction);
if (controllersNames.size() > 0) {
for (String str : controllersNames) {
// String tooltip = "<html>how many of these 12 M <br>average size 1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
String tooltip = "";
propertyList.add(new BioPaxObjectProperty("Controlled by", str, interaction, tooltip));
}
}
// get the kinetic laws (if any)
Set<Control> controls = BioPAXUtil.getControlsOfInteraction(interaction, bioModel.getPathwayModel());
for (Control control : controls) {
ArrayList<SBEntity> sbEntities = control.getSBSubEntity();
for (SBEntity sbE : sbEntities) {
// the only SBSubEntities allowed in a control are kinetic laws
if (sbE.getID().contains("kineticLaw")) {
String str = new String();
if (control.getPhysicalControllers() != null) {
str += " for Controller(s): ";
for (PhysicalEntity ep : control.getPhysicalControllers()) {
if (ep.getName().size() > 0) {
str += ep.getName().get(0);
} else {
str += ep.getIDShort();
}
str += " ";
}
}
String sDetails = "";
ArrayList<SBVocabulary> sbTerms = sbE.getSBTerm();
for (SBVocabulary sbv : sbTerms) {
// type of kinetic law
String str1 = sbv.getID();
str1 = str1.substring(str1.lastIndexOf('#') + 1);
System.out.println(str1);
SBOTerm sboT = SBOListEx.sboMap.get(str1);
sDetails += "<font color=\"#660000\"><b>" + sboT.getName() + "</b></font>" + " " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
sDetails += "<br>";
}
ArrayList<SBEntity> klProperties = sbE.getSBSubEntity();
for (SBEntity klProperty : klProperties) {
if (klProperty instanceof SBMeasurable) {
SBMeasurable m = (SBMeasurable) klProperty;
String str1 = "";
String str2 = "";
String str3 = "";
if (m.hasTerm()) {
str1 += m.extractSBOTermAsString();
}
if (m.hasNumber()) {
str2 += m.getNumber().get(0);
}
if (m.hasUnit()) {
str3 += m.extractSBOUnitAsString();
}
// str1 is an SBO id, for example "SBO:0000064"
SBOTerm sboT = SBOListEx.sboMap.get(str1);
sDetails += sboT.getSymbol() + " (" + sboT.getName() + ")" + "<font color=\"#660000\"><b>" + str2 + str3 + "</b></font>" + " " + "<font color=\"#006600\">" + sboT.getDescription() + "</font>";
} else {
sDetails = klProperty.getIDShort() + " " + klProperty.getTypeLabel();
}
sDetails += "<br>";
}
// String tooltip = "<html>how many of these 12 M <br>average size 1.12345*E12 nm <br>temperature 37 degrees Celsius</html>";
String tooltip = "";
BioPaxObjectProperty bpop = new BioPaxObjectProperty("Kinetic Law" + str, sbE.getID(), sbE, tooltip);
bpop.setDetails(sDetails);
propertyList.add(bpop);
}
}
}
if (interaction instanceof Control) {
// TODO: is this ever being called?
