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");
}
/**
* Re-writes an unit description file by replacing the label names of the input vectors as defined
* by the given mapping file.
*
* @author Michael Dittenbach
* @author Rudolf Mayer
* @version $Id: VectorFileRewriter.java 4267 2012-04-03 14:51:20Z mayer $
*/
public class VectorFileRewriter implements SOMToolboxApp {
private static final Parameter[] OPTIONS =
new Parameter[] {
OptionFactory.getOptInputFileName(),
OptionFactory.getOptNameMappingFile(true),
OptionFactory.getOptOutputVector(),
OptionFactory.getOptMatchMode(false),
OptionFactory.getOptStrip(false),
OptionFactory.getSwitchOnlyLastPathSegment(false),
OptionFactory.getOptGZip(false, false)
};
public static String DESCRIPTION = "Replace labels in SOMLibVectorFiles";
public static String LONG_DESCRIPTION =
"Replaces labels in SOMLibVectorFiles by means of a mapping file; labels in the mapping file must be separated by a tab";
public static final Type APPLICATION_TYPE = Type.Helper;
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");
}
public static String getReplacement(
Hashtable<String, String> mapping, String[] keys, String token, MatchMode matchMode) {
if (matchMode == MatchMode.exact) {
return mapping.get(token);
} else if (matchMode == MatchMode.withoutPath) {
int index = token.lastIndexOf("/");
String searchToken = token.substring(index + 1);
return mapping.get(searchToken);
} else if (matchMode == MatchMode.endsWith) {
// FIXME: this is not at all efficient
for (String key : keys) {
if (token.endsWith(key)) {
return mapping.get(key);
}
}
return null;
} else {
throw new IllegalArgumentException("Unsupported MatchMode '" + matchMode + "'.");
}
}
private static Hashtable<String, String> readMappingFile(String fName) throws IOException {
Hashtable<String, String> res = new Hashtable<String, String>();
res.put("$MAPPED_VECS", "$MAPPED_VECS");
BufferedReader br = FileUtils.openFile("Mapping file", fName);
String line = null;
while ((line = br.readLine()) != null) {
String[] splits = line.split("\t", 2);
String origString = splits[0];
String targetString = splits[1];
res.put(origString, targetString);
}
br.close();
return res;
}
}