Examples with BioPaxObject org.vcell.pathway.BioPaxObject used on opensource projects

Example 1 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class PathwayMapping method createReactionStepFromPathway.

/*
	 * for reaction:
	 * 1. annotate the selected vcell object using linked pathway conversion
	 * 2. add non-existing speciesContexts from linked pathway conversion
	 * 3. add links between relative vcell objects and pathway objects
	 * Questions:
	 * - how to deal with the case that the reaction is existing in the model?
	 * 		+ add it in no matter what? 
	 * 				(this is the version we have now: 
	 * 					add the duplicated reactions in without name changing, 
	 * 				 	all duplicated reactions share the same participant objects)
	 *      + just modify the existing one?
	 */
private void createReactionStepFromPathway(BioModel bioModel, Process process, ReactionStep reactionStep, RelationshipObject relationshipObject, boolean addSubunits) throws Exception {
    // annotate the selected vcell object using linked pathway object
    // add non-existing speciesContexts from linked pathway conversion
    ReactionParticipant[] rpArray = parseReaction(reactionStep, bioModel, relationshipObject);
    // create a hashtable for interaction Participants
    Hashtable<String, BioPaxObject> participantTable = new Hashtable<String, BioPaxObject>();
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getLeft()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (BioPaxObject bpObject : ((Conversion) relationshipObject.getBioPaxObject()).getRight()) {
        if (((PhysicalEntity) bpObject).getName().size() == 0) {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getID()), bpObject);
        } else {
            participantTable.put(getSafetyName(((PhysicalEntity) bpObject).getName().get(0)), bpObject);
        }
    }
    for (ReactionParticipant rp : rpArray) {
        SpeciesContext speciesContext = rp.getSpeciesContext();
        if (bioModel.getModel().getSpeciesContext(speciesContext.getName()) == null) {
            // if the speciesContext is not existed, then add it to the bioModel and link it to the corresponding pathway object
            if (bioModel.getModel().getSpecies(speciesContext.getName()) == null) {
                bioModel.getModel().addSpecies(speciesContext.getSpecies());
            }
            bioModel.getModel().addSpeciesContext(speciesContext);
            RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
            bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
        } else {
            // if it is in the bioModel, then check whether it links to pathway object or not
            HashSet<RelationshipObject> linkedReObjects = bioModel.getRelationshipModel().getRelationshipObjects(bioModel.getModel().getSpeciesContext(speciesContext.getName()));
            if (linkedReObjects != null) {
                boolean isLinked = false;
                for (RelationshipObject reObject : linkedReObjects) {
                    if (reObject.getBioPaxObject() == participantTable.get(speciesContext.getName())) {
                        isLinked = true;
                        break;
                    }
                }
                if (!isLinked) {
                    RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                    bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
                }
            } else {
                RelationshipObject newSpeciesContext = new RelationshipObject(speciesContext, participantTable.get(speciesContext.getName()));
                bioModel.getRelationshipModel().addRelationshipObject(newSpeciesContext);
            }
        }
    }
    (reactionStep).setReactionParticipants(rpArray);
    // add Control to the reaction
    if (process.getControl() != null) {
        for (InteractionParticipant pe : process.getControl().getParticipants()) {
            SpeciesContext newSpeciescontext = createSpeciesContextFromBioPaxObject(bioModel, pe.getPhysicalEntity(), addSubunits);
            (reactionStep).addReactionParticipant(new Catalyst(null, reactionStep, newSpeciescontext));
        }
    }
    addKinetics(reactionStep, process);
}

Example 2 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class AnnotationMapping method annotation2BioPaxObject.

