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

[mothur.git] / removegroupscommand.cpp

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 9b537281b4abef7ecb9f270e1438993fca198e22..c9908fbc715f33eb33f75ff2005d51c9347678ff 100644 (file)
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -245,7 +245,7 @@ int RemoveGroupsCommand::execute(){
                if (listfile != "")                     {               readList();             }
                if (taxfile != "")                      {               readTax();              }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } return 0; }
                
                m->mothurOut("Removed " + toString(names.size()) + " sequences. From the groups: "); m->mothurOutEndLine();
                for (int i = 0; i < Groups.size(); i++) {       m->mothurOut(Groups[i]); m->mothurOut("\t" + toString(groupMap->getNumSeqs(Groups[i]))); m->mothurOutEndLine(); }
@@ -311,7 +311,7 @@ int RemoveGroupsCommand::readFasta(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        Sequence currSeq(in);
                        name = currSeq.getName();
@@ -366,7 +366,7 @@ int RemoveGroupsCommand::readList(){
                        
                        //for each bin
                        for (int i = 0; i < list.getNumBins(); i++) {
-                               if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                               if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                                
                                //parse out names that are in accnos file
                                string binnames = list.get(i);
@@ -429,7 +429,7 @@ int RemoveGroupsCommand::readName(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        in >> firstCol;         m->gobble(in);          
                        in >> secondCol;                        
@@ -505,7 +505,7 @@ int RemoveGroupsCommand::readGroup(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        in >> name;                             //read from first column
                        in >> group;                    //read from second column
@@ -547,7 +547,7 @@ int RemoveGroupsCommand::readTax(){
                bool wroteSomething = false;
                
                while(!in.eof()){
-                       if (m->control_pressed) { in.close();  out.close();  remove(outputFileName.c_str());  return 0; }
+                       if (m->control_pressed) { in.close();  out.close();  m->mothurRemove(outputFileName);  return 0; }
                        
                        in >> name;                             //read from first column
                        in >> tax;                      //read from second column