private Collection getNeighbors(CyNode node) {
Set result = new HashSet();
Collection edges = network.getAdjacentEdgeList(node, org.cytoscape.model.CyEdge.Type.ANY);
if (edges == null || edges.size() == 0) return result;
Long targetID = node.getSUID();
for (Iterator iterator = edges.iterator(); iterator.hasNext(); ) {
CyEdge curEdge = (CyEdge) iterator.next();
if (curEdge.getSource().getSUID() != targetID) result.add(curEdge.getSource());
else if (curEdge.getTarget().getSUID() != targetID) result.add(curEdge.getTarget());
}
return result;
}
public String getWeightName(CyEdge edge) {
return getName(edge.getSource())
+ "("
+ weights.get(edges.indexOf(edge))
+ ")"
+ getName(edge.getTarget());
}
private void addEdges() {
for (CyEdge edge : edgeList) {
PRNode sourceNode = idToNode.get(edge.getSource().getSUID());
PRNode targetNode = idToNode.get(edge.getTarget().getSUID());
PREdge prEdge = new PREdge(edge);
insertEdgeScore(prEdge, edgeTable, edgeAttributes);
graph.addEdge(prEdge, new Pair<>(sourceNode, targetNode), EdgeType.DIRECTED);
}
}
/**
* @param args the function arguments which must be either one object of type Double or Long
* @return the result of the function evaluation which is the natural logarithm of the first
* argument
*/
public Object evaluateFunction(final Object[] args) {
final Long edgeID = FunctionUtil.getArgAsLong(args[0]);
final CyNetwork currentNetwork = applicationManager.getCurrentNetwork();
if (currentNetwork == null) return (Long) (-1L);
final CyEdge edge = currentNetwork.getEdge(edgeID);
if (edge == null)
throw new IllegalArgumentException("\"" + edgeID + "\" is not a valid edge identifier.");
return edge.getSource().getSUID();
}
public void paintview(ArrayList<HashSet<String>> t, Color c, boolean flag) {
for (CyEdge e : network.getEdgeList()) {
HashSet<String> th = new HashSet<String>();
th.add(network.getRow(e.getSource()).get("name", String.class));
th.add(network.getRow(e.getTarget()).get("name", String.class));
if (t.contains(th)) {
networkView.getEdgeView(e).setLockedValue(BasicVisualLexicon.EDGE_PAINT, c);
if (flag) {
networkView
.getNodeView(e.getSource())
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, c);
networkView
.getNodeView(e.getTarget())
.setVisualProperty(BasicVisualLexicon.NODE_FILL_COLOR, c);
}
}
}
}
public BellmanFordStatsImpl findPath(
CyNetwork network, CyNode source, boolean directed, WeightFunction function) {
Map<CyNode, MetaNode> nodeToMetaNodeMap = new IdentityHashMap<CyNode, MetaNode>();
boolean negativeCycle = true;
for (CyNode node : network.getNodeList()) {
MetaNode metaNode = new MetaNode(node, Double.POSITIVE_INFINITY, null);
nodeToMetaNodeMap.put(node, metaNode);
}
nodeToMetaNodeMap.get(source).setDistance(0.0);
for (int i = 0; i < network.getNodeCount() - 1; i++) {
for (CyEdge edge : network.getEdgeList()) {
MetaNode sourceMetaNode = nodeToMetaNodeMap.get(edge.getSource());
MetaNode targetMetaNode = nodeToMetaNodeMap.get(edge.getTarget());
if (targetMetaNode.getDistance()
> sourceMetaNode.getDistance() + function.getWeight(edge)) {
targetMetaNode.setDistance(sourceMetaNode.getDistance() + function.getWeight(edge));
targetMetaNode.setPredecessor(sourceMetaNode.getNode());
}
}
}
for (CyEdge edge : network.getEdgeList()) {
MetaNode sourceMetaNode = nodeToMetaNodeMap.get(edge.getSource());
MetaNode targetMetaNode = nodeToMetaNodeMap.get(edge.getTarget());
if (targetMetaNode.getDistance() > sourceMetaNode.getDistance() + function.getWeight(edge))
negativeCycle = false;
}
return new BellmanFordStatsImpl(source, nodeToMetaNodeMap, negativeCycle);
}
private double getAdjacency(CyNode neighbor, Set<CyNode> clusterNodes) {
List<CyEdge> edgeList = network.getAdjacentEdgeList(neighbor, CyEdge.Type.ANY);
int totalEdges = edgeList.size();
if (totalEdges == 0) return 0;
int adjacentEdges = 0;
for (CyEdge edge : edgeList) {
if (clusterNodes.contains(edge.getSource()) || clusterNodes.contains(edge.getTarget())) {
adjacentEdges += 1;
}
}
return (double) adjacentEdges / (double) totalEdges;
}
@Override
public void serialize(CyNetworkView networkView, JsonGenerator jgen, SerializerProvider provider)
throws IOException, JsonProcessingException {
jgen.useDefaultPrettyPrinter();
jgen.writeStartObject();
jgen.writeStringField(
CytoscapeJsNetworkModule.FORMAT_VERSION_TAG, CytoscapeJsNetworkModule.FORMAT_VERSION);
jgen.writeStringField(CytoscapeJsNetworkModule.GENERATED_BY_TAG, "cytoscape-" + version);
jgen.writeStringField(
CytoscapeJsNetworkModule.TARGET_CYJS_VERSION_TAG,
CytoscapeJsNetworkModule.CYTOSCAPEJS_VERSION);
final CyNetwork network = networkView.getModel();
// Serialize network data table
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeObject(network.getRow(network));
jgen.writeEndObject();
jgen.writeObjectFieldStart(ELEMENTS.getTag());
// Write array
final List<CyNode> nodes = network.getNodeList();
final List<CyEdge> edges = network.getEdgeList();
jgen.writeArrayFieldStart(NODES.getTag());
for (final CyNode node : nodes) {
jgen.writeStartObject();
// Data field
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeStringField(ID.getTag(), node.getSUID().toString());
// Write CyRow in "data" field
jgen.writeObject(network.getRow(node));
jgen.writeEndObject();
// Position and other visual props
jgen.writeObject(networkView.getNodeView(node));
// Special case for cytoscape.js format:
// - Selected
jgen.writeBooleanField(
CyNetwork.SELECTED, network.getRow(node).get(CyNetwork.SELECTED, Boolean.class));
jgen.writeEndObject();
}
jgen.writeEndArray();
jgen.writeArrayFieldStart(EDGES.getTag());
for (final CyEdge edge : edges) {
jgen.writeStartObject();
jgen.writeObjectFieldStart(DATA.getTag());
jgen.writeStringField(ID.getTag(), edge.getSUID().toString());
jgen.writeStringField(SOURCE.getTag(), edge.getSource().getSUID().toString());
jgen.writeStringField(TARGET.getTag(), edge.getTarget().getSUID().toString());
// Write CyRow in "data" field
jgen.writeObject(network.getRow(edge));
jgen.writeEndObject();
// Special case for cytoscape.js format:
// - Selected
jgen.writeBooleanField(
CyNetwork.SELECTED, network.getRow(edge).get(CyNetwork.SELECTED, Boolean.class));
jgen.writeEndObject();
}
jgen.writeEndArray();
jgen.writeEndObject();
}