- int[] viscontigs = alview.getVisibleContigs();
- int spos = 0;
- int i = 0;
- if (viscontigs != null)
- {
- // Construct the delMap - mapping from the positions within the input to
- // Jnet to the contigs in the original sequence
-
- delMap = new int[seq.getEnd() - seq.getStart() + 1];
- int gapMap[] = seq.gapMap();
- for (int contig = 0; contig < viscontigs.length; contig += 2)
- {
-
- while (spos < gapMap.length && gapMap[spos] < viscontigs[contig])
- {
- spos++;
- }
- while (spos < gapMap.length
- && gapMap[spos] <= viscontigs[contig + 1])
- {
- delMap[i++] = spos++;
- }
- }
- int tmap[] = new int[i];
- System.arraycopy(delMap, 0, tmap, 0, i);
- delMap = tmap;
- }