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

Example 11 with Conversion

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

the class PathwayMapping method createReactionStep.

/*
	 * 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 createReactionStep(BioModel bioModel, Process process, ReactionStep reactionStep, RelationshipObject relationshipObject, ArrayList<ConversionTableRow> participants, boolean addSubunits) throws Exception {
    if (reactionStep == null || bioModel == null || bioModel.getRelationshipModel() == null || participants.size() < 1) {
        return;
    }
    ArrayList<ReactionParticipant> rplist = new ArrayList<ReactionParticipant>();
    // create and add reaction participants to list
    for (ConversionTableRow ctr : participants) {
        if (ctr.getBioPaxObject() instanceof Conversion)
            continue;
        int stoich = ctr.stoich().intValue();
        String safeId = getSafetyName(ctr.id());
        // get speciesContext object based on its name
        // if the speciesContext is not existed, create a new one
        createSpeciesContextFromTableRow(bioModel, (PhysicalEntity) ctr.getBioPaxObject(), ctr.stoich(), ctr.id(), ctr.location(), addSubunits);
        // add the existed speciesContext objects or new speciesContext objects to reaction participant list
        if (ctr.participantType().equals("Reactant")) {
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                rplist.add(new Reactant(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId), stoich));
            }
        } else if (ctr.participantType().equals("Product")) {
            if (reactionStep instanceof SimpleReaction || reactionStep instanceof FluxReaction) {
                rplist.add(new Product(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId), stoich));
            }
        }
    // we do not add catalysts
    }
    ReactionParticipant[] rpArray = rplist.toArray(new ReactionParticipant[0]);
    reactionStep.setReactionParticipants(rpArray);
    // add Controls to the reaction
    Set<PhysicalEntity> controllers = process.getControllers();
    for (ConversionTableRow ctr : participants) {
        if (controllers.contains(ctr.getBioPaxObject())) {
            if (ctr.participantType().equals("Catalyst")) {
                String safeId = getSafetyName(ctr.id());
                /* 
					 * using addCatalyst() to create catalyst in reaction: 
					 * this function cannot allow an object to be catalyst and (reactant/product) in the same reaction
					 */
                // reactionStep.addCatalyst(bioModel.getModel().getSpeciesContext(safeId));
                /* However, in pathway interaction object, an physicalEntity can be catalyst and (reactant/product) in the same reaction
					 * So we just call create catalyst for the reaction no matter what rolls the object is playing in the reaction
					 * Switch back to the addCatalyst() function when it is necessary, but exceptions make be reported for some reactions
					 */
                reactionStep.addReactionParticipant(new Catalyst(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId)));
            } else if (ctr.participantType().equals("Control")) {
                String safeId = getSafetyName(ctr.id());
                // reactionStep.addCatalyst(bioModel.getModel().getSpeciesContext(safeId));
                reactionStep.addReactionParticipant(new Catalyst(null, reactionStep, bioModel.getModel().getSpeciesContext(safeId)));
            }
        }
    }
}

Example 12 with Conversion

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

the class PathwayReaderBiopax3 method addObjectConversion.

private Conversion addObjectConversion(Element conversionElement) {
    if (conversionElement.getChildren().size() == 0) {
        ConversionProxy proxy = new ConversionProxy();
        addAttributes(proxy, conversionElement);
        pathwayModel.add(proxy);
        return proxy;
    }
    Conversion conversion = new ConversionImpl();
    addAttributes(conversion, conversionElement);
    for (Object child : conversionElement.getChildren()) {
        if (child instanceof Element) {
            if (!addContentConversion(conversion, conversionElement, (Element) child)) {
                showUnexpected((Element) child);
            }
        }
    }
    pathwayModel.add(conversion);
    return conversion;
}

Example 13 with Conversion

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

the class PathwayProducerBiopax3 method addContentConversion.

// right 						PhysicalEntity 	multiple
// participantStoichiometry 	Stoichiometry 	multiple
// left 						PhysicalEntity 	multiple
// spontaneous 				Boolean 		single
// conversionDirection 		String 			single
private Element addContentConversion(BioPaxObject bpObject, Element element) {
    element = addContentInteraction(bpObject, element);
    Conversion ob = (Conversion) bpObject;
    Element tmpElement = null;
    if (ob.getLeft() != null && ob.getLeft().size() > 0) {
        List<PhysicalEntity> list = ob.getLeft();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("left", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getRight() != null && ob.getRight().size() > 0) {
        List<PhysicalEntity> list = ob.getRight();
        for (PhysicalEntity item : list) {
            tmpElement = new Element("right", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getParticipantStoichiometry() != null && ob.getParticipantStoichiometry().size() > 0) {
        List<Stoichiometry> list = ob.getParticipantStoichiometry();
        for (Stoichiometry item : list) {
            tmpElement = new Element("participantStoichiometry", bp);
            addIDToProperty(tmpElement, item);
            mustPrintObject(item);
            element.addContent(tmpElement);
        }
    }
    if (ob.getSpontaneous() != null) {
        tmpElement = new Element("spontaneous", bp);
        tmpElement.setAttribute("datatype", schemaBoolean, rdf);
        tmpElement.setText(ob.getSpontaneous().toString());
        element.addContent(tmpElement);
    }
    if (ob.getConversionDirection() != null && ob.getConversionDirection().length() > 0) {
        tmpElement = new Element("conversionDirection", bp);
        tmpElement.setAttribute("datatype", schemaString, rdf);
        tmpElement.setText(ob.getConversionDirection());
        element.addContent(tmpElement);
    }
    return element;
}