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

[mothur.git] / collectcommand.cpp

diff --git a/collectcommand.cpp b/collectcommand.cpp
index 5bd9fd75c474aeafdf632d8800b9c184916ccc83..89ab0a49a7592a86638d801aaaf0257f63a34379 100644 (file)
--- a/collectcommand.cpp
+++ b/collectcommand.cpp
@@ -307,7 +307,7 @@ int CollectCommand::execute(){
        
                for (int p = 0; p < inputFileNames.size(); p++) {
                        
-                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());         }  m->Groups.clear();  return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]);        }  m->Groups.clear();  return 0; }
                        
                        if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
                        string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
@@ -413,7 +413,7 @@ int CollectCommand::execute(){
                        
                        if (m->control_pressed) {  
                                for(int i=0;i<cDisplays.size();i++){    delete cDisplays[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(); 
                                delete input;  
                                delete order; 
                                m->Groups.clear();
@@ -425,7 +425,7 @@ int CollectCommand::execute(){
                        
                                if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[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(); 
                                        delete input;  
                                        delete order; 
                                        m->Groups.clear();
@@ -474,7 +474,7 @@ int CollectCommand::execute(){
                        
                        if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[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(); 
                                        delete input;  
                                        m->Groups.clear();
                                        return 0;
@@ -506,7 +506,7 @@ int CollectCommand::execute(){
                                
                                if (m->control_pressed) { 
                                        for(int i=0;i<cDisplays.size();i++){    delete cDisplays[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(); 
                                        delete input;  
                                        delete order;
                                        m->Groups.clear();
@@ -520,7 +520,7 @@ int CollectCommand::execute(){
                        delete input;  
                }
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());         } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);        } return 0; }
                                
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -551,7 +551,7 @@ vector<string> CollectCommand::parseSharedFile(string filename) {
                
                //clears file before we start to write to it below
                for (int i=0; i<lookup.size(); i++) {
-                       remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
+                       m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                        filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
                }