public String annotation2BioPaxObject(BioModel bioModel, Identifiable identifiable) {
    String name = "";
    String type = "";
    ArrayList<String> componentInfo = getComponentInfo(bioModel, identifiable);
    if (componentInfo.size() > 0) {
        name = componentInfo.get(0);
        type = componentInfo.get(1);
    }
    String info = type + " : " + name;
    HashMap<String, String> refInfo = getRefInfo(bioModel, identifiable);
    // otherwise, create object and add link
    if (type.equals(VCID.CLASS_SPECIES)) {
        // lookup name by speciesContext
        ArrayList<SpeciesContext> speciesContextArrList = new ArrayList<SpeciesContext>(Arrays.asList(new SpeciesContext[] { bioModel.getModel().getSpeciesContext(name) }));
        if (speciesContextArrList.get(0) == null) {
            speciesContextArrList.clear();
            // lookup name by species
            for (int i = 0; i < bioModel.getModel().getSpeciesContexts().length; i++) {
                if (bioModel.getModel().getSpeciesContexts()[i].getSpecies().getCommonName().equals(name)) {
                    speciesContextArrList.add(bioModel.getModel().getSpeciesContexts()[i]);
                }
            }
        }
        for (int i = 0; i < speciesContextArrList.size(); i++) {
            SpeciesContext speciesContext = speciesContextArrList.get(i);
            if (bioModel.getRelationshipModel().getRelationshipObjects(speciesContext).size() == 0) {
                ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
                ArrayList<String> refName = getNameRef(xRef, name);
                BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_PHYSICALENTITY);
                if (bpObject == null) {
                    bpObject = createPhysicalEntity(xRef, refName, name);
                    bioModel.getPathwayModel().add(bpObject);
                }
                if (!isLinked(bioModel, bpObject, speciesContext)) {
                    // create linkage
                    RelationshipObject newRelationship = new RelationshipObject(speciesContext, bpObject);
                    bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
                    return info;
                }
            }
        }
    } else if (type.equals(VCID.CLASS_BIOMODEL)) {
    // BioPaxObject bpObject = bioModel.getPathwayModel().findFromName(refName.get(0), "Pathway");
    // if(bpObject == null){
    // bpObject = createPathway(componentInfo, refInfo);
    // bioModel.getPathwayModel().add(bpObject);
    // return info;
    // }
    } else if (type.equals(VCID.CLASS_REACTION_STEP)) {
        ReactionStep reactionStep = bioModel.getModel().getReactionStep(name);
        ArrayList<Xref> xRef = getXrefs(bioModel, refInfo);
        ArrayList<String> refName = getNameRef(xRef, name);
        if (bioModel.getRelationshipModel().getRelationshipObjects(reactionStep).size() == 0) {
            BioPaxObject bpObject = bioModel.getPathwayModel().findFromNameAndType(refName.get(0), EntityImpl.TYPE_INTERACTION);
            if (bpObject == null) {
                bpObject = createInteraction(reactionStep, xRef, refName);
                bioModel.getPathwayModel().add(bpObject);
            }
            if (!isLinked(bioModel, bpObject, reactionStep)) {
                // create linkage
                RelationshipObject newRelationship = new RelationshipObject(reactionStep, bpObject);
                bioModel.getRelationshipModel().addRelationshipObject(newRelationship);
                return info;
            }
        }
    }
    return null;
}

Example 3 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class PathwayProducerBiopax3 method addContentGroupObject.

private Element addContentGroupObject(BioPaxObject bpObject, Element element) {
    element = addContentEntity(bpObject, element);
    GroupObject ob = (GroupObject) bpObject;
    Element tmpElement = null;
    if (ob.getGroupedObjects() != null && ob.getGroupedObjects().size() > 0) {
        HashSet<BioPaxObject> list = ob.getGroupedObjects();
        for (BioPaxObject item : list) {
            tmpElement = new Element("groupedObject", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getType() != null) {
        tmpElement = new Element("type", bp);
        tmpElement.setAttribute("resource", ob.getType().toString(), rdf);
        tmpElement.setText(ob.getType().toString());
        element.addContent(tmpElement);
    }
    return element;
}

Example 4 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class PathwayProducerBiopax3 method getXML.

