Package org.openbel.framework.api.Kam

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

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    public KamNode getKamNode(final Kam kam, String belTermString) {
        if (noLength(belTermString))
            throw new InvalidArgument("belTermString", belTermString);
        KamInfo ki = kam.getKamInfo();
        if (!exists(ki)) return null;
        KamNode kamNode;
        Integer nodeID;
        try {
            nodeID = kamStoreDao(ki).getKamNodeId(belTermString);
            kamNode = kam.findNode(nodeID);
        } catch (SQLException e) {
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        try {
            ids = kamStoreDao(k.getKamInfo()).getKamNodeCandidates(
                    function, uuid);
            List<KamNode> kamNodeList = new ArrayList<KamNode>();
            for (Integer kamNodeId : ids) {
                KamNode kn = k.findNode(kamNodeId);
                if (kn != null)
                    kamNodeList.add(kn);
            }
            return kamNodeList;
        } catch (SQLException e) {
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        nf.add(ftcriteria);
        nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(2, nodes.size());
        Iterator<KamNode> nodeIt = nodes.iterator();
        KamNode n1 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n1.getFunctionType());
        KamNode n2 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n2.getFunctionType());
    }
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        nf.add(rtcriteria);
        Collection<KamNode> nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(4, nodes.size());
        Iterator<KamNode> nodeIt = nodes.iterator();
        KamNode n1 = nodeIt.next();
        assertEquals(COMPLEX_ABUNDANCE, n1.getFunctionType());
        KamNode n2 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n2.getFunctionType());
        KamNode n3 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n3.getFunctionType());
        KamNode n4 = nodeIt.next();
        assertEquals(KINASE_ACTIVITY, n4.getFunctionType());

        // Test exclude of PROTEIN_ABUNDANCE function type criteria yields 3 nodes
        nf = testKAM.createNodeFilter();
        FunctionTypeFilterCriteria ftcriteria =
                new FunctionTypeFilterCriteria();
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        nf.add(rtcriteria);
        Collection<KamNode> nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(2, nodes.size());
        Iterator<KamNode> nodeIt = nodes.iterator();
        KamNode n1 = nodeIt.next();
        assertEquals(KINASE_ACTIVITY, n1.getFunctionType());
        assertEquals(ABUNDANCE, n1.getFunctionType().getReturnType());
        KamNode n2 = nodeIt.next();
        assertEquals(BIOLOGICAL_PROCESS, n2.getFunctionType());
        assertEquals(ReturnType.BIOLOGICAL_PROCESS, n2.getFunctionType()
                .getReturnType());

        // Test include of PROTEIN_ABUNDANCE AND COMPLEX_ABUNDANCE function type
        // criterion yields 3 nodes
        nf = testKAM.createNodeFilter();
        FunctionTypeFilterCriteria ftcriteria =
                new FunctionTypeFilterCriteria();
        ftcriteria.setInclude(true);
        ftcriteria.add(PROTEIN_ABUNDANCE);
        ftcriteria.add(COMPLEX_ABUNDANCE);
        nf.add(ftcriteria);
        nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(3, nodes.size());
        nodeIt = nodes.iterator();
        n1 = nodeIt.next();
        assertEquals(COMPLEX_ABUNDANCE, n1.getFunctionType());
        n2 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n2.getFunctionType());
        KamNode n3 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n3.getFunctionType());
    }
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        nf.add(rtcriteria);
        Collection<KamNode> nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(3, nodes.size());
        Iterator<KamNode> nodeIt = nodes.iterator();
        KamNode n1 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n1.getFunctionType());
        assertEquals(ReturnType.PROTEIN_ABUNDANCE, n1.getFunctionType()
                .getReturnType());
        KamNode n2 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n2.getFunctionType());
        assertEquals(ReturnType.PROTEIN_ABUNDANCE, n2.getFunctionType()
                .getReturnType());
        KamNode n3 = nodeIt.next();
        assertEquals(KINASE_ACTIVITY, n3.getFunctionType());
        assertEquals(ABUNDANCE, n3.getFunctionType().getReturnType());

        // Test exclude of PROTEIN_ABUNDANCE AND BIOLOGICAL_PROCESS function
        // type criterion yields 2 nodes
        nf = testKAM.createNodeFilter();
        FunctionTypeFilterCriteria ftcriteria =
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        nf.add(rtcriteria);
        Collection<KamNode> nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(2, nodes.size());
        Iterator<KamNode> nodeIt = nodes.iterator();
        KamNode n1 = nodeIt.next();
        assertEquals(KINASE_ACTIVITY, n1.getFunctionType());
        KamNode n2 = nodeIt.next();
        assertEquals(BIOLOGICAL_PROCESS, n2.getFunctionType());
    }
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        nf.add(rtcriteria);
        Collection<KamNode> nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(5, nodes.size());
        Iterator<KamNode> nodeIt = nodes.iterator();
        KamNode n1 = nodeIt.next();
        assertEquals(COMPLEX_ABUNDANCE, n1.getFunctionType());
        KamNode n2 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n2.getFunctionType());
        KamNode n3 = nodeIt.next();
        assertEquals(PROTEIN_ABUNDANCE, n3.getFunctionType());
        KamNode n4 = nodeIt.next();
        assertEquals(KINASE_ACTIVITY, n4.getFunctionType());
        KamNode n5 = nodeIt.next();
        assertEquals(BIOLOGICAL_PROCESS, n5.getFunctionType());
    }
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        nf.add(rtcriteria);
        Collection<KamNode> nodes = testKAM.getNodes(nf);
        assertNotNull(nodes);
        assertEquals(3, nodes.size());
        Iterator<KamNode> nodeIt = nodes.iterator();
        KamNode n1 = nodeIt.next();
        assertEquals(COMPLEX_ABUNDANCE, n1.getFunctionType());
        KamNode n2 = nodeIt.next();
        assertEquals(KINASE_ACTIVITY, n2.getFunctionType());
        KamNode n3 = nodeIt.next();
        assertEquals(BIOLOGICAL_PROCESS, n3.getFunctionType());
    }
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        // Iterate over all the edges
        for (KamEdge kamEdge : kam.getEdges()) {
            Edge xEdge = new Edge();
            xEdge.id = kamEdge.getId();
            xEdge.rel = kamEdge.getRelationshipType();
            KamNode knsrc = kamEdge.getSourceNode();
            KamNode kntgt = kamEdge.getTargetNode();
            xEdge.source = knsrc.getId();
            xEdge.target = kntgt.getId();

            Node src = new Node();
            src.function = knsrc.getFunctionType();
            src.label = knsrc.getLabel();
            Node tgt = new Node();
            tgt.function = kntgt.getFunctionType();
            tgt.label = kntgt.getLabel();

            XGMMLUtility.writeEdge(src, tgt, xEdge, writer);
        }

        // Close out the writer
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Related Classes of org.openbel.framework.api.Kam.KamNode

  • org.openbel.framework.api.AbstractPathFinder
  • org.openbel.framework.api.BasicPathFinder
  • org.openbel.framework.api.DefaultOrthologize
  • org.openbel.framework.api.KamImpl
  • org.openbel.framework.api.KamImpl$KamNodeImpl
  • org.openbel.framework.api.KAMStoreImpl
  • org.openbel.framework.api.KamTestUtil
  • org.openbel.framework.api.KamUtils
  • org.openbel.framework.api.NodeFilterTest
  • org.openbel.framework.api.Resolver
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