- ifstream inFasta;
- openInputFile(fastafile, inFasta);
- length = 0;
- map<string, string>::iterator it;
-
- while (!inFasta.eof()) {
- Sequence temp(inFasta); //read seq
-
- if (temp.getName() != "") {
- if (namefile != "") {
- //make sure fasta and name files match
- it = names.find(temp.getName());
- if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
- }else { sizes[temp.getName()] = 1; }
-
- seqPNode tempNode(sizes[temp.getName()], temp);
- alignSeqs.push_back(tempNode);
- active[temp.getName()] = true;
- }
- gobble(inFasta);
- }
- inFasta.close();
-
- if (alignSeqs.size() != 0) { length = alignSeqs[0].seq.getAligned().length(); }
-
+// ifstream inFasta;
+// openInputFile(fastafile, inFasta);
+// length = 0;
+//// map<string, string>::iterator it;
+//
+// while (!inFasta.eof()) {
+// Sequence temp(inFasta); //read seq
+//
+// if (temp.getName() != "") {
+// if (namefile != "") {
+// //make sure fasta and name files match
+// it = names.find(temp.getName());
+// if (it == names.end()) { mothurOut(temp.getName() + " is not in your names file, please correct."); mothurOutEndLine(); exit(1); }
+// }else { sizes[temp.getName()] = 1; }
+//
+// seqPNode tempNode(sizes[temp.getName()], temp);
+// alignSeqs.push_back(tempNode);
+// active[temp.getName()] = true;
+// }
+// gobble(inFasta);
+// }
+// inFasta.close();
+//
+// if (alignSeqs.size() != 0) { length = alignSeqs[0].seq.getAligned().length(); }
+//