Examples of org.openbel.framework.api.Kam.KamNode

        kam = kam(kamName);
        info = kam.getKamInfo();
        Map<KamNode, KamNode> collapsed = orthokam.getCollapsedNodes();
        Set<Entry<KamNode, KamNode>> set = collapsed.entrySet();
        for (Entry<KamNode, KamNode> e : set) {
            KamNode collapsing = e.getKey();
            KamNode collapseTo = e.getValue();


            collapsing = kam.findNode(collapsing.getId());
            collapseTo = kam.findNode(collapseTo.getId());
            kamstore.collapseKamNode(info, collapsing, collapseTo);
        }


        // remove orthologous edges/statements
        kamstore.removeKamEdges(info, ORTHOLOGOUS);

        Map<Integer, Resource> termResources = new HashMap<Integer, Resource>();


        // handle kam nodes first
        Iterator<KamNode> kamNodes = kam.getNodes().iterator();
        while (kamNodes.hasNext()) {
            KamNode kamNode = kamNodes.next();


            // TODO: This is a sanity check that should be removed as LIST is not a KAM function type
            if (FunctionEnum.LIST == kamNode.getFunctionType()) {
                System.err.println("Invalid KAM node type found: "
                        + kamNode.getFunctionType().getDisplayValue());
                continue;
            }


            Resource functionResource = model.getResource(KAMVocabulary
                    .resourceForFunction(kamNode.getFunctionType()).getURI());


            // Retrieve seen KAMNode Resource or create a new Blank Node for it.
            Resource kamNodeResource;
            if (kamNodeResources.containsKey(kamNode)) {
                kamNodeResource = kamNodeResources.get(kamNode);
            } else {
                kamNodeResource = model.createResource(new AnonId(UUID
                        .randomUUID().toString()));


                // associate kam node with kam resource
                kamResource.addProperty(composedOf, kamNodeResource);
            }


            // node type KAMNode
            kamNodeResource.addProperty(RDF.type, KAMNode);


            // node hasFunction Function
            kamNodeResource.addProperty(hasFunction, functionResource);


            // node hasId "1"^^xsd:int
            kamNodeResource.addLiteral(hasId,
                    model.createTypedLiteral(kamNode.getId()));


            // node hasLabel "p(EG:207)"^^xsd:string
            kamNodeResource.addLiteral(hasLabel,
                    model.createTypedLiteral(kamNode.getLabel()));


            // hold on to kam node resources
            kamNodeResources.put(kamNode, kamNodeResource);


            // handle terms for this KAMNode
            // TODO Support nested terms instead of just Parameters!
            List<BelTerm> terms = kAMStore.getSupportingTerms(kamNode);
            for (BelTerm term : terms) {
                Resource termResource = model.createResource(new AnonId(UUID
                        .randomUUID().toString()));


                termResource.addProperty(RDF.type, Term);
                termResource.addProperty(hasId,
                        model.createTypedLiteral(term.getId()));
                termResource.addProperty(hasLabel,
                        model.createTypedLiteral(term.getLabel()));
                termResource.addProperty(hasFunction,
                        resourceForFunction(kamNode.getFunctionType()));


                RDFList argumentres = model.createList();


                List<TermParameter> termParameters =
                        kAMStore.getTermParameters(kamInfo, term);

Examples of org.openbel.framework.api.Kam.KamNode

Related Classes of org.openbel.framework.api.Kam.KamNode