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

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index 9c89f7f82f1f93cbaadfa1277d2b1002a7fa3f0b..5a33253ff1ec2b67a9e995b940f09349241494f5 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -184,14 +184,14 @@ int GetRAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  outputTypes.clear();  out.close(); remove(filename.c_str()); delete rabund; delete input; return 0; }
+               if (m->control_pressed) {  outputTypes.clear();  out.close(); m->mothurRemove(filename); delete rabund; delete input; return 0; }
                
                while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
                        if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
                                        
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
@@ -208,7 +208,7 @@ int GetRAbundCommand::execute(){
                                        
                                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0;  }
+                                       if (m->control_pressed) {   outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0;  }
                                        
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
@@ -246,7 +246,7 @@ int GetRAbundCommand::execute(){
                        
                        m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
                                        
-                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; delete rabund;  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; delete rabund;  return 0; }
                        
                        if(sorted)      {   rabund->print(out);                         }
                        else            {       rabund->nonSortedPrint(out);    }