+
+ while (!fastaString.eof()) { char c = fastaString.get(); if (c == 10 || c == 13){ break; } } // get rest of line if there's any crap there
+
+ sequence = getSequenceString(fastaString);
+ setAligned(sequence);
+ //setUnaligned removes any gap characters for us
+ setUnaligned(sequence);
+ }else{ m->mothurOut("Error in reading your fastafile, at position " + toString(fastaString.tellg()) + ". Blank name."); m->mothurOutEndLine(); }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Sequence", "Sequence");
+ exit(1);
+ }
+}
+//********************************************************************************************************************
+//this function will jump over commented out sequences, but if the last sequence in a file is commented out it makes a blank seq
+Sequence::Sequence(istringstream& fastaString, string JustUnaligned){
+ try {
+ m = MothurOut::getInstance();
+
+ initialize();
+ fastaString >> name;
+
+ if (name.length() != 0) {