added checks for ^C to quit command instead of program

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index df9754b14219548719305cd53498b5d46b05d42c..6b68c32cad7673b950eeb8acfe6423b160630130 100644 (file)
--- a/getrabundcommand.cpp
+++ b/getrabundcommand.cpp
@@ -11,7 +11,7 @@
 
 //**********************************************************************************************************************
 
-GetRAbundCommand::GetRAbundCommand(string option){
+GetRAbundCommand::GetRAbundCommand(string option)  {
        try {
                globaldata = GlobalData::getInstance();
                abort = false;
@@ -43,7 +43,7 @@ GetRAbundCommand::GetRAbundCommand(string option){
                        }
                        
                        //make sure the user has already run the read.otu command
-                       if (globaldata->getListFile() == "") { mothurOut("You must read a listfile before you can use the get.rabund command."); mothurOutEndLine(); abort = true; }
+                       if (globaldata->getListFile() == "") { m->mothurOut("You must read a listfile before you can use the get.rabund command."); m->mothurOutEndLine(); abort = true; }
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...
@@ -73,7 +73,7 @@ GetRAbundCommand::GetRAbundCommand(string option){
 
        }
        catch(exception& e) {
-               errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+               m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
                exit(1);
        }                       
 }
@@ -81,27 +81,25 @@ GetRAbundCommand::GetRAbundCommand(string option){
 
 void GetRAbundCommand::help(){
        try {
-               mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
-               mothurOut("The get.rabund command parameters are label and sorted.  No parameters are required.\n");
-               mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
-               mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
-               mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
-               mothurOut("Example get.rabund(sorted=F).\n");
-               mothurOut("The default value for label is all labels in your inputfile.\n");
-               mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
-               mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
+               m->mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
+               m->mothurOut("The get.rabund command parameters are label and sorted.  No parameters are required.\n");
+               m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
+               m->mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not.  The default is sorted.\n");
+               m->mothurOut("The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n");
+               m->mothurOut("Example get.rabund(sorted=F).\n");
+               m->mothurOut("The default value for label is all labels in your inputfile.\n");
+               m->mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
+               m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n\n");
        }
        catch(exception& e) {
-               errorOut(e, "GetRAbundCommand", "help");
+               m->errorOut(e, "GetRAbundCommand", "help");
                exit(1);
        }
 }
 
 //**********************************************************************************************************************
 
-GetRAbundCommand::~GetRAbundCommand(){
-       if (abort == false) {  globaldata->gListVector = NULL; }
-}
+GetRAbundCommand::~GetRAbundCommand(){}
 
 //**********************************************************************************************************************
 
@@ -122,13 +120,18 @@ int GetRAbundCommand::execute(){
                set<string> processedLabels;
                set<string> userLabels = labels;
                
+               if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; globaldata->gListVector = NULL;  return 0; }
+               
                while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
                        
                        if(allLines == 1 || labels.count(list->getLabel()) == 1){
-                                       mothurOut(list->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                                        rabund = new RAbundVector();                            
                                        *rabund = (list->getRAbundVector());
                                        
+                                       if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+
+                                       
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
                                        
@@ -144,10 +147,12 @@ int GetRAbundCommand::execute(){
                                        delete list;
                                        list = input->getListVector(lastLabel);
                                        
-                                       mothurOut(list->getLabel()); mothurOutEndLine();
+                                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                                        rabund = new RAbundVector();
                                        *rabund = (list->getRAbundVector());
                                        
+                                       if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+                                       
                                        if(sorted)      {   rabund->print(out);                         }
                                        else            {       rabund->nonSortedPrint(out);    }
 
@@ -170,12 +175,12 @@ int GetRAbundCommand::execute(){
                set<string>::iterator it;
                bool needToRun = false;
                for (it = userLabels.begin(); it != userLabels.end(); it++) {  
-                       mothurOut("Your file does not include the label " + *it); 
+                       m->mothurOut("Your file does not include the label " + *it); 
                        if (processedLabels.count(lastLabel) != 1) {
-                               mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+                               m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
                                needToRun = true;
                        }else {
-                               mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+                               m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
                        }
                }
                
@@ -184,23 +189,34 @@ int GetRAbundCommand::execute(){
                        if (list != NULL) {     delete list;    }
                        list = input->getListVector(lastLabel);
                        
-                       mothurOut(list->getLabel()); mothurOutEndLine();
+                       m->mothurOut(list->getLabel()); m->mothurOutEndLine();
                        rabund = new RAbundVector();
                        *rabund = (list->getRAbundVector());
                        
+                       if (m->control_pressed) {  out.close(); remove(filename.c_str()); delete read; delete input; delete list; delete rabund; globaldata->gListVector = NULL;  return 0; }
+                       
                        if(sorted)      {   rabund->print(out);                         }
                        else            {       rabund->nonSortedPrint(out);    }
 
                        delete rabund;
                        delete list;
                }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(filename); m->mothurOutEndLine();  
+               m->mothurOutEndLine();
 
+               
                out.close(); 
+               delete read; delete input;
+               globaldata->gListVector = NULL; 
+               
                return 0;               
        }
 
        catch(exception& e) {
-               errorOut(e, "GetRAbundCommand", "execute");
+               m->errorOut(e, "GetRAbundCommand", "execute");
                exit(1);
        }
 }