Package org.openbel.framework.common.protonetwork.model.ProtoEdgeTable

Examples of org.openbel.framework.common.protonetwork.model.ProtoEdgeTable.TableProtoEdge

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     */
    @Test
    public void testDistinctEdgesSingleCall() {
        final ProtoEdgeTable tbl = new ProtoEdgeTable();

        final TableProtoEdge edge1 = new TableProtoEdge(1, "INCREASES", 2);
        final TableProtoEdge edge2 =
                new TableProtoEdge(1, "DIRECTLY_DECREASES", 3);

        // for statement 0 add both edges in one call
        tbl.addEdges(0, edge1, edge2);

        // we should have one statement (0)
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     */
    @Test
    public void testDistinctEdgesSubsequentCall() {
        final ProtoEdgeTable tbl = new ProtoEdgeTable();

        final TableProtoEdge edge1 = new TableProtoEdge(1, "INCREASES", 2);
        final TableProtoEdge edge2 =
                new TableProtoEdge(1, "DIRECTLY_DECREASES", 3);

        // for statement 0 add both edges in subsequent calls
        tbl.addEdges(0, edge1);
        tbl.addEdges(0, edge2);

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    @Test
    public void testDuplicateEdges() {
        final ProtoEdgeTable tbl = new ProtoEdgeTable();

        // for statement 0, add edge triple "1 HAS_COMPONENT 2"
        final TableProtoEdge edge1 = new TableProtoEdge(1, "HAS_COMPONENT", 2);
        tbl.addEdges(0, edge1);

        // for statement 1, add the same edge
        final TableProtoEdge edge2 = new TableProtoEdge(1, "HAS_COMPONENT", 2);
        tbl.addEdges(1, edge2);

        // we should have two statements (0 and 1)
        assertThat(tbl.getStatementEdges().size(), is(2));
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        final Map<TableProtoEdge, Integer> edgeCache =
                new HashMap<ProtoEdgeTable.TableProtoEdge, Integer>();
        final Map<Integer, Integer> revEq = new HashMap<Integer, Integer>();
        int eq = 0;
        for (int i = 0, n = edges.size(); i < n; i++) {
            final TableProtoEdge edge = edges.get(i);

            // translate into a proto node equivalent edge
            final Integer eqs = eqn.get(edge.getSource());
            final Integer eqt = eqn.get(edge.getTarget());
            final TableProtoEdge eqEdge =
                    new TableProtoEdge(eqs, edge.getRel(), eqt);

            // we have seen this proto edge so equivalence
            Integer cachedEdge = edgeCache.get(eqEdge);
            if (cachedEdge != null) {
                // reassign equivalence index to previously seen equivalent edge
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                    "SourceProtoNodeIndex", "Relationship",
                    "TargetProtoNodeIndex", "EquivalenceIndex");

            final List<TableProtoEdge> edges = pet.getProtoEdges();
            for (int i = 0, n = edges.size(); i < n; i++) {
                final TableProtoEdge edge = edges.get(i);

                final String ei = String.valueOf(i);
                final String source = String.valueOf(edge.getSource());
                final String rel = edge.getRel();
                final String target = String.valueOf(edge.getTarget());

                String eqIndex = edgeEq.get(i).toString();

                tdvWriter.writeNext(new String[] { ei, source, rel, target,
                        eqIndex });
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        Map<Integer, Integer> nodeTermIndex = nt.getNodeTermIndex();

        TableProtoEdge[] remappedEdges = new TableProtoEdge[edgeIndices.size()];
        int i = 0;
        for (Integer edgeIndex : edgeIndices) {
            TableProtoEdge edge = edges.get(edgeIndex);
            int sourceBefore = edge.getSource();
            int targetBefore = edge.getTarget();

            Integer sourceTerm = nodeTermIndex.get(sourceBefore);
            Integer targetTerm = nodeTermIndex.get(targetBefore);
            Integer newSource = termMap.get(sourceTerm);
            if (newSource == null) {
                newSource = mergeTerm(sourceTerm, protoNetwork1, protoNetwork2,
                        documentId, termMap);
            }

            Integer newTarget = termMap.get(targetTerm);
            if (newTarget == null) {
                newTarget = mergeTerm(targetTerm, protoNetwork1, protoNetwork2,
                        documentId, termMap);
            }

            remappedEdges[i++] = new TableProtoEdge(newSource, edge.getRel(),
                    newTarget);
        }
        ProtoEdgeTable edgeTable = protoNetwork1.getProtoEdgeTable();
        edgeTable.addEdges(newStatementIndex, remappedEdges);
    }
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                continue;
            }

            added.add(eqId);

            final TableProtoEdge edge = edges.get(i);

            // XXX offset
            keps.setInt(1, eqId + 1);
            // XXX offset
            keps.setInt(2, eqn.get(edge.getSource()) + 1);
            // XXX offset
            keps.setInt(3, eqn.get(edge.getTarget()) + 1);

            RelationshipType r = RelationshipType.getRelationshipType(edge
                    .getRel());
            keps.setInt(4, r.getValue());
            keps.addBatch();
        }
        added.clear();
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Related Classes of org.openbel.framework.common.protonetwork.model.ProtoEdgeTable.TableProtoEdge

  • org.openbel.framework.common.protonetwork.model.ProtoEdgeTableTest
  • org.openbel.framework.core.equivalence.StatementEquivalencer
  • org.openbel.framework.core.kam.JdbcKAMLoaderImpl
  • org.openbel.framework.core.protonetwork.ProtoNetworkMerger
  • org.openbel.framework.core.protonetwork.TextProtoNetworkExternalizer
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