use of org.vcell.pathway.Protein in project vcell by virtualcell.
the class PathwayReaderBiopax3 method addContentControl.
private boolean addContentControl(Control control, Element element, Element childElement) {
if (addContentInteraction(control, element, childElement)) {
return true;
}
/**
* InteractionImpl controlledInteraction
* Pathway controlledPathway
* String controlType
* ArrayList<Pathway> pathwayControllers
* ArrayList<PhysicalEntity> physicalControllers
*/
if (childElement.getName().equals("controller")) {
// if (resourceAttribute != null){
if (childElement.getChildren().size() == 0) {
// if there are no children it must be a resource inside another object
// we don't know yet whether it's Interaction or Pathway, we make a proxy for each
// at the time when we solve the references we'll find out which is fake
PhysicalEntityProxy proxyE = new PhysicalEntityProxy();
addAttributes(proxyE, childElement);
pathwayModel.add(proxyE);
control.addPhysicalController(proxyE);
PathwayProxy proxyP = new PathwayProxy();
addAttributes(proxyP, childElement);
pathwayModel.add(proxyP);
control.getPathwayControllers().add(proxyP);
return true;
} else {
for (Object child : element.getChildren()) {
if (child instanceof Element) {
if (((Element) child).getName().equals("Pathway")) {
Pathway thingie = addObjectPathway((Element) child);
control.getPathwayControllers().add(thingie);
return true;
} else if (((Element) child).getName().equals("Complex")) {
Complex thingie = addObjectComplex((Element) child);
control.getPhysicalControllers().add(thingie);
return true;
} else if (((Element) child).getName().equals("Dna")) {
Dna thingie = addObjectDna((Element) child);
control.getPhysicalControllers().add(thingie);
return true;
} else if (((Element) child).getName().equals("DnaRegion")) {
DnaRegion thingie = addObjectDnaRegion((Element) child);
control.getPhysicalControllers().add(thingie);
return true;
} else if (((Element) child).getName().equals("Rna")) {
Rna thingie = addObjectRna((Element) child);
control.getPhysicalControllers().add(thingie);
return true;
} else if (((Element) child).getName().equals("RnaRegion")) {
RnaRegion thingie = addObjectRnaRegion((Element) child);
control.getPhysicalControllers().add(thingie);
return true;
} else if (((Element) child).getName().equals("Protein")) {
Protein thingie = addObjectProtein((Element) child);
control.getPhysicalControllers().add(thingie);
return true;
} else if (((Element) child).getName().equals("SmallMolecule")) {
SmallMolecule thingie = addObjectSmallMolecule((Element) child);
control.getPhysicalControllers().add(thingie);
return true;
} else {
return false;
}
}
}
}
return false;
} else if (childElement.getName().equals("controlled")) {
if (childElement.getChildren().size() == 0) {
InteractionProxy proxyI = new InteractionProxy();
addAttributes(proxyI, childElement);
pathwayModel.add(proxyI);
control.setControlledInteraction(proxyI);
PathwayProxy proxyP = new PathwayProxy();
addAttributes(proxyP, childElement);
pathwayModel.add(proxyP);
control.setControlledPathway(proxyP);
return true;
} else {
for (Object child : childElement.getChildren()) {
if (child instanceof Element) {
if (((Element) child).getName().equals("Pathway")) {
Pathway thingie = addObjectPathway((Element) child);
control.setControlledPathway(thingie);
return true;
} else {
Interaction thingie = (Interaction) addObjectBioPaxObjectSubclass((Element) child);
if (thingie == null) {
return false;
} else {
control.setControlledInteraction(thingie);
return true;
}
}
// if(((Element)child).getName().equals("Pathway")) {
// Pathway thingie = addObjectPathway((Element)child);
// control.setControlledPathway(thingie);
// return true;
// } else if(((Element)child).getName().equals("Interaction")) {
// Interaction thingie = addObjectInteraction((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("Control")) {
// Control thingie = addObjectControl((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("Modulation")) {
// Modulation thingie = addObjectModulation((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("Catalysis")) {
// Catalysis thingie = addObjectCatalysis((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("TemplateReactionRegulation")) {
// TemplateReactionRegulation thingie = addObjectTemplateReactionRegulation((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("Conversion")) {
// Conversion thingie = addObjectConversion((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("BiochemicalReaction")) {
// BiochemicalReaction thingie = addObjectBiochemicalReaction((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("TransportWithBiochemicalReaction")) {
// TransportWithBiochemicalReaction thingie = addObjectTransportWithBiochemicalReaction((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("ComplexAssembly")) {
// ComplexAssembly thingie = addObjectComplexAssembly((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("Degradation")) {
// Degradation thingie = addObjectDegradation((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("Transport")) {
// Transport thingie = addObjectTransport((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("GeneticInteraction")) {
// GeneticInteraction thingie = addObjectGeneticInteraction((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("MolecularInteraction")) {
// MolecularInteraction thingie = addObjectMolecularInteraction((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else if(((Element)child).getName().equals("TemplateReaction")) {
// TemplateReaction thingie = addObjectTemplateReaction((Element)child);
// control.setControlledInteraction(thingie);
// return true;
// } else {
// return false;
// }
}
}
}
return false;
} else if (childElement.getName().equals("controlType")) {
control.setControlType(childElement.getTextTrim());
return true;
} else {
return false;
}
}
use of org.vcell.pathway.Protein in project vcell by virtualcell.
