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

[mothur.git] / summarycommand.cpp

diff --git a/summarycommand.cpp b/summarycommand.cpp
index 2bb88770ec37651df7ff9da2954926abf3bf5153..629750bbccb5ed027edf5ef53dbba3686ddb4bba 100644 (file)
--- a/summarycommand.cpp
+++ b/summarycommand.cpp
@@ -337,7 +337,7 @@ int SummaryCommand::execute(){
                        }
                        
                        //if the users entered no valid calculators don't execute command
-                       if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } return 0; }
+                       if (sumCalculators.size() == 0) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } return 0; }
                        
                        ofstream outputFileHandle;
                        m->openOutputFile(fileNameRoot, outputFileHandle);
@@ -363,11 +363,11 @@ int SummaryCommand::execute(){
                        set<string> processedLabels;
                        set<string> userLabels = labels;
                        
-                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
                        
                        while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                                
-                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
                                
                                if(allLines == 1 || labels.count(sabund->getLabel()) == 1){                     
                                        
@@ -379,7 +379,7 @@ int SummaryCommand::execute(){
                                        for(int i=0;i<sumCalculators.size();i++){
                                                vector<double> data = sumCalculators[i]->getValues(sabund);
                                                
-                                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
+                                               if (m->control_pressed) { outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input;  return 0;  }
 
                                                outputFileHandle << '\t';
                                                sumCalculators[i]->print(outputFileHandle);
@@ -402,7 +402,7 @@ int SummaryCommand::execute(){
                                        for(int i=0;i<sumCalculators.size();i++){
                                                vector<double> data = sumCalculators[i]->getValues(sabund);
                                                
-                                               if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete sabund;  delete input;  return 0;  }
+                                               if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {      m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; } delete sabund;  delete input;  return 0;  }
                                                
                                                outputFileHandle << '\t';
                                                sumCalculators[i]->print(outputFileHandle);
@@ -420,7 +420,7 @@ int SummaryCommand::execute(){
                                sabund = input->getSAbundVector();
                        }
                        
-                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
+                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 
                        //output error messages about any remaining user labels
                        set<string>::iterator it;
@@ -445,7 +445,7 @@ int SummaryCommand::execute(){
                                for(int i=0;i<sumCalculators.size();i++){
                                        vector<double> data = sumCalculators[i]->getValues(sabund);
                                        
-                                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input; return 0;  }
+                                       if (m->control_pressed) {  outputFileHandle.close(); for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }  delete sabund;  delete input; return 0;  }
 
                                        outputFileHandle << '\t';
                                        sumCalculators[i]->print(outputFileHandle);
@@ -457,19 +457,19 @@ int SummaryCommand::execute(){
                        
                        outputFileHandle.close();
                        
-                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
+                       if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }   delete input;  return 0;  }
 
                        
                        delete input;  
                        for(int i=0;i<sumCalculators.size();i++){  delete sumCalculators[i]; }
                }
                
-               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;  }
                
                //create summary file containing all the groups data for each label - this function just combines the info from the files already created.
                if ((sharedfile != "") && (groupMode)) {   outputNames.push_back(createGroupSummaryFile(numLines, numCols, outputNames));  }
                
-               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();
@@ -498,7 +498,7 @@ vector<string> SummaryCommand::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"));
                }
                
@@ -592,7 +592,7 @@ string SummaryCommand::createGroupSummaryFile(int numLines, int numCols, vector<
                        files[outputNames[i]] = thisFilesLines;
                        
                        temp.close();
-                       remove(outputNames[i].c_str());
+                       m->mothurRemove(outputNames[i]);
                }
                
                //output label line to new file