changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / consensusseqscommand.cpp

diff --git a/consensusseqscommand.cpp b/consensusseqscommand.cpp
index 4f8c53bc9b8cd70fab82a13cd8507a8e5719a07a..55ec8023270cd17d38b830f519ad9f62518e635e 100644 (file)
--- a/consensusseqscommand.cpp
+++ b/consensusseqscommand.cpp
@@ -142,7 +142,7 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                        }else { m->setFastaFile(fastafile); }   
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
                        else { m->setNameFile(namefile); }
                        
@@ -163,7 +163,11 @@ ConsensusSeqsCommand::ConsensusSeqsCommand(string option)  {
                        
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(fastafile);      }
-
+                       
+                       if (namefile == ""){
+                               vector<string> files; files.push_back(fastafile); 
+                               parser.getNameFile(files);
+                       }
                }
        }
        catch(exception& e) {
@@ -649,38 +653,29 @@ int ConsensusSeqsCommand::readFasta(){
 
 int ConsensusSeqsCommand::readNames(){
         try{
-                
-                ifstream in;
-                m->openInputFile(namefile, in);
-                
-                string thisname, repnames;
-                map<string, string>::iterator it;
-                
-                bool error = false;
-                
-                while(!in.eof()){
-                        
-                        if (m->control_pressed) { break; }
-                        
-                        in >> thisname;                m->gobble(in);          //read from first column
-                        in >> repnames;                        //read from second column
-                        
-                        it = nameMap.find(thisname);
+         map<string, string> temp;
+         map<string, string>::iterator it;
+         bool error = false;
+         
+         m->readNames(namefile, temp); //use central buffered read
+         
+         for (map<string, string>::iterator itTemp = temp.begin(); itTemp != temp.end(); itTemp++) {
+             string thisname, repnames;
+             thisname = itTemp->first;
+             repnames = itTemp->second;
+             
+             it = nameMap.find(thisname);
                         if (it != nameMap.end()) { //then this sequence was in the fastafile
-                                
+                                nameFileMap[thisname] = repnames;      //for later when outputting the new namesFile if the list file is unique
+                 
                                 vector<string> splitRepNames;
                                 m->splitAtComma(repnames, splitRepNames);
                                 
-                                nameFileMap[thisname] = repnames;      //for later when outputting the new namesFile if the list file is unique
                                 for (int i = 0; i < splitRepNames.size(); i++) { nameMap[splitRepNames[i]] = thisname; }
                                 
                         }else{ m->mothurOut("[ERROR]: " + thisname + " is not in the fasta file, please correct."); m->mothurOutEndLine(); error = true; }
-                        
-                        m->gobble(in);
-                }
-                
-                in.close();
-                
+         }
+         
                 if (error) { m->control_pressed = true; }
  
                 return 0;