Control c = (Control) interaction;
// catalysis::controlled
Interaction controlledInteraction = c.getControlledInteraction();
if (controlledInteraction != null) {
String controlledName = controlledInteraction.getIDShort();
if (controlledInteraction.getName().size() > 0) {
controlledName = controlledInteraction.getName().get(0);
}
propertyList.add(new BioPaxObjectProperty("Controlled Interaction", controlledName, controlledInteraction));
}
}
} else if (entity instanceof GroupObject) {
// ---------------------- GROUP OBJECT ------------------
GroupObject groupObject = (GroupObject) entity;
for (BioPaxObject bpo : groupObject.getGroupedObjects()) {
propertyList.add(new BioPaxObjectProperty("Element::" + bpo.getTypeLabel(), getEntityName((Entity) bpo), bpo));
}
}
// entity::comments
for (String comment : entity.getComments()) {
propertyList.add(new BioPaxObjectProperty("Comment", comment));
}
// entity::xRef
ArrayList<Xref> xrefList = ((Entity) bioPaxObject).getxRef();
for (Xref xref : xrefList) {
if (xref instanceof UnificationXref) {
propertyList.add(new BioPaxObjectProperty("Xref", xref.getDb() + ":" + xref.getId(), xref));
}
}
for (Xref xref : xrefList) {
if (xref instanceof RelationshipXref) {
propertyList.add(new BioPaxObjectProperty("Xref (related)", xref.getDb() + ":" + xref.getId(), xref));
}
}
for (Xref xref : xrefList) {
if (xref instanceof PublicationXref) {
propertyList.add(new BioPaxObjectProperty("Publication", xref.getDb() + ":" + xref.getId(), xref));
}
}
// for(SBVocabulary sbVocab : sbEntity.getSBTerm()) {
// propertyList.add(new BioPaxObjectProperty("SBO Term", SBPAXLabelUtil.makeLabel(sbVocab)));
// }
// if(sbEntity instanceof Interaction) {
// // TODO: this goes away
// Interaction interaction = (Interaction) sbEntity;
// Set<SBEntity> subEntities = new HashSet<SBEntity>();
// subEntities.add(interaction);
// Set<Control> controls = BioPAXUtil.findAllControls(interaction, bioModel.getPathwayModel());
// subEntities.addAll(controls);
// subEntities = SBPAX3Util.extractAllEntities(subEntities);
// for(SBEntity subEntity : subEntities) {
// if(subEntity instanceof SBMeasurable) {
// propertyList.add(new BioPaxObjectProperty("Measured quantity", SBPAXLabelUtil.makeLabel(subEntity)));
// }
// }
// }
tableModel.setData(propertyList);
}
use of org.vcell.pathway.Complex in project vcell by virtualcell.
the class PathwayGraphModel method refreshAll.
@Override
public void refreshAll() {
if (pathwayModel == null) {
clearAllShapes();
fireGraphChanged();
return;
}
unwantedShapes = new HashSet<Shape>();
unwantedShapes.addAll(getShapes());
pathwayContainerShape = (PathwayContainerShape) getShapeFromModelObject(pathwayModel);
if (pathwayContainerShape == null) {
pathwayContainerShape = new PathwayContainerShape(this, pathwayModel);
pathwayContainerShape.getSpaceManager().setSize(400, 300);
addShape(pathwayContainerShape);
}
unwantedShapes.remove(pathwayContainerShape);
Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(pathwayModel.getDisplayableBioPaxObjectList());
for (BioPaxObject bpObject : bioPaxObjects) {
BioPaxShape bpObjectShape = (BioPaxShape) getShapeFromModelObject(bpObject);
if (bpObjectShape == null) {
if (bpObject instanceof Conversion) {
bpObjectShape = new BioPaxConversionShape((Conversion) bpObject, this);
} else if (bpObject instanceof MolecularInteraction) {
bpObjectShape = new BioPaxMolecularInteractionShape((MolecularInteraction) bpObject, this);
} else if (bpObject instanceof Protein) {
bpObjectShape = new BioPaxProteinShape((Protein) bpObject, this);
} else if (bpObject instanceof Complex) {
bpObjectShape = new BioPaxComplexShape((Complex) bpObject, this);
} else if (bpObject instanceof SmallMolecule) {
bpObjectShape = new BioPaxSmallMoleculeShape((SmallMolecule) bpObject, this);
} else if (bpObject instanceof Dna) {
bpObjectShape = new BioPaxDnaShape((Dna) bpObject, this);
} else if (bpObject instanceof Rna) {
bpObjectShape = new BioPaxRnaShape((Rna) bpObject, this);
} else if (bpObject instanceof PhysicalEntity) {
bpObjectShape = new BioPaxPhysicalEntityShape((PhysicalEntity) bpObject, this);
} else if (bpObject instanceof GroupObject) {
bpObjectShape = new BioPaxGroupShape((GroupObject) bpObject, this);
} else {
bpObjectShape = new BioPaxObjectShape(bpObject, this);
}
if (!(bpObject instanceof Control)) {
// the Control objects will not be displayed on the diagram
pathwayContainerShape.addChildShape(bpObjectShape);
addShape(bpObjectShape);
}
Dimension shapeSize = bpObjectShape.getSpaceManager().getSize();
Rectangle boundary = getContainerLayout().getBoundaryForAutomaticLayout(pathwayContainerShape);
int xPos = boundary.x + random.nextInt(boundary.width - shapeSize.width);
int yPos = boundary.y + random.nextInt(boundary.height - shapeSize.height);
bpObjectShape.setAbsPos(xPos, yPos);
}
unwantedShapes.remove(bpObjectShape);
}
for (BioPaxObject bpObject : bioPaxObjects) {
if (bpObject instanceof Conversion) {
refreshInteraction((Conversion) bpObject);
} else if (bpObject instanceof MolecularInteraction) {
refreshInteraction((MolecularInteraction) bpObject);
} else if (bpObject instanceof Control) {
refreshControl((Control) bpObject);
} else if (bpObject instanceof GroupObject) {
refreshGroupObject((GroupObject) bpObject);
}
}
for (Shape unwantedShape : unwantedShapes) {
removeShape(unwantedShape);
}
refreshRelationshipInfo();
fireGraphChanged();
}
use of org.vcell.pathway.Complex in project vcell by virtualcell.
