fix to summary.tax for 1.28.0

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index 57afd85943e956b6bf4364d0b7c0b8bf27657cc3..b7c4f1790b152371a6e302f3d56ae79fc60badf1 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -49,6 +49,26 @@ string GetListCountCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string GetListCountCommand::getOutputFileNameTag(string type, string inputName=""){    
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "otu") {  outputFileName =  "otu"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "GetListCountCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
+//**********************************************************************************************************************
 GetListCountCommand::GetListCountCommand(){    
        try {
                abort = true; calledHelp = true; 
@@ -149,7 +169,7 @@ int GetListCountCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+               if (m->control_pressed) { 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))) {
                        
@@ -157,7 +177,7 @@ int GetListCountCommand::execute(){
                        
                                process(list);
                                
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -171,7 +191,7 @@ int GetListCountCommand::execute(){
                                
                                process(list);
                                
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
 
                                                                                                        
                                processedLabels.insert(list->getLabel());
@@ -208,7 +228,7 @@ int GetListCountCommand::execute(){
                                
                        process(list);  
                        
-                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                        
                        delete list;  
                }
@@ -234,7 +254,7 @@ void GetListCountCommand::process(ListVector* list) {
        try {
                string binnames;
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + ".otu";
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + list->getLabel() + "." +getOutputFileNameTag("otu");
                m->openOutputFile(outputFileName, out);
                outputNames.push_back(outputFileName); outputTypes["otu"].push_back(outputFileName);