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

[mothur.git] / getrelabundcommand.cpp

diff --git a/getrelabundcommand.cpp b/getrelabundcommand.cpp
index 693e36d000891339b843115fa11bd338dbc7a103..26d795808e826e9f13279bc8dcbbcfe9fc7ba14a 100644 (file)
--- a/getrelabundcommand.cpp
+++ b/getrelabundcommand.cpp
@@ -170,7 +170,7 @@ int GetRelAbundCommand::execute(){
                //as long as you are not at the end of the file or done wih the lines you want
                while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
-                       if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->Groups.clear(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
        
                        if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){                  
 
@@ -202,13 +202,13 @@ int GetRelAbundCommand::execute(){
                        //prevent memory leak
                        for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
                        
-                       if (m->control_pressed) {  outputTypes.clear();  m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) {  outputTypes.clear();  m->Groups.clear(); delete input;  out.close(); m->mothurRemove(outputFileName); return 0; }
 
                        //get next line to process
                        lookup = input->getSharedRAbundVectors();                               
                }
                
-               if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input;  out.close(); remove(outputFileName.c_str());  return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->Groups.clear(); delete input;  out.close(); m->mothurRemove(outputFileName);  return 0; }
 
                //output error messages about any remaining user labels
                set<string>::iterator it;
@@ -240,7 +240,7 @@ int GetRelAbundCommand::execute(){
                delete input; 
                out.close();
                
-               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
+               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();