{
String[] seqs=new String[sequences.length];
for (int n=0; n<sequences.length; n++) {
- seqs[n] = sequences[n].getSequenceString(c);
+ String fullseq = sequences[n].getSequenceString(c);
+ if (contigs != null)
+ {
+ seqs[n] = "";
+ int p = 0;
+ for (int h = 0; h < contigs.length; h += 3)
+ {
+ seqs[n] += fullseq.substring(p, contigs[h + 1]);
+ p = contigs[h + 1] + contigs[h + 2];
+ }
+ seqs[n] += fullseq.substring(p);
+ } else
+ seqs[n] = fullseq;
}
return seqs;
}