/*.................................................................................................................*/
public int[] getTaxonNumberTranslation(Taxa taxa) {
int max = -1;
for (int it = 0; it < taxa.getNumTaxa(); it++) {
long translateNumber = getTaxonNumberInTree(taxa, it);
if (MesquiteLong.isCombinable(translateNumber) && translateNumber > max) {
max = (int) translateNumber;
}
}
int[] translate = new int[max + 1];
for (int it = 0; it < data.getNumTaxa(); it++) {
long translateNumber = getTaxonNumberInTree(taxa, it);
if (MesquiteLong.isCombinable(translateNumber) && translateNumber >= 0) {
translate[(int) translateNumber] = it;
}
}
return translate;
}
/*.................................................................................................................*/
public void processOutputFiles() {
if (outputFileProcessor != null && outputFilePaths != null && lastModified != null) {
String[] paths = outputFileProcessor.modifyOutputPaths(outputFilePaths);
for (int i = 0; i < paths.length && i < lastModified.length; i++) {
File file = new File(paths[i]);
long lastMod = file.lastModified();
if (!MesquiteLong.isCombinable(lastModified[i]) || lastMod > lastModified[i]) {
outputFileProcessor.processOutputFile(paths, i);
lastModified[i] = lastMod;
}
}
}
}