the class PathwayReaderBiopax3 method addObjectPhysicalEntity.
private PhysicalEntity addObjectPhysicalEntity(Element element) {
if (element.getChildren().size() == 0) {
// we got lucky: no children, it means a reference -> create a proxy
PhysicalEntityProxy proxy = new PhysicalEntityProxy();
addAttributes(proxy, element);
pathwayModel.add(proxy);
return proxy;
}
for (Object child : element.getChildren()) {
if (child instanceof Element) {
Element childElement = (Element) child;
// </bp:component>
if (childElement.getName().equals("Complex")) {
Complex thingie = addObjectComplex(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("Dna")) {
Dna thingie = addObjectDna(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("DnaRegion")) {
DnaRegion thingie = addObjectDnaRegion(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("Rna")) {
Rna thingie = addObjectRna(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("RnaRegion")) {
RnaRegion thingie = addObjectRnaRegion(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("Protein")) {
Protein thingie = addObjectProtein(childElement);
pathwayModel.add(thingie);
return thingie;
} else if (childElement.getName().equals("SmallMolecule")) {
SmallMolecule thingie = addObjectSmallMolecule(childElement);
pathwayModel.add(thingie);
return thingie;
}
}
}
PhysicalEntity physicalEntity = new PhysicalEntity();
if (element.getAttributes().size() > 0) {
// real PhysicalEntity, with ID and everything
addAttributes(physicalEntity, element);
}
for (Object child : element.getChildren()) {
if (child instanceof Element) {
Element childElement = (Element) child;
if (!addContentPhysicalEntity(physicalEntity, element, childElement)) {
showUnexpected(childElement);
}
}
}
pathwayModel.add(physicalEntity);
return physicalEntity;
}
use of org.vcell.pathway.Protein in project vcell by virtualcell.
the class PathwayReaderBiopax3 method addObjectProtein.
private Protein addObjectProtein(Element element) {
Protein protein = new Protein();
addAttributes(protein, element);
for (Object child : element.getChildren()) {
if (child instanceof Element) {
Element childElement = (Element) child;
if (!addContentProtein(protein, element, childElement)) {
showUnexpected(childElement);
}
}
}
pathwayModel.add(protein);
return protein;
}
use of org.vcell.pathway.Protein in project vcell by virtualcell.
the class BioModelEditorPathwayDiagramPanel method collapse2Complex.
private GroupObject collapse2Complex(BioPaxObject bpObject) {
PathwayGrouping pathwayGrouping = new PathwayGrouping();
GroupObject groupObject = null;
HashSet<BioPaxObject> hiddenobjects = new HashSet<BioPaxObject>();
if (bpObject instanceof Complex) {
// collapse components
Complex complex = (Complex) bpObject;
Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
for (PhysicalEntity pe : complex.getComponents()) {
if (bioPaxObjects.contains(pe)) {
hiddenobjects.add(pe);
}
}
if (hiddenobjects.size() > 0) {
hiddenobjects.add(bpObject);
String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), ((Entity) bpObject).getName(), id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
} else {
// error message
DialogUtils.showErrorDialog(this, "No Collapse action happened because the components of the complex, " + getEntityName(complex) + ", haven't been imported to pathway model.");
}
} else if (bpObject instanceof Protein || bpObject instanceof SmallMolecule) {
Set<BioPaxObject> bioPaxObjects = new HashSet<BioPaxObject>(bioModel.getPathwayModel().getBiopaxObjects());
ArrayList<String> name = new ArrayList<String>();
List<BioPaxObject> parents = bioModel.getPathwayModel().getParents(bpObject);
if (parents.isEmpty()) {
DialogUtils.showErrorDialog(this, "No Collapse action happened because protein, " + getEntityName((Entity) bpObject) + ", doesn't involve in any complexes in the pathway data.");
return null;
}
for (BioPaxObject bpo : bioModel.getPathwayModel().getParents(bpObject)) {
if (bpo instanceof Complex && bioPaxObjects.contains(bpo)) {
hiddenobjects.add(bpo);
name.addAll(((Complex) bpo).getName());
for (PhysicalEntity pe : ((Complex) bpo).getComponents()) {
if (bioPaxObjects.contains(pe)) {
hiddenobjects.add(pe);
}
}
}
}
if (hiddenobjects.size() > 0) {
hiddenobjects.add(bpObject);
String id = pathwayGrouping.groupIdGenerator(bioModel.getPathwayModel());
if (name.size() == 0) {
name.add(id);
}
groupObject = pathwayGrouping.createGroupObject(bioModel.getPathwayModel(), name, id, hiddenobjects, GroupObject.Type.GROUPEDCOMPLEX);
} else {
// error message
DialogUtils.showErrorDialog(this, "No Collapse action happened because complexes that relate to protein, " + getEntityName((Entity) bpObject) + ", haven't been imported to pathway model.");
}
}
return groupObject;
}
use of org.vcell.pathway.Protein 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);
}
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