working on current change

[mothur.git] / getsabundcommand.cpp

diff --git a/getsabundcommand.cpp b/getsabundcommand.cpp
index 820868416b7bfc9bebcc27c8f73c24c6ddb7bbb4..799d8dced192019f65a633e946262db92c1e615f 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