+ string temp;
+
+ while(!in.eof()){
+ Sequence currSeq(in);
+ name = currSeq.getName();
+
+ 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 = name;
+ }else { // its a duplicate.
+ data[sequence].names += "," + name;
+// data[sequence].groupnumber++;
+ }
+
+ gobble(in);
+ }
+ in.close();
+ }
+ catch(exception& e) {
+ errorOut(e, "FastaMap", "readFastaFile");
+ exit(1);
+ }
+}
+
+/*******************************************************************************/
+
+void FastaMap::readFastaFile(string inFastaFile, string oldNameFileName){ //prints data