/**
* Inform User of Network Stats.
*
* @param taskMonitor
*/
private void informUserOfGraphStats(CyNetwork newNetwork, TaskMonitor taskMonitor) {
NumberFormat formatter = new DecimalFormat("#,###,###");
StringBuffer sb = new StringBuffer();
// Give the user some confirmation
sb.append("Successfully loaded network from: ");
sb.append(url);
sb.append("\n\nNetwork contains " + formatter.format(newNetwork.getNodeCount()));
sb.append(" nodes and " + formatter.format(newNetwork.getEdgeCount()));
sb.append(" edges.\n\n");
// TODO: Port this
// if (newNetwork.getNodeCount() < Integer.parseInt(CytoscapeInit.getProperties()
//
// .getProperty("viewThreshold"))) {
// sb.append("Network is under "
// + CytoscapeInit.getProperties().getProperty("viewThreshold")
// + " nodes. A view will be automatically created.");
// } else {
// sb.append("Network is over "
// + CytoscapeInit.getProperties().getProperty("viewThreshold")
// + " nodes. A view has not been created."
// + " If you wish to view this network, use "
// + "\"Create View\" from the \"Edit\" menu.");
// }
taskMonitor.setStatusMessage(sb.toString());
}
@Test
public void testRemoveNodeIndexStaysConstant() {
assertEquals(0, net.getNodeCount());
CyNode n0 = net.addNode();
CyNode n1 = net.addNode();
long n0i = n0.getSUID();
long n1i = n1.getSUID();
net.removeNodes(Collections.singletonList(n0));
long nnli = n1.getSUID();
assertEquals(nnli, n1i);
}
@Test
public void testRemoveNodeGetNodeFromIndex() {
assertEquals(0, net.getNodeCount());
CyNode n0 = net.addNode();
CyNode n1 = net.addNode();
long n0i = n0.getSUID();
long n1i = n1.getSUID();
assertEquals(net.getNode(n0i), n0);
assertEquals(net.getNode(n1i), n1);
assertTrue(net.removeNodes(Collections.singletonList(n0)));
assertNull(net.getNode(n0i));
assertEquals(n1, net.getNode(n1i));
}
/** Assuming we only create one network. */
protected CyNetwork checkSingleNetwork(List<CyNetworkView> views, int numNodes, int numEdges) {
assertNotNull(views);
assertEquals(1, views.size());
CyNetwork net = views.get(0).getModel();
assertNotNull(net);
assertEquals(numNodes, net.getNodeCount());
assertEquals(numEdges, net.getEdgeCount());
return net;
}
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);
}