- System.err.println("Warn - no match for redundant hit "
- + repseq + "/" + alisqfrom + "-" + alisqto);
- }
- if (ofound > 1)
- {
- System.err.println("Warn - multiple matches for redundant hit "
- + repseq + "/" + alisqfrom + "-" + alisqto);
+ int ofound = 0;
+ for (SequenceI oth : other)
+ {
+ if (oth.getStart() == alisqfrom && oth.getEnd() == alisqto)
+ {
+ ofound++;
+ repgroup.addSequence(oth, false);
+ }
+ }
+ if (ofound == 0)
+ {
+ System.err.println("Warn - no match for redundant hit "
+ + repseq + "/" + alisqfrom + "-" + alisqto);
+ }
+ if (ofound > 1)
+ {
+ System.err
+ .println("Warn - multiple matches for redundant hit "
+ + repseq + "/" + alisqfrom + "-" + alisqto);
+ }