/**
* GML File constructor. STILL IN DEVELOPMENT: If the file has .xml extension, it considers that
* it is a Syntren file, and converts it before building
*
* @param inputPath File path with TRN information
*/
public NetworkData(String inputPath) {
String ext = SyntrenFilter.getExtension(inputPath);
if (ext.equals("xml")) {
TRNParser.syntren2GML(inputPath, "es/usal/bicoverlapper/data/TRN.xml");
f = new File("es/usal/bicoverlapper/data/TRN.xml");
} else if (ext.equals("txt")) {
TRNParser.tab2GML(inputPath, "es/usal/bicoverlapper/data/TRN.xml");
f = new File("es/usal/bicoverlapper/data/TRN.xml");
} else f = new File(inputPath);
gr = new GraphMLReader();
try {
g = gr.readGraph(f); // takes some time for 2600 nodes, not too much
} catch (DataIOException dioe) {
System.out.println("Error reading " + f + ": " + dioe.getMessage());
System.exit(1);
}
nNodes = g.getNodeCount();
nEdges = g.getEdgeCount();
g.addColumn("id", int.class);
// Motifs (pruebas)
// countFFLs(); //TODO: Improve the search with long number of nodes, for 2600 is terribly slow
}
/** @see java.lang.Runnable#run() */
public void run() {
while (true) {
Entry e = null;
synchronized (s_queue) {
if (s_queue.size() > 0) e = (Entry) s_queue.remove(0);
}
if (e != null) {
try {
if (e.listener != null) e.listener.preQuery(e);
e.ds.getData(e.table, e.query, e.keyField, e.lock);
if (e.listener != null) e.listener.postQuery(e);
} catch (DataIOException dre) {
s_logger.warning(dre.getMessage() + "\n" + StringLib.getStackTrace(dre));
}
} else {
// nothing to do, chill out until notified
try {
synchronized (this) {
wait();
}
} catch (InterruptedException ex) {
}
}
}
}
/**
* Syntren File constructor. Builds a GML file from a Syntren file, saving it to disk and building
* the TRNData
*
* @param inputPath Syntren input file path
* @param outputPath GML output file path
*/
public NetworkData(String inputPath, String outputPath) {
TRNParser.syntren2GML(inputPath, outputPath);
// System.out.println("Termina el conversor");
f = new File(outputPath);
gr = new GraphMLReader();
try {
g = gr.readGraph(f);
} catch (DataIOException dioe) {
System.out.println("Error reading " + f + ": " + dioe.getMessage());
System.exit(1);
}
// System.out.println("Hemos terminado de crear el grafo sin problemas");
System.out.println("Network with " + g.getNodeCount() + " nodes");
System.out.println("Network with " + g.getEdgeCount() + " edges");
nNodes = g.getNodeCount();
nEdges = g.getEdgeCount();
// countFFLs();
System.out.println("Number of FFLs found: " + ffls.size());
}