/*.................................................................................................................*/ 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; } } } }