created mothurOut class to handle logfiles

[mothur.git] / getrabundcommand.cpp

diff --git a/getrabundcommand.cpp b/getrabundcommand.cpp
index df9754b14219548719305cd53498b5d46b05d42c..5a192c5066d6f23921e356ed7a2785abbd967631 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);
        }                       
 }
@@ -81,18 +81,18 @@ 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);
        }
 }
@@ -125,7 +125,7 @@ int GetRAbundCommand::execute(){
                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());
                                        
@@ -144,7 +144,7 @@ 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());
                                        
@@ -170,12 +170,12 @@ 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();
                        }
                }
                
@@ -184,7 +184,7 @@ 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());
                        
@@ -194,13 +194,19 @@ int GetRAbundCommand::execute(){
                        delete rabund;
                        delete list;
                }
+               
+               m->mothurOutEndLine();
+               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut(filename); m->mothurOutEndLine();  
+               m->mothurOutEndLine();
 
+               
                out.close(); 
                return 0;               
        }
 
        catch(exception& e) {
-               errorOut(e, "GetRAbundCommand", "execute");
+               m->errorOut(e, "GetRAbundCommand", "execute");
                exit(1);
        }
 }