the class BioModelEditorPathwayDiagramPanel method collapseBioPaxObject.
private void collapseBioPaxObject() {
HashSet<BioPaxObject> selected = new HashSet<BioPaxObject>(getSelectedBioPaxObjects());
if (selected.size() == 0)
return;
if (bioModel == null || bioModel.getPathwayModel() == null)
return;
PathwayGrouping pathwayGrouping = new PathwayGrouping();
GroupObject groupObject = null;
HashSet<BioPaxObject> hiddenobjects = new HashSet<BioPaxObject>();
for (BioPaxObject bpObject : selected) {
hiddenobjects.clear();
if (bpObject instanceof Complex || bpObject instanceof Protein || bpObject instanceof SmallMolecule) {
// collapse complex with physicalEntities
groupObject = collapse2Complex(bpObject);
} else if (bpObject instanceof Interaction) {
for (InteractionParticipant itp : ((Interaction) bpObject).getParticipants()) {
hiddenobjects.add(itp.getPhysicalEntity());
}
hiddenobjects.add(bpObject);
String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), ((Entity) bpObject).getName(), id, hiddenobjects, GroupObject.Type.GROUPEDINTERACTION);
}
}
if (groupObject != null) {
bioModel.getPathwayModel().add(groupObject);
bioModel.getPathwayModel().refreshGroupMap();
// set the grouped object to be selected
graphCartoonTool.getGraphModel().setSelectedObjects(new GroupObject[] { groupObject });
pathwayGraphModel.refreshAll();
}
}
use of org.vcell.pathway.Complex in project vcell by virtualcell.
the class BioModelEditorPathwayDiagramPanel method deleteSelectedBioPaxObjects.
public static void deleteSelectedBioPaxObjects(Component guiRequester, BioModel bioModel, GraphModel graphModel) {
StringBuilder warning = new StringBuilder("You can NOT delete the following pathway objects:\n\n");
StringBuilder text = new StringBuilder("You are going to DELETE the following pathway objects:\n\n");
// all objects required by user
List<BioPaxObject> selected = getSelectedBioPaxObjects(graphModel);
// the user required objects that can be deleted
List<BioPaxObject> selectedBioPaxObjects = new ArrayList<BioPaxObject>();
// all objects that will be deleted from the pathway model
List<BioPaxObject> completeSelectedBioPaxObjects = new ArrayList<BioPaxObject>();
// used for recover group objects
HashSet<GroupObject> undeletedGroupObjects = new HashSet<GroupObject>();
// all objects required by user + grouped elements contained in selected group objects
List<BioPaxObject> allSelectedBioPaxObjects = new ArrayList<BioPaxObject>();
// build a list of selected objects with selected grouped elements
for (BioPaxObject bpObject : selected) {
if (bpObject instanceof GroupObject) {
// all elements of the groupObject will be deleted
allSelectedBioPaxObjects.add(bpObject);
// check all elements
allSelectedBioPaxObjects.addAll(getAllGroupedObjects((GroupObject) bpObject));
} else {
allSelectedBioPaxObjects.add(bpObject);
}
}
// if so, whether participants and catalysts of a selected reaction can be deleted
for (BioPaxObject bpObject : allSelectedBioPaxObjects) {
if (canDelete(bioModel, allSelectedBioPaxObjects, bpObject)) {
selectedBioPaxObjects.add(bpObject);
text.append(" " + bpObject.getTypeLabel() + ": \'" + PhysiologyRelationshipTableModel.getLabel(bpObject) + "\'\n");
completeSelectedBioPaxObjects.add(bpObject);
if (bpObject instanceof Conversion) {
// check each participant
