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

[mothur.git] / readcluster.cpp

diff --git a/readcluster.cpp b/readcluster.cpp
index d8227101b2c339b3904e95144d11f5cccb068dd3..b6cb71de5fdbb888f4a7c1614987f74cd0bf8b1a 100644 (file)
--- a/readcluster.cpp
+++ b/readcluster.cpp
@@ -109,7 +109,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
                                        
                                        for(int j=0;j<i;j++){
                                        
-                                               if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
                                                
                                                in >> distance;
                                                
@@ -126,7 +126,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
                                        
                                        for(int j=0;j<i;j++){
                                                
-                                               if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
                                                
                                                in >> distance;
                                                
@@ -148,7 +148,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
                                if(nameMap == NULL){
                                        list->set(i, name);
                                        for(int j=0;j<nseqs;j++){
-                                               if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
                                                
                                                in >> distance;
                                        
@@ -163,7 +163,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
                                        if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
                                        
                                        for(int j=0;j<nseqs;j++){
-                                               if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); return 0; }
+                                               if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); return 0; }
                                                
                                                in >> distance;
                         
@@ -201,7 +201,7 @@ int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
                float dist;
                
                while (in2) {
-                       if (m->control_pressed) { in2.close(); out2.close(); remove(tempFile.c_str()); remove(outputFile.c_str()); return 0; }
+                       if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(tempFile); m->mothurRemove(outputFile); return 0; }
                        
                        in2 >> first >> second >> dist;
                        out2 << rowToName[first] << '\t' << rowToName[second] << '\t' << dist << endl;
@@ -210,10 +210,10 @@ int ReadCluster::convertPhylip2Column(NameAssignment*& nameMap){
                in2.close();
                out2.close();
                
-               remove(tempFile.c_str());
+               m->mothurRemove(tempFile);
                distFile = outputFile;
        
-               if (m->control_pressed) {  remove(outputFile.c_str());  }
+               if (m->control_pressed) {  m->mothurRemove(outputFile);  }
 
                return 0;
        }