// This constructor works for tbt file
public void getClusters(TagsByTaxa tbt) {
ArrayList<cluster> clList = new ArrayList();
TagMatchFinder tmf = new TagMatchFinder(tbt);
for (int i = 0; i < tbt.getTagCount(); i++) {
long[] qTag = tbt.getTag(i);
TreeMap<Integer, Integer> hitDiv = tmf.findMatchesWithIntLengthWords(qTag, 1, false);
for (Entry<Integer, Integer> each : hitDiv.entrySet()) {
if (each.getValue() > 0) {
clList.add(new cluster(i, each.getKey(), hitDiv.size(), true));
}
}
}
cls = clList.toArray(new cluster[clList.size()]);
// Arrays.sort(cls);
}
/** Inserts tag count values into the RandomAccessFile created by @link{createMergeOutfile}. */
public static final void fillMergeOutfile(String[] infiles, String outfile) {
TagsByTaxa tbtOut = newTBT(outfile);
tbtOut.setMethodByRows(true);
int count = 0;
int filesRead = 0;
for (String inName : infiles) {
filesRead++;
myLogger.info("Scanning " + inName + " (file " + filesRead + " of " + infiles.length + ").");
TagsByTaxa tbtFM = newTBT(inName);
if (combineSynonymousTaxa) {
tbtFM.truncateTaxonNames();
}
int[] theTR = taxaRedirect(tbtFM.getTaxaNames(), tbtOut.getTaxaNames());
for (int i = 0; i < tbtFM.getTagCount(); i++) {
int toTag = tbtOut.getTagIndex(tbtFM.getTag(i));
if (toTag < 0) {
continue;
}
for (int t = 0; t < tbtFM.getTaxaCount(); t++) {
if (theTR[t] < 0) {
continue;
}
int tagCount =
tbtOut.getReadCountForTagTaxon(toTag, theTR[t]) + tbtFM.getReadCountForTagTaxon(i, t);
if (tagCount > 0) {
tbtOut.setReadCountForTagTaxon(toTag, theTR[t], tagCount);
count++;
}
}
if (count % 100000 == 0) {
System.out.printf("Tag:%d BitSet:%d %n", i, count);
}
}
}
tbtOut.getFileReadyForClosing();
}