public void getXML(PathwayModel pathwayModel, Element rootElement) {
    objectsToPrint.addAll(pathwayModel.getBiopaxObjects());
    biopaxElement = rootElement;
    biopaxElement.addNamespaceDeclaration(bp);
    biopaxElement.addNamespaceDeclaration(rdf);
    if (pathwayModel.getDiagramObjects().size() > 0) {
        for (String diagramObjectID : pathwayModel.getDiagramObjects()) {
            if (diagramObjectID != null) {
                Element e = new Element("DiagramObjectsID");
                e.setText(diagramObjectID);
                biopaxElement.addContent(e);
            }
        }
    }
    while (objectsToPrint.size() > 0) {
        BioPaxObject bpObject = objectsToPrint.iterator().next();
        if (bpObject == null) {
            System.out.println("PathwayProducerBiopax3: null BioPaxObject in the PathwayModel.");
            continue;
        }
        String className = bpObject.getClass().getName().substring(1 + bpObject.getClass().getName().lastIndexOf('.'));
        // System.out.println("object: " + className);
        if (className.equals("Test")) {
            System.out.println("PathwayProducerBiopax3::getXML()");
        // sbPAX section
        } else if (className.equals("SBMeasurable")) {
            biopaxElement.addContent(addObjectSBMeasurable(bpObject, className));
        } else if (className.equals("SBState")) {
            biopaxElement.addContent(addObjectSBState(bpObject, className));
        } else if (className.equals("SBVocabulary")) {
            biopaxElement.addContent(addObjectSBVocabulary(bpObject, className));
        // bioPAX section
        } else if (className.equals("Pathway")) {
            biopaxElement.addContent(addObjectPathway(bpObject, className));
        } else if (className.equals("BiochemicalReactionImpl")) {
            biopaxElement.addContent(addObjectBiochemicalReaction(bpObject, "BiochemicalReaction"));
        } else if (className.equals("ConversionImpl")) {
            biopaxElement.addContent(addObjectConversion(bpObject, "Conversion"));
        } else if (className.equals("CellularLocationVocabulary")) {
            biopaxElement.addContent(addObjectCellularLocationVocabulary(bpObject, className));
        } else if (className.equals("CellVocabulary")) {
            biopaxElement.addContent(addObjectCellVocabulary(bpObject, className));
        } else if (className.equals("EntityReferenceTypeVocabulary")) {
            biopaxElement.addContent(addObjectEntityReferenceTypeVocabulary(bpObject, className));
        } else if (className.equals("EvidenceCodeVocabulary")) {
            biopaxElement.addContent(addObjectEvidenceCodeVocabulary(bpObject, className));
        } else if (className.equals("ExperimentalFormVocabulary")) {
            biopaxElement.addContent(addObjectExperimentalFormVocabulary(bpObject, className));
        } else if (className.equals("InteractionVocabulary")) {
            biopaxElement.addContent(addObjectInteractionVocabulary(bpObject, className));
        } else if (className.equals("PhenotypeVocabulary")) {
            biopaxElement.addContent(addObjectPhenotypeVocabulary(bpObject, className));
        } else if (className.equals("RelationshipTypeVocabulary")) {
            biopaxElement.addContent(addObjectRelationshipTypeVocabulary(bpObject, className));
        } else if (className.equals("SequenceModificationVocabulary")) {
            biopaxElement.addContent(addObjectSequenceModificationVocabulary(bpObject, className));
        } else if (className.equals("SequenceRegionVocabulary")) {
            biopaxElement.addContent(addObjectSequenceRegionVocabulary(bpObject, className));
        } else if (className.equals("TissueVocabulary")) {
            biopaxElement.addContent(addObjectTissueVocabulary(bpObject, className));
        } else if (className.equals("PublicationXref")) {
            biopaxElement.addContent(addObjectPublicationXref(bpObject, className));
        } else if (className.equals("RelationshipXref")) {
            biopaxElement.addContent(addObjectRelationshipXref(bpObject, className));
        } else if (className.equals("UnificationXref")) {
            biopaxElement.addContent(addObjectUnificationXref(bpObject, className));
        } else if (className.equals("DnaReference")) {
            biopaxElement.addContent(addObjectDnaReference(bpObject, className));
        } else if (className.equals("DnaRegionReference")) {
            biopaxElement.addContent(addObjectDnaRegionReference(bpObject, className));
        } else if (className.equals("ProteinReference")) {
            biopaxElement.addContent(addObjectProteinReference(bpObject, className));
        } else if (className.equals("RnaReference")) {
            biopaxElement.addContent(addObjectRnaReference(bpObject, className));
        } else if (className.equals("RnaRegionReference")) {
            biopaxElement.addContent(addObjectRnaRegionReference(bpObject, className));
        } else if (className.equals("SmallMoleculeReference")) {
            biopaxElement.addContent(addObjectSmallMoleculeReference(bpObject, className));
        } else if (className.equals("Provenance")) {
            biopaxElement.addContent(addObjectProvenance(bpObject, className));
        } else if (className.equals("Control")) {
            biopaxElement.addContent(addObjectControl(bpObject, className));
        } else if (className.equals("Catalysis")) {
            biopaxElement.addContent(addObjectCatalysis(bpObject, className));
