+ // find the end of this run of set bits
+ int nextp = grp.nextClearBit(p)-1;
+ int[] pos = ((MappableContactMatrixI)matrix).getMappedPositionsFor(rseq, p,nextp);
+ p=nextp;
+
+ if (pos!=null)
+ {
+ for (int pos_p = pos[0];pos_p<=pos[1];pos_p++)
+ {
+ int col = rseq.findIndex(pos_p)-1;
+ if (col>=0 && (!av.hasHiddenColumns() || hc.isVisible(col)))
+ {
+ cs.addElement(col);
+ }
+ }
+ }
+ } else {
+ int offp = (rseq != null)
+ ? rseq.findIndex(rseq.getStart() - 1 + p)
+ : p;
+
+ if (!av.hasHiddenColumns() || hc.isVisible(offp))
+ {
+ cs.addElement(offp);
+ }