+void Sequence::padToPos(int start){
+
+ for(int j = startPos-1; j < start-1; j++) {
+ aligned[j] = '.';
+ }
+ startPos = start;
+
+}
+//********************************************************************************************************************
+
+int Sequence::filterToPos(int start){
+
+ if (start > aligned.length()) { start = aligned.length(); m->mothurOut("[ERROR]: start to large.\n"); }
+
+ for(int j = 0; j < start-1; j++) {
+ aligned[j] = '.';
+ }
+
+ //things like ......----------AT become ................AT
+ for(int j = start-1; j < aligned.length(); j++) {
+ if (isalpha(aligned[j])) { break; }
+ else { aligned[j] = '.'; }
+ }
+ setUnaligned(aligned);
+
+ return 0;
+
+}
+//********************************************************************************************************************
+
+int Sequence::filterFromPos(int end){
+
+ if (end > aligned.length()) { end = aligned.length(); m->mothurOut("[ERROR]: end to large.\n"); }
+
+ for(int j = end; j < aligned.length(); j++) {
+ aligned[j] = '.';
+ }
+
+ for(int j = aligned.length()-1; j < 0; j--) {
+ if (isalpha(aligned[j])) { break; }
+ else { aligned[j] = '.'; }
+ }
+
+ setUnaligned(aligned);
+
+ return 0;
+}
+//********************************************************************************************************************
+