- errorOut(e, "PreClusterCommand", "execute");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int PreClusterCommand::readFASTA(){
- try {
-// 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(); }
-//
- return alignSeqs.size();
- }
- catch(exception& e) {
- errorOut(e, "PreClusterCommand", "readFASTA");