rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index d065b3a37c5ac41f9c6c3b59eb9ca3832f8697a9..7b1a04f3658bcb0a3e919fefe34a30dedcfaa882 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -244,7 +244,7 @@ int ClassifyOtuCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) { outputTypes.clear(); delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  }  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  }  return 0; }
        
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -252,7 +252,7 @@ int ClassifyOtuCommand::execute(){
                        
                                        m->mothurOut(list->getLabel() + "\t" + toString(list->size())); m->mothurOutEndLine();
                                        process(list);
-                                       if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
+                                       if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } delete input; delete list; return 0; }
                                                                                
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
@@ -267,7 +267,7 @@ int ClassifyOtuCommand::execute(){
                                        process(list);
                                
                                        
-                                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
+                                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } delete input; delete list; return 0; }
                                                                                
                                        processedLabels.insert(list->getLabel());
                                        userLabels.erase(list->getLabel());
@@ -303,12 +303,12 @@ int ClassifyOtuCommand::execute(){
                        process(list);
                        delete list;
                        
-                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } delete input; delete list; return 0; }
+                       if (m->control_pressed) { outputTypes.clear();  for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } delete input; delete list; return 0; }
                }
                
                delete input;  
                                
-               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   remove(outputNames[i].c_str());  } return 0; }
+               if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {   m->mothurRemove(outputNames[i]);  } return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -451,7 +451,7 @@ vector<string> ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* th
                phylo->assignHeirarchyIDs(0);
                
                TaxNode currentNode = phylo->get(0);
-               
+               int myLevel = 0;        
                //at each level
                while (currentNode.children.size() != 0) { //you still have more to explore
                
@@ -480,6 +480,7 @@ vector<string> ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* th
                                }else{
                                        conTax += bestChild.name + ";";
                                }
+                               myLevel++;
                        }else{ //if no, quit
                                break;
                        }
@@ -488,7 +489,12 @@ vector<string> ClassifyOtuCommand::findConsensusTaxonomy(int bin, ListVector* th
                        currentNode = bestChild;
                }
                
-                               
+               if (myLevel != phylo->getMaxLevel()) {
+                       while (myLevel != phylo->getMaxLevel()) {
+                               conTax += "unclassified;";
+                               myLevel++;
+                       }
+               }               
                if (conTax == "") {  conTax = "no_consensus;";  }
                
                delete phylo;   
@@ -570,6 +576,35 @@ int ClassifyOtuCommand::process(ListVector* processList) {
                exit(1);
        }
 }
+/**************************************************************************************************/
+string ClassifyOtuCommand::addUnclassifieds(string tax, int maxlevel) {
+       try{
+               string newTax, taxon;
+               int level = 0;
+               
+               //keep what you have counting the levels
+               while (tax.find_first_of(';') != -1) {
+                       //get taxon
+                       taxon = tax.substr(0,tax.find_first_of(';'))+';';
+                       tax = tax.substr(tax.find_first_of(';')+1, tax.length());
+                       newTax += taxon;
+                       level++;
+               }
+               
+               //add "unclassified" until you reach maxLevel
+               while (level < maxlevel) {
+                       newTax += "unclassified;";
+                       level++;
+               }
+               
+               return newTax;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "ClassifyOtuCommand", "addUnclassifieds");
+               exit(1);
+       }
+}
+
 /**************************************************************************************************/
 void ClassifyOtuCommand::removeConfidences(string& tax) {
        try {