+ oldNameFile.close();
+
+ ifstream inFASTA;
+ openInputFile(inFastaFile, inFASTA);
+ string sequence;
+ while(!inFASTA.eof()){
+ Sequence currSeq(inFASTA);
+ name = currSeq.getName();
+
+ if (name != "") {
+ if(currSeq.getIsAligned()) { sequence = currSeq.getAligned(); }
+ else { sequence = currSeq.getUnaligned(); }
+
+ seqmap[name] = sequence;
+ map<string,group>::iterator it = data.find(sequence);
+ if (it == data.end()) { //it's unique.
+ data[sequence].groupname = name; //group name will be the name of the first duplicate sequence found.
+ // data[sequence].groupnumber = 1;
+ data[sequence].names = oldNameMap[name];
+ }else { // its a duplicate.
+ data[sequence].names += "," + oldNameMap[name];
+ // data[sequence].groupnumber++;
+ }
+ }
+ gobble(inFASTA);
+ }
+
+
+ inFASTA.close();