for (InteractionParticipant ip : ((Conversion) bpObject).getParticipants()) {
if (canDelete(bioModel, allSelectedBioPaxObjects, ip.getPhysicalEntity())) {
completeSelectedBioPaxObjects.add(ip.getPhysicalEntity());
// the complex of the pysicalEntity will be removed
for (Complex complex : getComplex(bioModel, ip.getPhysicalEntity())) {
if (canDelete(bioModel, allSelectedBioPaxObjects, complex))
completeSelectedBioPaxObjects.add(complex);
}
}
}
// check catalysts
for (BioPaxObject bp : bioModel.getPathwayModel().getBiopaxObjects()) {
if (bp instanceof Control) {
Control control = (Control) bp;
if (control.getControlledInteraction() == bpObject) {
completeSelectedBioPaxObjects.add(bp);
for (PhysicalEntity pe : control.getPhysicalControllers()) {
if (canDelete(bioModel, allSelectedBioPaxObjects, pe))
completeSelectedBioPaxObjects.add(pe);
}
}
}
}
} else if (bpObject instanceof GroupObject) {
// all elements of the groupObject will be deleted
completeSelectedBioPaxObjects.add(bpObject);
// check all elements
completeSelectedBioPaxObjects.addAll(getAllGroupedObjects((GroupObject) bpObject));
}
} else {
warning.append(" " + bpObject.getTypeLabel() + ": \'" + PhysiologyRelationshipTableModel.getLabel(bpObject) + "\'\n");
if (bpObject instanceof GroupObject) {
undeletedGroupObjects.add((GroupObject) bpObject);
}
}
}
warning.append("\nThey are either required by other reactions or linked with other physiological objects.\n\n");
// for(GroupObject gObject : undeletedGroupObjects){
// for (BioPaxObject bpo : gObject.getGroupedObjects()){
// completeSelectedBioPaxObjects.remove(bpo);
// }
// }
StringBuilder finalWarningMessage = new StringBuilder();
if (allSelectedBioPaxObjects.size() > selectedBioPaxObjects.size()) {
finalWarningMessage.append(warning.toString() + "\n\n");
}
if (selectedBioPaxObjects.size() > 0) {
text.append("\nContinue?");
finalWarningMessage.append(text.toString());
}
if (finalWarningMessage.length() == 0) {
return;
}
String confirm = DialogUtils.showOKCancelWarningDialog(guiRequester, "Deleting pathway objects", finalWarningMessage.toString());
if (confirm.equals(UserMessage.OPTION_CANCEL)) {
return;
}
if (completeSelectedBioPaxObjects.size() > 0) {
bioModel.getPathwayModel().remove(completeSelectedBioPaxObjects);
bioModel.getPathwayModel().cleanGroupObjects();
bioModel.getRelationshipModel().removeRelationshipObjects(completeSelectedBioPaxObjects);
}
}
use of org.vcell.pathway.Complex in project vcell by virtualcell.
the class PathwayMapping method generateSpeciesPattern.
private SpeciesPattern generateSpeciesPattern(BioModel bioModel, PhysicalEntity bioPaxObject, boolean addSubunits) {
SpeciesPattern sp = new SpeciesPattern();
if (bioPaxObject instanceof Complex) {
Complex c = (Complex) bioPaxObject;
for (PhysicalEntity pc : c.getComponents()) {
MolecularType mt = createMolecularTypeFromBioPaxObject(bioModel, pc, addSubunits);
MolecularTypePattern mtp = new MolecularTypePattern(mt);
sp.addMolecularTypePattern(mtp);
}
return sp;
} else {
// else if(!(bioPaxObject instanceof Complex))
MolecularType mt = createMolecularTypeFromBioPaxObject(bioModel, bioPaxObject, addSubunits);
MolecularTypePattern mtp = new MolecularTypePattern(mt);
sp.addMolecularTypePattern(mtp);
return sp;
}
// return null;
}
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