- //if this spot is not a gap
- if (filterString[j] == '1') {
- newAligned += seqAligned[j];
- baseSpots[i][count] = baseCount;
- count++;
- }
+ //if this spot is not a gap
+ if (filterString[j] == '1') {
+ newAligned += seqAligned[j];
+ baseSpots[0][count] = baseCount;
+ count++;
+ }
+ }
+
+ q.setAligned(newAligned);
+
+ seqAligned = pA.getAligned();
+ newAligned = "";
+
+ baseCount = 0;
+ count = 0;
+ for (int j = 0; j < seqAligned.length(); j++) {
+ //are you a base
+ if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N')) { baseCount++; }
+
+ //if this spot is not a gap
+ if (filterString[j] == '1') {
+ newAligned += seqAligned[j];
+ baseSpots[1][count] = baseCount;
+ count++;