pat's ../ bug fix

[mothur.git] / preclustercommand.cpp

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index d97ffc7934484c3b7ba29a3674418c672b77133a..fa5329b1e4094b4c87d60b5b4dfbd211f1bc1aeb 100644 (file)
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -179,43 +179,11 @@ int 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");
-               exit(1);
-       }
-}
+
 /**************************************************************************************************/
-//this seems to require the names and fasta file to be in the same order???
+
+//this requires the names and fasta file to be in the same order
+
 int PreClusterCommand::readFASTA(){
        try {
                //ifstream inNames;
@@ -316,7 +284,9 @@ void PreClusterCommand::printData(string newfasta, string newname){
                exit(1);
        }
 }
+
 /**************************************************************************************************/
+
 void PreClusterCommand::readNameFile(){
        try {
                ifstream in;