lengths[l] = seqNums.elementAt(l).length - 1;
}
- // todo ? remove '*' (unused?) from score matrix and
- // use getSize() here instead of getSize() - 1 ??
- final int symbolCount = blosum62.getSize() - 1; // 24;
+ final int symbolCount = blosum62.getSize();
int gapIndex = blosum62.getGapIndex();
for (j = startRes; j <= endRes; j++)