private void createEdge(final Interaction itr, final CySubNetwork subNetwork) {
CyNode sourceNode = nMap.get(itr.getSource());
if (sourceNode == null) {
sourceNode = subNetwork.addNode();
subNetwork.getRow(sourceNode).set(CyNetwork.NAME, itr.getSource());
nMap.put(itr.getSource(), subNetwork.getRootNetwork().getNode(sourceNode.getSUID()));
}
for (final String target : itr.getTargets()) {
CyNode targetNode = nMap.get(target);
if (targetNode == null) {
targetNode = subNetwork.addNode();
subNetwork.getRow(targetNode).set(CyNetwork.NAME, target);
nMap.put(target, subNetwork.getRootNetwork().getNode(targetNode.getSUID()));
}
// Add the sourceNode and targetNode to subNetwork
if (!subNetwork.containsNode(sourceNode)) {
subNetwork.addNode(sourceNode);
}
if (!subNetwork.containsNode(targetNode)) {
subNetwork.addNode(targetNode);
}
final CyEdge edge = subNetwork.addEdge(sourceNode, targetNode, true);
subNetwork.getRow(edge).set(CyNetwork.NAME, getEdgeName(itr, target));
subNetwork.getRow(edge).set(CyEdge.INTERACTION, itr.getType());
}
}
private void readInput(TaskMonitor tm) throws IOException {
this.parentTaskMonitor = tm;
tm.setProgress(0.0);
String line;
final BufferedReader br =
new BufferedReader(
new InputStreamReader(inputStream, Charset.forName("UTF-8").newDecoder()), 128 * 1024);
String networkCollectionName = this.rootNetworkList.getSelectedValue().toString();
CySubNetwork subNetwork;
if (networkCollectionName.equalsIgnoreCase(CRERATE_NEW_COLLECTION_STRING)) {
// This is a new network collection, create a root network and a subnetwork, which is a base
// subnetwork
CyNetwork rootNetwork = cyNetworkFactory.createNetwork();
subNetwork = this.cyRootNetworkManager.getRootNetwork(rootNetwork).addSubNetwork();
} else {
// Add a new subNetwork to the given collection
subNetwork = this.name2RootMap.get(networkCollectionName).addSubNetwork();
}
// Build a Map based on the key attribute for the entire collection,
// For SIF network, the 'shared name' attribute is the primary key
this.initNodeMap(subNetwork.getRootNetwork(), "shared " + CyNetwork.NAME);
tm.setProgress(0.1);
// Generate bundled event to avoid too many events problem.
final String firstLine = br.readLine();
if (firstLine.contains(TAB)) delimiter = TAB;
createEdge(new Interaction(firstLine.trim(), delimiter), subNetwork);
tm.setProgress(0.15);
tm.setStatusMessage("Processing the interactions...");
int numInteractionsRead = 0;
while ((line = br.readLine()) != null) {
if (cancelled) {
// Cancel called. Clean up the garbage.
nMap.clear();
nMap = null;
subNetwork = null;
br.close();
return;
}
if (line.trim().length() <= 0) continue;
try {
final Interaction itr = new Interaction(line, delimiter);
createEdge(itr, subNetwork);
} catch (Exception e) {
// Simply ignore invalid lines.
continue;
}
if ((++numInteractionsRead % 1000) == 0)
tm.setStatusMessage("Processed " + numInteractionsRead + " interactions so far.");
}
br.close();
tm.setStatusMessage("Processed " + numInteractionsRead + " interactions in total.");
nMap.clear();
nMap = null;
this.cyNetworks = new CyNetwork[] {subNetwork};
tm.setProgress(1.0);
logger.debug("SIF file loaded: ID = " + subNetwork.getSUID());
}
