Package org.openbel.framework.api.internal.KAMStoreDaoImpl

Examples of org.openbel.framework.api.internal.KAMStoreDaoImpl.TermParameter

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    private KamNode wrapNode(KamNode kamNode) {
        if (kamNode == null) {
            return null;
        }

        TermParameter param = ntp.get(kamNode.getId());
        if (param != null) {
            return new OrthologousNode(kamNode, param);
        }

        return kamNode;
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    private KamEdge wrapEdge(KamEdge kamEdge) {
        if (kamEdge == null) {
            return null;
        }

        TermParameter param = etp.get(kamEdge.getId());
        if (param != null) {
            return new OrthologousEdge(kamEdge, param);
        }

        return kamEdge;
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                    "http://resource.belframework.org/belframework/1.0/namespace/rgd-approved-symbols.belns");

            when(kamstore.getNamespaces(info)).thenReturn(
                    Arrays.asList(eg, hgnc, mgi, rgd));

            final TermParameter mgiMapk1 = createTermParameter(0, mgi, "Mapk1");
            final TermParameter eg26413 = createTermParameter(1, eg, "26413");
            final TermParameter hgncMAPK1 = createTermParameter(2, hgnc,
                    "MAPK1");
            final TermParameter eg116590 = createTermParameter(3, eg, "116590");
            final TermParameter rgdMapk1 = createTermParameter(4, rgd, "Mapk1");

            Collection<KamNode> kn = kam.getNodes();
            final KamNode[] nodes = kn.toArray(new KamNode[kn.size()]);
            BelTerm belTerm = createBelTerm(0,
                    "kinaseActivity(proteinAbundance(MGI:Mapk1))");
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                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-protein-families.belns");

            when(kamstore.getNamespaces(info)).thenReturn(
                    Arrays.asList(pfh, pfm, pfr));

            final TermParameter pfh1433 = createTermParameter(0, pfh,
                    "14-3-3 Family");
            final TermParameter pfm1433 = createTermParameter(1, pfm,
                    "14-3-3 Family");
            final TermParameter pfr1433 = createTermParameter(2, pfr,
                    "14-3-3 Family");

            final Collection<KamNode> kn = kam.getNodes();
            final KamNode[] nodes = kn.toArray(new KamNode[kn.size()]);
            BelTerm belTerm = createBelTerm(0,
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                    "http://resource.belframework.org/belframework/1.0/namespace/selventa-named-rat-complexes.belns");

            when(kamstore.getNamespaces(info)).thenReturn(
                    Arrays.asList(nch, ncm, ncr));

            final TermParameter nchAP1 = createTermParameter(0, nch,
                    "AP-1 Complex");
            final TermParameter ncmAP1 = createTermParameter(1, ncm,
                    "AP-1 Complex");
            final TermParameter ncrAP1 = createTermParameter(2, ncr,
                    "AP-1 Complex");

            final Collection<KamNode> kn = kam.getNodes();
            final KamNode[] nodes = kn.toArray(new KamNode[kn.size()]);
            BelTerm belTerm = createBelTerm(0,
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                // invalid; skip orthologous self edges
                if (edgeSource == edgeTarget) {
                    continue;
                }

                TermParameter speciesParam = findParameter(kam, kAMStore,
                        edgeSource, rlocs);
                if (speciesParam != null) {
                    // source node matches target species
                    Integer id = edgeSource.getId();
                    Set<Integer> adjacentEdges = oedges.get(id);
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        Map<Integer, TermParameter> etp = sizedHashMap(species.size());
        for (final KamNode snode : species) {
            if (snode != null) {
                // XXX term parameter looked up 2x; may impact perf/determinism
                // TODO redesign orthologousNodes / inferOrthologs
                TermParameter p = findParameter(kam, kAMStore, snode, rlocs);

                // recurse incoming connections from species node
                recurseConnections(kam, snode, p, inferf, REVERSE, ortho, ntp, etp);
                // recurse outgoing connections from species node
                recurseConnections(kam, snode, p, inferf, FORWARD, ortho, ntp, etp);
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        return new Namespace(id, prefix, resourceLocation);
    }

    public static TermParameter createTermParameter(final Integer id,
            Namespace ns, String value) {
        return new TermParameter(id, ns, value);
    }
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Related Classes of org.openbel.framework.api.internal.KAMStoreDaoImpl.TermParameter

  • org.openbel.framework.api.DefaultOrthologize
  • org.openbel.framework.api.internal.KamStoreUtil
  • org.openbel.framework.api.OrthologizedKam
  • org.openbel.framework.api.SpeciesKamTest
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