Example #1
0
 /**
  * Determine if the given loc overlaps any loc in the sorted set
  *
  * @param loc the location to test
  * @return
  */
 public boolean overlaps(final GenomeLoc loc) {
   for (final GenomeLoc e : mArray) {
     if (e.overlapsP(loc)) {
       return true;
     }
   }
   return false;
 }
Example #2
0
  public GenomeLocSortedSet subtractRegions(GenomeLocSortedSet toRemoveSet) {
    LinkedList<GenomeLoc> good = new LinkedList<GenomeLoc>();
    Stack<GenomeLoc> toProcess = new Stack<GenomeLoc>();
    Stack<GenomeLoc> toExclude = new Stack<GenomeLoc>();

    // initialize the stacks
    toProcess.addAll(mArray);
    Collections.reverse(toProcess);
    toExclude.addAll(toRemoveSet.mArray);
    Collections.reverse(toExclude);

    int i = 0;
    while (!toProcess.empty()) { // while there's still stuff to process
      if (toExclude.empty()) {
        good.addAll(toProcess); // no more excludes, all the processing stuff is good
        break;
      }

      GenomeLoc p = toProcess.peek();
      GenomeLoc e = toExclude.peek();

      if (p.overlapsP(e)) {
        toProcess.pop();
        for (GenomeLoc newP : p.subtract(e)) toProcess.push(newP);
      } else if (p.compareContigs(e) < 0) {
        good.add(toProcess.pop()); // p is now good
      } else if (p.compareContigs(e) > 0) {
        toExclude.pop(); // e can't effect anything
      } else if (p.getStop() < e.getStart()) {
        good.add(toProcess.pop()); // p stops before e starts, p is good
      } else if (e.getStop() < p.getStart()) {
        toExclude.pop(); // p starts after e stops, e is done
      } else {
        throw new ReviewedStingException("BUG: unexpected condition: p=" + p + ", e=" + e);
      }

      if (i++ % 10000 == 0) logger.debug("removeRegions operation: i = " + i);
    }

    return createSetFromList(genomeLocParser, good);
  }