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

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 3e31691e6c8340d3ff7f02c0f316085f246f1b6b..9ed887a72ff7354c9396ba2d2c63f3b4a460afd3 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -394,7 +394,7 @@ int GetOTURepCommand::execute(){
                        //openfile for getMap to use
                        m->openInputFile(distFile, inRow);
                        
-                       if (m->control_pressed) { inRow.close(); remove(distFile.c_str()); return 0; }
+                       if (m->control_pressed) { inRow.close(); m->mothurRemove(distFile); return 0; }
                }
                
                
@@ -417,7 +417,7 @@ int GetOTURepCommand::execute(){
                
                                
                if (m->control_pressed) { 
-                       if (large) {  inRow.close(); remove(distFile.c_str());  }
+                       if (large) {  inRow.close(); m->mothurRemove(distFile);  }
                        return 0; 
                }
                
@@ -446,7 +446,7 @@ int GetOTURepCommand::execute(){
                set<string> userLabels = labels;
                
                if (m->control_pressed) { 
-                       if (large) {  inRow.close(); remove(distFile.c_str());  }
+                       if (large) {  inRow.close(); m->mothurRemove(distFile);  }
                        delete input; delete list; return 0; 
                }
                
@@ -460,8 +460,8 @@ int GetOTURepCommand::execute(){
                                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
                                        
                                        if (m->control_pressed) { 
-                                               if (large) {  inRow.close(); remove(distFile.c_str());  }
-                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                                               if (large) {  inRow.close(); m->mothurRemove(distFile);  }
+                                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                                delete input; delete list; return 0; 
                                        }
                                        
@@ -479,8 +479,8 @@ int GetOTURepCommand::execute(){
                                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
                                        
                                        if (m->control_pressed) { 
-                                               if (large) {  inRow.close(); remove(distFile.c_str());  }
-                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                                               if (large) {  inRow.close(); m->mothurRemove(distFile);  }
+                                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                                delete input; delete list; return 0; 
                                        }
                                        
@@ -519,8 +519,8 @@ int GetOTURepCommand::execute(){
                        if (error == 1) { return 0; } //there is an error in hte input files, abort command
                        
                        if (m->control_pressed) { 
-                                       if (large) {  inRow.close(); remove(distFile.c_str());  }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  } outputTypes.clear();
+                                       if (large) {  inRow.close(); m->mothurRemove(distFile);  }
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);  } outputTypes.clear();
                                        delete input; delete list; return 0; 
                        }
                }
@@ -528,7 +528,7 @@ int GetOTURepCommand::execute(){
                //close and remove formatted matrix file
                if (large) {
                        inRow.close();
-                       remove(distFile.c_str());
+                       m->mothurRemove(distFile);
                }
                
                delete input;  
@@ -954,7 +954,7 @@ int GetOTURepCommand::processNames(string filename, string label) {
                out.close();
                out2.close();
                
-               remove(filename.c_str());
+               m->mothurRemove(filename);
                rename(tempNameFile.c_str(), filename.c_str());
                
                return 0;