        } else if (className.equals("Modulation")) {
            biopaxElement.addContent(addObjectModulation(bpObject, className));
        } else if (className.equals("TemplateReactionRegulation")) {
            biopaxElement.addContent(addObjectTemplateReactionRegulation(bpObject, className));
        } else if (className.equals("Complex")) {
            biopaxElement.addContent(addObjectComplex(bpObject, className));
        } else if (className.equals("Protein")) {
            biopaxElement.addContent(addObjectProtein(bpObject, className));
        } else if (className.equals("Dna")) {
            biopaxElement.addContent(addObjectDna(bpObject, className));
        } else if (className.equals("DnaRegion")) {
            biopaxElement.addContent(addObjectDnaRegion(bpObject, className));
        } else if (className.equals("Rna")) {
            biopaxElement.addContent(addObjectRna(bpObject, className));
        } else if (className.equals("RnaRegion")) {
            biopaxElement.addContent(addObjectRnaRegion(bpObject, className));
        } else if (className.equals("SmallMolecule")) {
            biopaxElement.addContent(addObjectSmallMolecule(bpObject, className));
        } else if (className.equals("BioSource")) {
            biopaxElement.addContent(addObjectBioSource(bpObject, className));
        } else if (className.equals("EntityFeature")) {
            biopaxElement.addContent(addObjectEntityFeature(bpObject, className));
        } else if (className.equals("ModificationFeature")) {
            biopaxElement.addContent(addObjectModificationFeature(bpObject, className));
        } else if (className.equals("CovalentBindingFeature")) {
            biopaxElement.addContent(addObjectCovalentBindingFeature(bpObject, className));
        } else if (className.equals("FragmentFeature")) {
            biopaxElement.addContent(addObjectFragmentFeature(bpObject, className));
        } else if (className.equals("BindingFeature")) {
            biopaxElement.addContent(addObjectBindingFeature(bpObject, className));
        } else if (className.equals("SequenceInterval")) {
            biopaxElement.addContent(addObjectSequenceInterval(bpObject, className));
        } else if (className.equals("SequenceSite")) {
            biopaxElement.addContent(addObjectSequenceSite(bpObject, className));
        } else if (className.equals("Stoichiometry")) {
            biopaxElement.addContent(addObjectStoichiometry(bpObject, className));
        } else if (className.equals("PathwayStep")) {
            biopaxElement.addContent(addObjectPathwayStep(bpObject, className));
        } else if (className.equals("BiochemicalPathwayStep")) {
            biopaxElement.addContent(addObjectBiochemicalPathwayStep(bpObject, className));
        } else if (className.equals("PhysicalEntity")) {
            biopaxElement.addContent(addObjectPhysicalEntity(bpObject, className));
        // 
        // // not found "as is" in tested sample
        } else if (className.equals("Gene")) {
            biopaxElement.addContent(addObjectGene(bpObject, className));
        } else if (className.equals("Ontology")) {
        // showIgnored(bpObject, className);
        } else if (className.equals("Interaction")) {
            biopaxElement.addContent(addObjectInteraction(bpObject, className));
        } else if (className.equals("Transport")) {
            biopaxElement.addContent(addObjectTransport(bpObject, className));
        } else if (className.equals("TransportWithBiochemicalReaction")) {
            biopaxElement.addContent(addObjectTransportWithBiochemicalReaction(bpObject, className));
        } else if (className.equals("GeneticInteraction")) {
            biopaxElement.addContent(addObjectGeneticInteraction(bpObject, className));
        } else if (className.equals("MolecularInteraction")) {
            biopaxElement.addContent(addObjectMolecularInteraction(bpObject, className));
        } else if (className.equals("TemplateReaction")) {
            biopaxElement.addContent(addObjectTemplateReaction(bpObject, className));
        } else if (className.equals("ComplexAssembly")) {
            biopaxElement.addContent(addObjectComplexAssembly(bpObject, className));
        } else if (className.equals("Degradation")) {
            biopaxElement.addContent(addObjectDegradation(bpObject, className));
        } else if (className.equals("ChemicalStructure")) {
            biopaxElement.addContent(addObjectChemicalStructure(bpObject, className));
        } else if (className.equals("DeltaG")) {
            biopaxElement.addContent(addObjectDeltaG(bpObject, className));
        } else if (className.equals("Evidence")) {
            biopaxElement.addContent(addObjectEvidence(bpObject, className));
        } else if (className.equals("ExperimentalForm")) {
            biopaxElement.addContent(addObjectExperimentalForm(bpObject, className));
        } else if (className.equals("KPrime")) {
            biopaxElement.addContent(addObjectKPrime(bpObject, className));
        } else if (className.equals("Score")) {
            biopaxElement.addContent(addObjectScore(bpObject, className));
        } else if (className.equals("GroupObject")) {
            biopaxElement.addContent(addObjectGroupObject(bpObject, className));
        } else {
            showUnexpected(bpObject);
        }
        objectsPrinted.add(bpObject);
        objectsToPrint.remove(bpObject);
    }
    return;
}

