added make.group command

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 39f28d09e8c19f1ed4ab2d3a1e7a57d42c7e30f9..85883282ed841c4f22bba3dda6e39e83fe5287c7 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -413,8 +413,6 @@ int ClassifySeqsCommand::execute(){
                                //delete inFileName;
 
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPINewTax);   MPI_File_close(&outMPITempTax);  delete classify; return 0;  }
-
-                               if(namefile != "") {  MPIReadNamesFile(namefileNames[s]);  }
                                
                                if (pid == 0) { //you are the root process 
                                        
@@ -465,22 +463,7 @@ int ClassifySeqsCommand::execute(){
                                MPI_File_close(&outMPITempTax);
                                
 #else
-                       //read namefile
-                       if(namefile != "") {
-                               nameMap.clear(); //remove old names
-                               
-                               ifstream inNames;
-                               openInputFile(namefileNames[s], inNames);
-                               
-                               string firstCol, secondCol;
-                               while(!inNames.eof()) {
-                                       inNames >> firstCol >> secondCol; gobble(inNames);
-                                       nameMap[firstCol] = getNumNames(secondCol);  //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
-                               }
-                               inNames.close();
-                       }
-
-       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                        if(processors == 1){
                                ifstream inFASTA;
                                openInputFile(fastaFileNames[s], inFASTA);
@@ -545,6 +528,32 @@ int ClassifySeqsCommand::execute(){
 
                #ifdef USE_MPI  
                        if (pid == 0) {  //this part does not need to be paralellized
+                       
+                               if(namefile != "") { m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();  MPIReadNamesFile(namefileNames[s]);  m->mothurOut("  Done."); m->mothurOutEndLine(); }
+               #else
+                       //read namefile
+                       if(namefile != "") {
+                       
+                           m->mothurOut("Reading " + namefileNames[s] + "..."); cout.flush();
+                               
+                               nameMap.clear(); //remove old names
+                               
+                               ifstream inNames;
+                               openInputFile(namefileNames[s], inNames);
+                               
+                               string firstCol, secondCol;
+                               while(!inNames.eof()) {
+                                       inNames >> firstCol >> secondCol; gobble(inNames);
+                                       
+                                       vector<string> temp;
+                                       splitAtComma(secondCol, temp);
+                       
+                                       nameMap[firstCol] = temp;  
+                               }
+                               inNames.close();
+                               
+                               m->mothurOut("  Done."); m->mothurOutEndLine();
+                       }
                #endif
 
                        m->mothurOutEndLine();
@@ -557,7 +566,7 @@ int ClassifySeqsCommand::execute(){
                        PhyloSummary taxaSum(taxonomyFileName, group);
                        
                        if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str()); } delete classify; return 0; }
-                       
+               
                        if (namefile == "") {  taxaSum.summarize(tempTaxonomyFile);  }
                        else {
                                ifstream in;
@@ -565,6 +574,7 @@ int ClassifySeqsCommand::execute(){
                                
                                //read in users taxonomy file and add sequences to tree
                                string name, taxon;
+                               
                                while(!in.eof()){
                                        in >> name >> taxon; gobble(in);
                                        
@@ -573,9 +583,11 @@ int ClassifySeqsCommand::execute(){
                                        if (itNames == nameMap.end()) { 
                                                m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
                                        }else{
-                                               for (int i = 0; i < itNames->second; i++) { 
-                                                       taxaSum.addSeqToTree(name, taxon);  //add it as many times as there are identical seqs
+                                               for (int i = 0; i < itNames->second.size(); i++) { 
+                                                       taxaSum.addSeqToTree(itNames->second[i], taxon);  //add it as many times as there are identical seqs
                                                }
+                                               itNames->second.clear();
+                                               nameMap.erase(itNames->first);
                                        }
                                }
                                in.close();
@@ -886,7 +898,11 @@ int ClassifySeqsCommand::MPIReadNamesFile(string nameFilename){
                string firstCol, secondCol;
                while(!iss.eof()) {
                        iss >> firstCol >> secondCol; gobble(iss);
-                       nameMap[firstCol] = getNumNames(secondCol);  //ex. seq1 seq1,seq3,seq5 -> seq1 = 3.
+                       
+                       vector<string> temp;
+                       splitAtComma(secondCol, temp);
+                       
+                       nameMap[firstCol] = temp;  
                }
        
                MPI_File_close(&inMPI);