Package org.openbel.framework.api.Kam

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

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                }
            }

            // TODO Handle terms that may not have UUID parameters!
            if (missing) {
                KamNode kamNode = kAMStore.getKamNode(kam, belTerm);
                return kamNode;
            }

            // find kam node by term signature / uuids
            return kAMStore.getKamNodeForTerm(kam, termSignature,
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        if (null == belTerm) {
            throw new InvalidArgument("belTerm", belTerm);
        }

        KamNode kamNode = null;

        try {
            // If we parsed Ok we can go ahead and lookup the string in the KAMStore
            kamNode = kAMStore.getKamNode(kam, belTerm);
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            throw new InvalidArgument(
                    "null parameter(s) provided to resolve API.");
        }

        // resolve subject bel term to kam node.
        final KamNode subjectKamNode = resolve(kam, kAMStore, subject, nsmap, eq);
        if (subjectKamNode == null) return null;

        // resolve object bel term to kam node.
        final KamNode objectKamNode = resolve(kam, kAMStore, object, nsmap, eq);
        if (objectKamNode == null) return null;

        // only resolve edge if kam nodes resolved
        return resolveEdge(kam, subjectKamNode, r, objectKamNode);
    }
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            throw new InvalidArgument(
                    "null parameter(s) provided to resolve API.");
        }

        // resolve subject bel term to kam node.
        final KamNode subjectKamNode = resolve(kam, kAMStore, subjectBelTerm);
        if (subjectKamNode == null) {
            return null;
        }

        // resolve object bel term to kam node.
        final KamNode objectKamNode = resolve(kam, kAMStore, objectBelTerm);

        return resolveEdge(kam, subjectKamNode, rtype, objectKamNode);
    }
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                    testKamNode.functionType,
                    testKamNode.label));
        }

        for (final TestKamEdge testKamEdge : testKamEdges) {
            final KamNode newSource = newNodes.get(testKamEdge.sourceNode);
            final KamNode newTarget = newNodes.get(testKamEdge.targetNode);

            if (newSource == null || newTarget == null) {
                throw new IllegalStateException(
                        "Test KAM nodes could not be found.");
            }
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     * @return Kam array
     */
    Kam[] kams(KamNode... nodes) {
        List<Kam> kams = new ArrayList<Kam>(nodes.length);
        for (int i = 0; i < nodes.length; i++) {
            KamNode node = nodes[i];
            kams.add(node.getKam());
        }
        return kams.toArray(new Kam[0]);
    }
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        }

        final Collection<KamEdge> edges = kam.getEdges();
        if (hasItems(edges)) {
            for (final KamEdge edge : edges) {
                final KamNode source = copy.findNode(edge.getSourceNode()
                        .getId());
                final KamNode target = copy.findNode(edge.getTargetNode()
                        .getId());

                assert source != null;
                assert target != null;
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        }

        // build out target set, check that each node is in the KAM
        final Set<KamNode> targetSet = new HashSet<KamNode>(sources.length);
        for (int i = 0; i < sources.length; i++) {
            final KamNode source = sources[i];

            if (!kam.contains(source)) {
                throw new InvalidArgument("Source does not exist in KAM.");
            }
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        // get adjacent edges
        final Set<KamEdge> edges = kam.getAdjacentEdges(cnode, BOTH);

        for (final KamEdge edge : edges) {
            if (pushEdge(edge, nodeStack, edgeStack)) {
                final KamNode edgeOppositeNode = nodeStack.peek();

                // we have found a path from source to target
                if (targets.contains(edgeOppositeNode)) {
                    final SimplePath newPath =
                            new SimplePath(kam, source, nodeStack.peek(),
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        if (edgeStack.contains(edge)) {
            return false;
        }

        final KamNode currentNode = nodeStack.peek();
        final KamNode edgeOppositeNode =
                (edge.getSourceNode() == currentNode ? edge
                        .getTargetNode() : edge.getSourceNode());

        if (nodeStack.contains(edgeOppositeNode)) {
            return false;
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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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