Example 5 with BioPaxObject

use of org.vcell.pathway.BioPaxObject in project vcell by virtualcell.

the class PathwayGrouping method computeNeighbors.

// get the neighbor of a given groupObject
public HashSet<BioPaxObject> computeNeighbors(PathwayModel pathwayModel, BioPaxObject bioPaxObject) {
    Map<BioPaxObject, HashSet<BioPaxObject>> parentMap = pathwayModel.refreshParentMap();
    HashSet<BioPaxObject> neighbors_temp = new HashSet<BioPaxObject>();
    HashSet<BioPaxObject> components = new HashSet<BioPaxObject>();
    if (bioPaxObject instanceof GroupObject) {
        components = ((GroupObject) bioPaxObject).getGroupedObjects();
        for (BioPaxObject bpObject : components) {
            if (bpObject instanceof GroupObject) {
                // compute neighbors for group object
                neighbors_temp.addAll(computeNeighbors(pathwayModel, parentMap, (GroupObject) bpObject));
            } else {
                if (parentMap.get(bpObject) != null) {
                    neighbors_temp.addAll(parentMap.get(bpObject));
                }
                neighbors_temp.addAll(pathwayModel.getBioPaxElements(bpObject));
            }
        }
    } else {
        neighbors_temp.addAll(pathwayModel.getBioPaxElements(bioPaxObject));
        if (parentMap.get(bioPaxObject) != null) {
            neighbors_temp.addAll(parentMap.get(bioPaxObject));
        }
    }
    Map<BioPaxObject, BioPaxObject> groupMap = pathwayModel.getGroupMap();
    HashSet<BioPaxObject> neighbors = new HashSet<BioPaxObject>();
    for (BioPaxObject bpo : neighbors_temp) {
        neighbors.add(findGroupAncestor(groupMap, bpo));
    }
    neighbors.removeAll(components);
    neighbors.remove(null);
    neighbors.remove(bioPaxObject);
    HashSet<BioPaxObject> notImported = new HashSet<BioPaxObject>();
    for (BioPaxObject bpo : neighbors) {
        if (!pathwayModel.getBiopaxObjects().contains(bpo)) {
            notImported.add(bpo);
        }
    }
    neighbors.remove(notImported);
    return neighbors;
}