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()); }