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

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index ebfa839161fc3d59cd27f9a2f8e2e24743b85e7e..4ae2eaa004f9df9cc75c12b63626ffa7fad71ea7 100644 (file)
--- a/getsabundcommand.cpp
+++ b/getsabundcommand.cpp
@@ -67,6 +67,7 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -113,12 +114,12 @@ GetSAbundCommand::GetSAbundCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else {  format = "list"; inputfile = listfile; }
+                       else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
-                       else {  format = "rabund"; inputfile = rabundfile; }
+                       else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
                        
                
                                                //check for optional parameter and set defaults
@@ -177,7 +178,7 @@ int GetSAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input; return 0; }
+               if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input; return 0; }
 
                
                while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
@@ -186,9 +187,8 @@ int GetSAbundCommand::execute(){
                                        m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
                                        
                                        sabund->print(out);
-                                       delete sabund;
                                        
-                               if (m->control_pressed) { outputTypes.clear();  out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+                               if (m->control_pressed) { outputTypes.clear();  out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
@@ -202,9 +202,8 @@ int GetSAbundCommand::execute(){
                                        
                                        m->mothurOut(sabund->getLabel());  m->mothurOutEndLine();
                                        sabund->print(out);
-                                       delete sabund;
                                        
-                                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete sabund; delete input;  return 0; }
+                                       if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete sabund; delete input;  return 0; }
 
                                        processedLabels.insert(sabund->getLabel());
                                        userLabels.erase(sabund->getLabel());
@@ -242,7 +241,7 @@ int GetSAbundCommand::execute(){
                        sabund->print(out);
                        delete sabund;
                        
-                       if (m->control_pressed) {  outputTypes.clear(); out.close(); remove(filename.c_str());  delete input; return 0; }
+                       if (m->control_pressed) {  outputTypes.clear(); out.close(); m->mothurRemove(filename);  delete input; return 0; }
                        
                }