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

[mothur.git] / secondarystructurecommand.cpp

diff --git a/secondarystructurecommand.cpp b/secondarystructurecommand.cpp
index cc53ee0f02741cbe0fc6358a3a08cd56e891cd09..fe80b7810e716264152835060f25d1f2e45c1fed 100644 (file)
--- a/secondarystructurecommand.cpp
+++ b/secondarystructurecommand.cpp
@@ -183,7 +183,7 @@ int AlignCheckCommand::execute(){
                
                int count = 0;
                while(!in.eof()){
-                       if (m->control_pressed) { in.close(); out.close(); remove(outfile.c_str()); return 0; }
+                       if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outfile); return 0; }
                        
                        Sequence seq(in);  m->gobble(in);
                        if (seq.getName() != "") {
@@ -220,7 +220,7 @@ int AlignCheckCommand::execute(){
                in.close();
                out.close();
                
-               if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+               if (m->control_pressed) {  m->mothurRemove(outfile); return 0; }
                
                sort(pound.begin(), pound.end());
                sort(dash.begin(), dash.end());
@@ -238,7 +238,7 @@ int AlignCheckCommand::execute(){
                int ptile97_5   = int(size * 0.975);
                int ptile100    = size - 1;
                
-               if (m->control_pressed) {  remove(outfile.c_str()); return 0; }
+               if (m->control_pressed) {  m->mothurRemove(outfile); return 0; }
                
                m->mothurOutEndLine();
                m->mothurOut("\t\tPound\tDash\tPlus\tEqual\tLoop\tTilde\tTotal"); m->mothurOutEndLine();