/** Initializes a new instance of <code>Plugin</code>. */
public Plugin(CySwingApplication swingApp) {
try {
// Initiate default visual settings
SettingsSerializer.initVisualSettings();
// If initialization fails, the following lines are not executed:
} catch (SecurityException ex) {
Utils.showErrorBox(swingApp.getJFrame(), Messages.DT_SECERROR, Messages.SM_SECERROR1);
System.err.println(Messages.SM_SECERROR1);
} catch (InnerException ex) {
final ByteArrayOutputStream os = new ByteArrayOutputStream();
final PrintStream ps = new PrintStream(os);
ex.printStackTrace(ps);
ps.flush();
if (os.toString().contains("NoClassDefFoundError:")) {
// Library is missing
logger.error(Messages.SM_LOGERROR, ex);
} else {
// NetworkAnalyzer internal error
logger.error(Messages.SM_LOGERROR, ex);
}
}
}
/*
* (non-Javadoc)
*
* @see cytoscape.util.SwingWorker#construct()
*/
@Override
public Object construct() {
progress = 0;
for (final File inputFile : inputFiles) {
// Make a new network in cytoscape from a filename in
// the network-directory
CyNetwork network = null;
try {
write(Messages.SM_LOADING + inputFile.getName() + " ... ");
if (!inputFile.isFile()) {
throw new RuntimeException();
}
CyNetworkReader reader =
cyNetworkViewReaderMgr.getReader(inputFile.toURI(), inputFile.getName());
try {
// TODO Use the Task's task monitor
reader.run(new SampleTaskMonitor());
} catch (Exception ex) {
return null;
}
network = reader.getNetworks()[0];
network.getRow(network).set(CyNetwork.NAME, inputFile.getName());
} catch (RuntimeException e) {
writeLine(Messages.SM_READERROR);
reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_NOT_OPENED));
progress += PROGRESS_PER_NET;
continue;
}
// Get all possible interpretations for the network
NetworkInspection inspection = null;
try {
inspection = CyNetworkUtils.inspectNetwork(network);
} catch (IllegalArgumentException e) {
writeLine(Messages.SM_DONE);
reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_EMPTY));
unloadNetwork(inputFile, network);
continue;
} catch (NullPointerException e) {
reports.add(new NetworkAnalysisReport(inputFile, null, AnalysisError.NETWORK_FILE_INVALID));
progress += PROGRESS_PER_NET;
continue;
}
final NetworkInterpretation[] interprs =
filterInterpretations(getInterpretations(inspection));
final int intCount = interprs.length;
final int advance = PROGRESS_PER_NET / intCount;
// Run NetworkAnalyzer on all accepted interpretations
writeLine(Messages.SM_DONE);
for (int j = 0; j < intCount; progress += advance, ++j) {
if (cancelled) {
writeLine(Messages.SM_ANALYSISC);
return null;
}
// Run the analysis for an interpretation
final NetworkInterpretation interpretation = interprs[j];
try {
if (interpretation.isDirected()) {
analyzer = new DirNetworkAnalyzer(network, null, interpretation);
} else {
analyzer = new UndirNetworkAnalyzer(network, null, interpretation);
}
writeLine(
Messages.DI_ANALYZINGINTERP1 + (j + 1) + Messages.DI_ANALYZINGINTERP2 + intCount);
final int maxProgress = analyzer.getMaxProgress();
scale = (double) advance / (double) maxProgress;
analyzing = true;
subProgress = 0;
analyzer.computeAll();
analyzing = false;
if (cancelled) {
writeLine(Messages.SM_ANALYSISC);
return null;
}
final NetworkStats stats = analyzer.getStats();
synchronized (this) {
analyzer = null;
}
final String networkName = network.getRow(network).get("name", String.class);
stats.setTitle(networkName + interpretation.getInterpretSuffix());
final String extendedName = networkName + createID(interpretation);
try {
if (SettingsSerializer.getPluginSettings().getUseNodeAttributes()) {
if (!saveNodeAttributes(
network, interpretation.isDirected(), outputDir, extendedName)) {
writeLine(Messages.SM_ATTRIBUTESNOTSAVED);
}
}
File netstatFile = new File(outputDir, extendedName + ".netstats");
StatsSerializer.save(stats, netstatFile);
writeLine(Messages.SM_RESULTSSAVED);
reports.add(new NetworkAnalysisReport(inputFile, interpretation, netstatFile));
} catch (SecurityException ex) {
writeError(Messages.SM_SAVEERROR);
reports.add(
new NetworkAnalysisReport(
inputFile, interpretation, AnalysisError.OUTPUT_NOT_CREATED));
} catch (FileNotFoundException ex) {
writeError(Messages.SM_SAVEERROR);
reports.add(
new NetworkAnalysisReport(
inputFile, interpretation, AnalysisError.OUTPUT_NOT_CREATED));
} catch (IOException e) {
writeError(Messages.SM_SAVEERROR);
reports.add(
new NetworkAnalysisReport(
inputFile, interpretation, AnalysisError.OUTPUT_IO_ERROR));
}
if (cancelled) {
writeLine(Messages.SM_ANALYSISC);
return null;
}
} catch (Exception e) {
reports.add(
new NetworkAnalysisReport(inputFile, interpretation, AnalysisError.INTERNAL_ERROR));
}
}
unloadNetwork(inputFile, network);
}
return null;
}