working on current change

[mothur.git] / catchallcommand.cpp

diff --git a/catchallcommand.cpp b/catchallcommand.cpp
index 3effaf4eaafe09659252e6f93fa81f31dcc4e1db..fd51664a21ffa6373ebf9fd46d0fe5f586eb288c 100644 (file)
--- a/catchallcommand.cpp
+++ b/catchallcommand.cpp
@@ -8,7 +8,6 @@
  */
 
 #include "catchallcommand.h"
-#include "globaldata.hpp"
 
 //**********************************************************************************************************************
 vector<string> CatchAllCommand::setParameters(){       
@@ -73,6 +72,7 @@ CatchAllCommand::CatchAllCommand(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();
@@ -119,10 +119,12 @@ CatchAllCommand::CatchAllCommand(string option)  {
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }
                        else if (sabundfile == "not found") { sabundfile = "";  }
+                       else { m->setSabundFile(sabundfile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }
                        else if (sharedfile == "not found") { sharedfile = "";   }
+                       else { m->setSharedFile(sharedfile); }
                        
                        string label = validParameter.validFile(parameters, "label", false);                    
                        if (label == "not found") { label = ""; }