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

[mothur.git] / formatphylip.cpp

diff --git a/formatphylip.cpp b/formatphylip.cpp
index 0390a806f97c5397d046c1384c1b4356280e78d9..de49daa32a31c6aa2a4bfbac97257ca993656a03 100644 (file)
--- a/formatphylip.cpp
+++ b/formatphylip.cpp
@@ -75,7 +75,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                        
                                        for(int j=0;j<i;j++){
                                        
-                                               if (m->control_pressed) { outTemp.close(); remove(tempFile.c_str()); fileHandle.close();  delete reading; return 0; }
+                                               if (m->control_pressed) { outTemp.close(); m->mothurRemove(tempFile); fileHandle.close();  delete reading; return 0; }
                                                                                        
                                                fileHandle >> distance;
                                                
@@ -104,7 +104,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                        system(command.c_str());
                                #endif
                                
-                               if (m->control_pressed) { remove(tempFile.c_str()); remove(outfile.c_str());  delete reading; return 0; }
+                               if (m->control_pressed) { m->mothurRemove(tempFile); m->mothurRemove(outfile);  delete reading; return 0; }
 
                                //output to new file distance for each row and save positions in file where new row begins
                                ifstream in;
@@ -128,7 +128,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                for(int k = 0; k < firstString.length(); k++)  {   in.putback(firstString[k]);  }
                                
                                while(!in.eof()) {
-                                       if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); remove(distFile.c_str()); remove(outfile.c_str());  delete reading; return 0; }
+                                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); m->mothurRemove(distFile); m->mothurRemove(outfile);  delete reading; return 0; }
 
                                        in >> first >> second >> dist; m->gobble(in);
                                        
@@ -170,10 +170,10 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                in.close();
                                out.close();
                                
-                               remove(tempFile.c_str());
-                               remove(outfile.c_str());
+                               m->mothurRemove(tempFile);
+                               m->mothurRemove(outfile);
                                
-                               if (m->control_pressed) {  remove(distFile.c_str());   delete reading; return 0; }
+                               if (m->control_pressed) {  m->mothurRemove(distFile);   delete reading; return 0; }
 
                        }
                        else{ //square matrix convert directly to formatted row file
@@ -188,7 +188,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                        list->set(i, name);
                                        
                                        for(int j=0;j<nseqs;j++){
-                                               if (m->control_pressed) {  fileHandle.close(); out.close(); remove(distFile.c_str());   delete reading; return 0; }
+                                               if (m->control_pressed) {  fileHandle.close(); out.close(); m->mothurRemove(distFile);   delete reading; return 0; }
                                                
                                                fileHandle >> distance;
                                        
@@ -222,7 +222,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                        fileHandle.close();
                        out.close();
                        
-                       if (m->control_pressed) { remove(distFile.c_str());  return 0; }
+                       if (m->control_pressed) { m->mothurRemove(distFile);  return 0; }
                        
                        list->setLabel("0");