private boolean parseArgs(String[] args) {
if (args.length < 1) {
System.out.println(
"Usage: java hclustering (<filename>:<16s-23s|23s-5s>:[<lowerThreshold>]:"
+ "[<upperThreshold>]:[<single|average|complete|ward>])+");
System.exit(1);
}
try {
for (String arg : args) {
System.out.println("arg: " + arg);
File dataFile;
FileSettings currFileSettings = new FileSettings();
String[] subArgs = arg.split(ARG_SEPARATOR);
/*
* subArg indices:
* 0 - filename
* 1 - region
* 3 - lowerthreshold
* 4 - upperthreshold
* 5 - distanceType
*/
dataFile = new File(subArgs[0]);
currFileSettings.setRegion(IsolateRegion.getRegion(subArgs[1]));
currFileSettings.setLowerThreshold(
subArgs.length >= 3 ? Double.parseDouble(subArgs[2]) : mLowerThreshold);
currFileSettings.setUpperThreshold(
subArgs.length >= 4 ? Double.parseDouble(subArgs[3]) : mUpperThreshold);
// use reflection for distance measure
/*
distanceMode = args.length >= 3 ?
(DistanceMeasure) Class.forName(args[2]).newInstance() :
new EuclideanDistanceMeasure();
*/
currFileSettings.setDistanceType(
subArgs.length >= 5
? Cluster.distType.valueOf(subArgs[4].toUpperCase())
: Cluster.distType.AVERAGE);
dataFileMap.put(dataFile, currFileSettings);
}
} catch (NumberFormatException formatErr) {
System.out.printf("Invalid threshold values: %d or %d\n", args[2], args[3]);
System.exit(1);
}
return true;
}
public boolean cluster(String[] args) {
boolean success = false;
// handle command line arguments; sets dataFile and threshold
success = parseArgs(args);
Map<String, Map<Integer, List<Isolate>>> dataMap =
new HashMap<String, Map<Integer, List<Isolate>>>();
/*
* Each isolate similarity matrix holds a correlation for both regions
*/
IsolateSimilarityMatrix partialCorrelations = new IsolateSimilarityMatrix();
Map<Connectivity, IsolateSimilarityMatrix> isolateNetworks =
new HashMap<Connectivity, IsolateSimilarityMatrix>();
isolateNetworks.put(Connectivity.STRONG, new IsolateSimilarityMatrix());
isolateNetworks.put(Connectivity.WEAK, new IsolateSimilarityMatrix());
Cluster.distType type = null;
String dataFileName = null;
double lowerThreshold = -1, upperThreshold = -1;
for (File dataFile : dataFileMap.keySet()) {
FileSettings settings = dataFileMap.get(dataFile);
dataFileName = dataFile.getName();
IsolateRegion region = settings.getRegion();
type = settings.getDistanceType();
lowerThreshold = settings.getLowerThreshold();
upperThreshold = settings.getUpperThreshold();
if (dataFile != null) {
IsolateFileParser parser = new IsolateFileParser(dataFile, settings);
// MARKER old code
// isolateMap = parser.extractData(similarityMatrix);
// mIsolateNetworks = parser.extractData();
parser.extractData(isolateNetworks, partialCorrelations);
}
System.out.println("strong Network size: " + isolateNetworks.get(Connectivity.STRONG).size());
}
// each point is a cluster, and we will combine two clusters in each iteration
List<ClusterDendogram> clustDends = clusterIsolates(type, isolateNetworks);
// System.err.println("clustDends length: " + clustDends.size());
// if the isolates yielded NO clusters (wtf data disappear?) or
// if clusterIsolates returned null, then this was *NOT* a success
success = clustDends != null && !clustDends.isEmpty();
String outputFileDir =
String.format("ClusterResults/%s_%.02f_%.02f", type, lowerThreshold, upperThreshold);
/*
String outputFileName = String.format("%s/%s", outputFileDir,
dataFile.getName().substring(0,
dataFile.getName().indexOf(".csv")));
*/
String origFileName =
HClustering.mOutputFileName.equals("")
? dataFileName.substring(0, dataFileName.indexOf(".csv"))
: HClustering.mOutputFileName;
System.out.println(
"Writing to file "
+ origFileName
+ " even though outputFilename should be "
+ HClustering.mOutputFileName);
String outputFileName = String.format("%s/%s", outputFileDir, origFileName);
IsolateOutputWriter.outputClusters(clustDends, outputFileDir, outputFileName + ".xml");
IsolateOutputWriter.outputCytoscapeFormat(clustDends, outputFileName);
IsolateOutputWriter.outputTemporalClusters(clustDends, outputFileName);
IsolateOutputWriter.outputTemporalCharts(clustDends, outputFileName);
return success;
}