Example #1
0
 // 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();
 }