public static void main(String[] args) throws IOException, SOMToolboxException {
// register and parse all options for the
JSAPResult config =
OptionFactory.parseResults(
args,
OptionFactory.getOptInputVectorFile(true),
OptionFactory.getOptClassInformationFile(true),
OptionFactory.getOptOutputFileName(true),
OptionFactory.getOptOutputDirectory(false));
String vectorFileName = config.getString("inputVectorFile");
String classInfoFile = config.getString("classInformationFile");
String outputDir = config.getString("outputDirectory", ".");
String outputFileName = config.getString("output");
SOMLibSparseInputData inputData = new SOMLibSparseInputData(vectorFileName);
SOMLibClassInformation classInfo = new SOMLibClassInformation(classInfoFile);
classInfo.removeNotPresentElements(inputData);
InputDataWriter.writeAsSOMLib(classInfo, outputDir + File.separator + outputFileName);
}
public static void main(String[] args) throws IOException {
// register and parse all options
JSAPResult config = OptionFactory.parseResults(args, OPTIONS);
String inputFileName = AbstractOptionFactory.getFilePath(config, "input");
String mappingFile = AbstractOptionFactory.getFilePath(config, "nameMappingFile");
String outputFileName = AbstractOptionFactory.getFilePath(config, "output");
String stripFromLabel = config.getString("stripFromString");
boolean onlyLastPathSegment = config.getBoolean("onlyLastPathSegment");
boolean gzip = config.getBoolean("gzip");
MatchMode matchMode = MatchMode.valueOf(config.getString("matchMode"));
Hashtable<String, String> mapping = readMappingFile(mappingFile);
String[] keys = null;
if (matchMode == MatchMode.endsWith) {
// defining the keys ones as String[] is still slow, but faster than using Hashmap#keySet()
// often
keys = mapping.keySet().toArray(new String[mapping.size()]);
}
OutputStream out =
gzip
? new GZIPOutputStream(new FileOutputStream(outputFileName))
: new FileOutputStream(outputFileName);
BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(out));
HashMap<String, String> headers =
FileUtils.readSOMLibFileHeaders(
FileUtils.openFile("Input vector", inputFileName), "input vector");
int totalVectorCount = Integer.parseInt(headers.get("$XDIM"));
BufferedReader br = FileUtils.openFile("Input vector", inputFileName);
String line = null;
StdErrProgressWriter progress =
new StdErrProgressWriter(totalVectorCount, "rewriting vector ", 100);
int written = 0;
int skipped = 0;
while ((line = br.readLine()) != null) {
if (line.startsWith("$")) {
bw.write(line);
bw.newLine();
} else {
int lastPos = line.lastIndexOf(" ");
String label = line.substring(lastPos + 1);
// System.out.println(stripFromLabel);
// System.out.print(label);
label = label.replaceAll(stripFromLabel, "");
if (onlyLastPathSegment && label.contains("/")) {
label = label.substring(label.lastIndexOf("/") + 1);
}
// System.out.println("=>" + label);
String target = getReplacement(mapping, keys, label, matchMode);
if (target != null) {
bw.write(line.substring(0, lastPos));
bw.write(" " + target);
bw.newLine();
written++;
} else {
// System.out.println("No label found for " + label);
skipped++;
}
progress.progress();
}
}
br.close();
bw.close();
System.out.println(
"Wrote "
+ written
+ " vectors, skipped "
+ skipped
+ " because no label found in matching file");
}