Examples with CyEdge org.cytoscape.model.CyEdge used on opensource projects

Example 31 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class NodeInteractionFilter method isHit.

private boolean isHit(CyNode pNode, List<CyEdge> edges) {
    // Get the list of relevant edges for this node
    List<CyEdge> adjacentEdges = null;
    if (nodeType == NODE_SOURCE) {
        adjacentEdges = network.getAdjacentEdgeList(pNode, Type.OUTGOING);
    } else if (nodeType == NODE_TARGET) {
        adjacentEdges = network.getAdjacentEdgeList(pNode, Type.INCOMING);
    } else if (nodeType == NODE_SOURCE_TARGET) {
        adjacentEdges = network.getAdjacentEdgeList(pNode, Type.ANY);
    } else {
        // nodeType == NODE_UNDEFINED --Neither source or target is selected
        return false;
    }
    if (adjacentEdges == null || adjacentEdges.size() == 0) {
        return false;
    }
    BitSet passFilter_edgeBits = passFilter.getEdgeBits();
    if (passFilter_edgeBits == null)
        return false;
    int edgeIndex = -1;
    for (int i = 0; i < adjacentEdges.size(); i++) {
        edgeIndex = edges.indexOf(adjacentEdges.get(i));
        if (passFilter_edgeBits.get(edgeIndex) == true) {
            return true;
        }
    }
    return false;
}

Example 32 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class NodeInteractionFilter method apply.

public void apply() {
    if (!childChanged)
        return;
    if (network == null) {
        setNetwork(applicationManager.getCurrentNetwork());
    }
    if (network == null) {
        return;
    }
    // Make sure the pass filter is current
    if (passFilter == null) {
        passFilter = new CompositeFilter("None");
    }
    if (!passFilter.getName().equalsIgnoreCase("None")) {
        passFilter.setNetwork(network);
        passFilter.apply();
    }
    List<CyNode> nodes_list = network.getNodeList();
    List<CyEdge> edges = network.getEdgeList();
    // NodeInteractionFilter will select node only
    int objectCount = nodes_list.size();
    // all the bits are false at very beginning
    nodeBits = new BitSet(objectCount);
    if ((nodeType != NODE_UNDEFINED) && (!passFilter.getName().equalsIgnoreCase("None"))) {
        for (int i = 0; i < objectCount; i++) {
            if (isHit(nodes_list.get(i), edges)) {
                nodeBits.set(i);
            }
        }
    }
    if (negation) {
        nodeBits.flip(0, objectCount);
    }
    childChanged = false;
}

Example 33 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class EdgeInteractionFilter method apply.

public void apply() {
    if (!childChanged)
        return;
    if (network == null) {
        setNetwork(applicationManager.getCurrentNetwork());
    }
    if (network == null) {
        return;
    }
    // Make sure the pass filter is current
    if (passFilter == null) {
        passFilter = new CompositeFilter("None");
    }
    if (!passFilter.getName().equalsIgnoreCase("None")) {
        passFilter.setNetwork(network);
        passFilter.apply();
    }
    BitSet passFilter_nodeBits = passFilter.getNodeBits();
    List<CyEdge> edges_list = network.getEdgeList();
    List<CyNode> nodes = network.getNodeList();
    // EdgeInteractionFilter will select edge only
    int objectCount = edges_list.size();
    // all the bits are false at very beginning
    edgeBits = new BitSet(objectCount);
    if (nodeType != NODE_UNDEFINED) {
        for (int i = 0; i < objectCount; i++) {
            if (isHit(edges_list.get(i), passFilter_nodeBits, nodes)) {
                edgeBits.set(i);
            }
        }
    }
    if (negation) {
        edgeBits.flip(0, objectCount);
    }
    childChanged = false;
}

Example 34 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class EnhancedSearchIndex method BuildIndex.

private void BuildIndex(RAMDirectory idx, CyNetwork network) {
    try {
        // Make a writer to create the index, empty set of stop words (redmine #3808)
        StandardAnalyzer analyzer = new StandardAnalyzer(Version.LUCENE_30, Collections.emptySet());
        analyzer.setMaxTokenLength(1024 * 10);
        IndexWriter writer = new IndexWriter(idx, analyzer, IndexWriter.MaxFieldLength.UNLIMITED);
        // Add a document for each graph object - node and edge
        List<CyNode> nodeList = network.getNodeList();
        this.taskMonitor.setProgress(0.1);
        for (CyNode cyNode : nodeList) {
            writer.addDocument(createDocument(network, cyNode, EnhancedSearch.NODE_TYPE, cyNode.getSUID()));
        }
        this.taskMonitor.setProgress(0.6);
        List<CyEdge> edgeList = network.getEdgeList();
        for (CyEdge cyEdge : edgeList) {
            writer.addDocument(createDocument(network, cyEdge, EnhancedSearch.EDGE_TYPE, cyEdge.getSUID()));
        }
        // Optimize and close the writer to finish building the index
        writer.optimize();
        writer.close();
    } catch (IOException ioe) {
        ioe.printStackTrace();
    }
    this.taskMonitor.setProgress(0.95);
}

Example 35 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class SelectTask method getResults.

public Object getResults(Class type) {
    List<CyIdentifiable> identifiables = new ArrayList();
    if (selectedNodes != null)
        identifiables.addAll(selectedNodes);
    if (selectedEdges != null)
        identifiables.addAll(selectedEdges);
    if (type.equals(List.class)) {
        return identifiables;
    } else if (type.equals(String.class)) {
        if (identifiables.size() == 0)
            return "<none>";
        String ret = "";
        if (selectedNodes != null && selectedNodes.size() > 0) {
            ret += "Nodes selected: \n";
            for (CyNode node : selectedNodes) {
                ret += "   " + network.getRow(node).get(CyNetwork.NAME, String.class) + "\n";
            }
        }
        if (selectedEdges != null && selectedEdges.size() > 0) {
            ret += "Edges selected: \n";
            for (CyEdge edge : selectedEdges) {
                ret += "   " + network.getRow(edge).get(CyNetwork.NAME, String.class) + "\n";
            }
        }
        return ret;
    } else if (type.equals(JSONResult.class)) {
        JSONResult res = () -> {
            if (identifiables == null || identifiables.size() == 0)
                return "{}";
            else {
                CyJSONUtil cyJSONUtil = registrar.getService(CyJSONUtil.class);
                String result = "{\"nodes\":";
                if (selectedNodes == null || selectedNodes.size() == 0)
                    result += "[]";
                else
                    result += cyJSONUtil.cyIdentifiablesToJson(selectedNodes);
                result += ", \"edges\":";
                if (selectedEdges == null || selectedEdges.size() == 0)
                    result += "[]";
                else
                    result += cyJSONUtil.cyIdentifiablesToJson(selectedEdges);
                return result + "}";
            }
        };
        return res;
    }
    return identifiables;
}