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

[mothur.git] / parsimonycommand.cpp

diff --git a/parsimonycommand.cpp b/parsimonycommand.cpp
index 6e69cad4f8dbde50541a8daad71dbcce712b8953..ff1209287b4e17b2fcc58678703123aae2cadbc1 100644 (file)
--- a/parsimonycommand.cpp
+++ b/parsimonycommand.cpp
@@ -241,7 +241,7 @@ int ParsimonyCommand::execute() {
                                        
                                        if (m->control_pressed) { 
                                                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
-                                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                                m->Groups.clear();
                                                return 0;
                                        }
@@ -296,7 +296,7 @@ int ParsimonyCommand::execute() {
                        delete reading; delete pars; delete output;
                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                        if (randomtree == "") {  outSum.close();  }
-                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                        m->Groups.clear();
                        return 0;
                }
@@ -321,7 +321,7 @@ int ParsimonyCommand::execute() {
                                        delete reading; delete pars; delete output;
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                        if (randomtree == "") {  outSum.close();  }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                        m->Groups.clear();
                                        return 0;
                                }
@@ -359,7 +359,7 @@ int ParsimonyCommand::execute() {
                                if (m->control_pressed) { 
                                        delete reading; delete pars; delete output; delete randT;
                                        if (randomtree == "") {  outSum.close();  }
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                        delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                        m->Groups.clear();
                                        return 0;
@@ -397,7 +397,7 @@ int ParsimonyCommand::execute() {
                                if (m->control_pressed) { 
                                        delete reading; delete pars; delete output; delete randT;
                                        delete tmap; 
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                        m->Groups.clear();
                                        return 0;
                                }
@@ -409,7 +409,7 @@ int ParsimonyCommand::execute() {
                                if (m->control_pressed) { 
                                        delete reading; delete pars;  delete output; delete randT;
                                        delete tmap; 
-                                       for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                                       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                        m->Groups.clear();
                                        return 0;
                                }
@@ -466,7 +466,7 @@ int ParsimonyCommand::execute() {
                                delete reading; delete pars; delete output;
                                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                                if (randomtree == "") {  outSum.close();  }
-                               for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); } outputTypes.clear();
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } outputTypes.clear();
                                m->Groups.clear();
                                return 0;
                }
@@ -485,7 +485,7 @@ int ParsimonyCommand::execute() {
                delete pars; delete output; 
                delete tmap; for (int i = 0; i < T.size(); i++) { delete T[i]; }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } outputTypes.clear(); return 0;}
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); } outputTypes.clear(); return 0;}
                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();