bug fixes

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index 0e23461c39803cd49cac67023d6c99255284f851..b724a68fb2ec34b63e740ae5bcaa3d9981af8ed8 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -245,7 +245,7 @@ int ClassifyOtuCommand::readNamesFile() {
                
                string name, names;
        
-               while(inNames){
+               while(!inNames.eof()){
                        inNames >> name;                        //read from first column  A
                        inNames >> names;               //read from second column  A,B,C,D
                        m->gobble(inNames);
@@ -313,9 +313,10 @@ string ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* thisList,
                
                size = 0;
                for (int i = 0; i < names.size(); i++) {
-               
+       
                        //if namesfile include the names
                        if (namefile != "") {
+       
                                //is this sequence in the name file - namemap maps seqName -> repSeqName
                                it2 = nameMap.find(names[i]);
                                
@@ -327,7 +328,8 @@ string ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* thisList,
                                        it = taxMap.find(it2->second);
                        
                                        if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
-                                               if (names[i] != it->second) { m->mothurOut(names[i] + " is represented by " +  it2->second + " and is not in your taxonomy file.  I will not include it in the consensus."); m->mothurOutEndLine(); }
+                                       
+                                               if (names[i] != it2->second) { m->mothurOut(names[i] + " is represented by " +  it2->second + " and is not in your taxonomy file.  I will not include it in the consensus."); m->mothurOutEndLine(); }
                                                else {  m->mothurOut(names[i] + " is not in your taxonomy file.  I will not include it in the consensus."); m->mothurOutEndLine(); }
                                        }else{
                                
@@ -426,8 +428,9 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                
                //for each bin in the list vector
                for (int i = 0; i < processList->getNumBins(); i++) {
+       
                        conTax  = findConsensusTaxonomy(i, processList, size);
-                       
+               
                        if (m->control_pressed) { out.close();  return 0; }
                        
                        //output to new names file