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

[mothur.git] / sharedcommand.cpp

diff --git a/sharedcommand.cpp b/sharedcommand.cpp
index 38bc480836ba114e3ed55d0c1aa65f4e33d4218a..040fad846245c4c275a016391cf179eb64b763e1 100644 (file)
--- a/sharedcommand.cpp
+++ b/sharedcommand.cpp
@@ -219,7 +219,7 @@ int SharedCommand::execute(){
                
                //clears file before we start to write to it below
                for (int i=0; i<Groups.size(); i++) {
-                       remove((fileroot + Groups[i] + ".rabund").c_str());
+                       m->mothurRemove((fileroot + Groups[i] + ".rabund"));
                        outputNames.push_back((fileroot + Groups[i] + ".rabund"));
                        outputTypes["rabund"].push_back((fileroot + Groups[i] + ".rabund"));
                }
@@ -239,8 +239,8 @@ int SharedCommand::execute(){
                if (m->control_pressed) { 
                        delete input; delete SharedList; delete groupMap; 
                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
-                       out.close(); remove(filename.c_str()); 
-                       for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
+                       out.close(); m->mothurRemove(filename); 
+                       for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
                        return 0; 
                }
                                
@@ -248,7 +248,7 @@ int SharedCommand::execute(){
                        m->mothurOut("Your group file contains " + toString(groupMap->getNumSeqs()) + " sequences and list file contains " + toString(SharedList->getNumSeqs()) + " sequences. Please correct."); m->mothurOutEndLine(); 
                        
                        out.close();
-                       remove(filename.c_str()); //remove blank shared file you made
+                       m->mothurRemove(filename); //remove blank shared file you made
                        
                        createMisMatchFile();
                        
@@ -296,8 +296,8 @@ int SharedCommand::execute(){
                        if (m->control_pressed) { 
                                delete input; delete SharedList; delete groupMap;
                                for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
-                               out.close(); remove(filename.c_str()); 
-                               for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
+                               out.close(); m->mothurRemove(filename); 
+                               for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
                                return 0; 
                        }
                
@@ -314,8 +314,8 @@ int SharedCommand::execute(){
                                                delete input; delete SharedList; delete groupMap; 
                                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                                                for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
-                                               out.close(); remove(filename.c_str()); 
-                                               for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
+                                               out.close(); m->mothurRemove(filename); 
+                                               for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
                                                return 0; 
                                        }
                                        
@@ -344,8 +344,8 @@ int SharedCommand::execute(){
                                                delete input; delete SharedList; delete groupMap; 
                                                for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
                                                for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;  }
-                                               out.close(); remove(filename.c_str()); 
-                                               for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
+                                               out.close(); m->mothurRemove(filename); 
+                                               for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
                                                return 0; 
                                        }
                                        
@@ -390,8 +390,8 @@ int SharedCommand::execute(){
                        if (m->control_pressed) { 
                                delete input;  delete groupMap;
                                        for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {  delete it3->second;   }
-                                       out.close(); remove(filename.c_str()); 
-                                       for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
+                                       out.close(); m->mothurRemove(filename); 
+                                       for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
                                        return 0; 
                        }
                        
@@ -410,8 +410,8 @@ int SharedCommand::execute(){
                delete input; delete groupMap;
                
                if (m->control_pressed) { 
-                               remove(filename.c_str()); 
-                               for (int i=0; i<Groups.size(); i++) {  remove((fileroot + Groups[i] + ".rabund").c_str());              }
+                               m->mothurRemove(filename); 
+                               for (int i=0; i<Groups.size(); i++) {  m->mothurRemove((fileroot + Groups[i] + ".rabund"));             }
                                return 0; 
                }
                
@@ -564,7 +564,7 @@ int SharedCommand::createMisMatchFile() {
                        
                        //go through list and if group returns "not found" output it
                        for (int i = 0; i < SharedList->getNumBins(); i++) {
-                               if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; } 
+                               if (m->control_pressed) { outMisMatch.close(); m->mothurRemove(outputMisMatchName); return 0; } 
                        
                                string names = SharedList->get(i); 
                                
@@ -635,7 +635,7 @@ int SharedCommand::createMisMatchFile() {
                        
                        //loop through names in seqNames and if they aren't in namesIn list output them
                        for (int i = 0; i < seqNames.size(); i++) {
-                               if (m->control_pressed) { outMisMatch.close(); remove(outputMisMatchName.c_str()); return 0; } 
+                               if (m->control_pressed) { outMisMatch.close(); m->mothurRemove(outputMisMatchName); return 0; } 
                                
                                itMatch = namesInList.find(seqNames[i]);