protected CyEdge getEdgeByName(CyNetwork net, String name) {
for (CyEdge e : net.getEdgeList()) {
if (name.equals(net.getRow(e).get(NAME, String.class))) return e;
}
return null;
}
private void initVariables() {
edgeAttributes = context.getSelectedEdgeAttributes();
graph = new DirectedSparseMultigraph<>();
idToNode = new HashMap<>();
nodeList = network.getNodeList();
edgeList = network.getEdgeList();
nodeTable = network.getDefaultNodeTable();
edgeTable = network.getDefaultEdgeTable();
}
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);
}
@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();
}
void cyLoad(CyNetwork gp) {
net = gp;
nodes = new ArrayList<CyNode>(net.getNodeList());
edges = new ArrayList<CyEdge>(net.getEdgeList());
}