some bug fixes

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index aac16371f1251fc4c7b78639427f95896aa4c223..00f04b08d6a6d42437faced7e76c736e6075d5cb 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -250,7 +250,11 @@ int ClassifyOtuCommand::readNamesFile() {
                        inNames >> names;               //read from second column  A,B,C,D
                        gobble(inNames);
                        
-                       nameMap[name] = names;
+                       //parse names into vector
+                       vector<string> theseNames;
+                       splitAtComma(names, theseNames);
+
+                       for (int i = 0; i < theseNames.size(); i++) {  nameMap[theseNames[i]] = name;  }
                        
                        if (m->control_pressed) { inNames.close(); nameMap.clear(); return 0; }
                }
@@ -309,41 +313,46 @@ string ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* thisList,
                
                size = 0;
                for (int i = 0; i < names.size(); i++) {
-                       
-                       if (m->control_pressed) { delete phylo; return conTax; }
-                       
-                       //is this sequence in the taxonomy file
-                       it = taxMap.find(names[i]);
-                       
-                       if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
-                               m->mothurOut(names[i] + " is not in your taxonomy file.  I will not include it in the consensus."); m->mothurOutEndLine();
-                       }else{
+               
+                       //if namesfile include the names
+                       if (namefile != "") {
+                               //is this sequence in the name file - namemap maps seqName -> repSeqName
+                               it2 = nameMap.find(names[i]);
                                
-                               //if namesfile include the names
-                               if (namefile != "") {
-                                       //is this sequence in the name file
-                                       it2 = nameMap.find(names[i]);
+                               if (it2 == nameMap.end()) { //this name is not in name file, skip it
+                                       m->mothurOut(names[i] + " is not in your name file.  I will not include it in the consensus."); m->mothurOutEndLine();
+                               }else{
                                        
-                                       if (it2 == nameMap.end()) { //this name is not in name file, skip it
-                                               m->mothurOut(names[i] + " is not in your name file.  I will not include it in the consensus."); m->mothurOutEndLine();
+                                       //is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
+                                       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(); }
+                                               else {  m->mothurOut(names[i] + " is not in your taxonomy file.  I will not include it in the consensus."); m->mothurOutEndLine(); }
                                        }else{
-                                               
-                                               vector<string> nameFileNames;
-                                               splitAtComma(it2->second, nameFileNames);
-                                               
-                                               for (int j = 0; j < nameFileNames.size(); j++) {
-                                                       //add seq to tree
-                                                       phylo->addSeqToTree(nameFileNames[j], it->second);
-                                                       size++;
-                                               }
+                               
+                                               //add seq to tree
+                                               phylo->addSeqToTree(names[i], it->second);
+                                               size++;
                                        }
-                                       
+                               }
+                               
+                       }else{
+                               //is this sequence in the taxonomy file - look for repSeqName since we are assuming the taxonomy file is unique
+                               it = taxMap.find(names[i]);
+               
+                               if (it == taxMap.end()) { //this name is not in taxonomy file, skip it
+                                       m->mothurOut(names[i] + " is not in your taxonomy file.  I will not include it in the consensus."); m->mothurOutEndLine();
                                }else{
                                        //add seq to tree
                                        phylo->addSeqToTree(names[i], it->second);
                                        size++;
                                }
                        }
+
+                       
+                       if (m->control_pressed) { delete phylo; return conTax; }
+                       
                }
                
                //build tree