changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / getlistcountcommand.cpp

diff --git a/getlistcountcommand.cpp b/getlistcountcommand.cpp
index eb9c980075a069b1e0f08f6f01fc64e4f1a6b358..980c886cc0cb79f51f892ee13fe4dc2c3061b812 100644 (file)
--- a/getlistcountcommand.cpp
+++ b/getlistcountcommand.cpp
@@ -69,6 +69,7 @@ GetListCountCommand::GetListCountCommand(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();
@@ -113,6 +114,7 @@ GetListCountCommand::GetListCountCommand(string option)  {
                                else {  m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                
                        //check for optional parameter and set defaults
@@ -147,7 +149,7 @@ int GetListCountCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
-               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
@@ -155,7 +157,7 @@ int GetListCountCommand::execute(){
                        
                                process(list);
                                
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                                                        
                                processedLabels.insert(list->getLabel());
                                userLabels.erase(list->getLabel());
@@ -169,7 +171,7 @@ int GetListCountCommand::execute(){
                                
                                process(list);
                                
-                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                               if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
 
                                                                                                        
                                processedLabels.insert(list->getLabel());
@@ -206,7 +208,7 @@ int GetListCountCommand::execute(){
                                
                        process(list);  
                        
-                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     remove(outputNames[i].c_str()); } return 0;  }
+                       if (m->control_pressed) { delete input; delete list; for (int i = 0; i < outputNames.size(); i++) {     m->mothurRemove(outputNames[i]);        } return 0;  }
                        
                        delete list;  
                }