- alseqs_string[i]=alseqs[i].getRefSeq().
- getSequence().substring(alseqs[i].start,alseqs[i].end);
- gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i], gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})
+ alseqs_string[i] = alseqs[i].getRefSeq().
+ getSequenceAsString(alseqs[i].start, alseqs[i].end);
+ gs_regions[i] = alseqs[i].getSequenceAndDeletions(alseqs_string[i],
+ gapCharacter); // gapped sequence, {start, start col, end. endcol}, hidden regions {{start, end, col}})