/**
* 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());
}
public Data[] execute() {
LogService logger = (LogService) context.getService(LogService.class.getName());
String fileHandler = (String) data[0].getData();
File inData = new File(fileHandler);
try {
if (validateGraphMLHeader(inData)) {
(new GraphMLReader()).readGraph(new FileInputStream(fileHandler));
Data[] dm = new Data[] {new BasicData(inData, "file:text/graphml+xml")};
dm[0].getMetaData().put(DataProperty.LABEL, "Prefuse GraphML file: " + fileHandler);
dm[0].getMetaData().put(DataProperty.TYPE, DataProperty.NETWORK_TYPE);
return dm;
} else return null;
} catch (DataIOException dioe) {
logger.log(
LogService.LOG_ERROR, "Might not be a GraphML file. Got the following exception");
logger.log(LogService.LOG_ERROR, "DataIOException", dioe);
dioe.printStackTrace();
return null;
} catch (SecurityException exception) {
logger.log(
LogService.LOG_ERROR, "Might not be a GraphML file. Got the following exception");
logger.log(LogService.LOG_ERROR, "SecurityException", exception);
exception.printStackTrace();
return null;
} catch (FileNotFoundException e) {
logger.log(LogService.LOG_ERROR, "FileNotFoundException", e);
e.printStackTrace();
return null;
} catch (IOException ioe) {
logger.log(LogService.LOG_ERROR, "IOException", ioe);
ioe.printStackTrace();
return null;
}
}
public static void main(String[] argv) {
// -- 1. load the data ------------------------------------------------
// load the socialnet.xml file. it is assumed that the file can be
// found at the root of the java classpath
Graph graph = null;
try {
graph = new GraphMLReader().readGraph(System.in);
} catch (DataIOException e) {
e.printStackTrace();
System.err.println("Error loading graph. Exiting...");
System.exit(1);
}
// -- 2. the visualization --------------------------------------------
// add the graph to the visualization as the data group "graph"
// nodes and edges are accessible as "graph.nodes" and "graph.edges"
Visualization vis = new Visualization();
vis.add("graph", graph);
vis.setInteractive("graph.edges", null, false);
// -- 3. the renderers and renderer factory ---------------------------
// draw the "name" label for NodeItems
LabelRenderer r = new LabelRenderer("label");
r.setRoundedCorner(8, 8); // round the corners
EdgeRenderer eRender =
new EdgeRenderer(Constants.EDGE_TYPE_CURVE, Constants.EDGE_ARROW_FORWARD);
// create a new default renderer factory
// return our name label renderer as the default for all non-EdgeItems
// includes straight line edges for EdgeItems by default
vis.setRendererFactory(new DefaultRendererFactory(r, eRender));
// -- 4. the processing actions ---------------------------------------
// create our nominal color palette
// pink for females, baby blue for males
int[] palette =
new int[] {
ColorLib.rgb(190, 190, 255), ColorLib.rgb(255, 180, 180), ColorLib.rgb(128, 128, 128),
};
// map nominal data values to colors using our provided palette
DataColorAction fill =
new DataColorAction(
"graph.nodes", "type", Constants.NOMINAL, VisualItem.FILLCOLOR, palette);
// use black for node text
ColorAction text = new ColorAction("graph.nodes", VisualItem.TEXTCOLOR, ColorLib.gray(0));
// use light grey for edges
ColorAction edges = new ColorAction("graph.edges", VisualItem.STROKECOLOR, ColorLib.gray(200));
ColorAction arrows = new ColorAction("graph.edges", VisualItem.FILLCOLOR, ColorLib.gray(200));
// create an action list containing all color assignments
ActionList color = new ActionList();
color.add(fill);
color.add(text);
color.add(edges);
color.add(arrows);
// Add a size action
DataSizeAction size = new DataSizeAction("graph.nodes", "type", 2, Constants.LINEAR_SCALE);
vis.putAction("size", size);
// create an action list with an animated layout
ActionList layout = new ActionList(Activity.INFINITY);
layout.add(new ForceDirectedLayout("graph"));
layout.add(new RepaintAction());
// add the actions to the visualization
vis.putAction("color", color);
vis.putAction("layout", layout);
// -- 5. the display and interactive controls -------------------------
Display d = new Display(vis);
d.setSize(720, 500); // set display size
// drag individual items around
d.addControlListener(new DragControl());
// pan with left-click drag on background
d.addControlListener(new PanControl());
// zoom with right-click drag
d.addControlListener(new ZoomControl());
// -- 6. launch the visualization -------------------------------------
// create a new window to hold the visualization
JFrame frame = new JFrame("IFDS Visualization");
// ensure application exits when window is closed
frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
frame.add(d);
frame.pack(); // layout components in window
frame.setVisible(true); // show the window
// assign the colors
vis.run("color");
// start up the animated layout
vis.run("layout");
}
