added load.logfile command. changed summary.single output for subsample=t.

[mothur.git] / getlabelcommand.cpp

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index 381a9508a0222e3bbec90930215513b7048a9770..8535db3203c6da354ce55e1a4f095f07b6d4e487 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -62,6 +62,7 @@ GetlabelCommand::GetlabelCommand(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();
@@ -112,17 +113,17 @@ GetlabelCommand::GetlabelCommand(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); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
-                       else {  format = "sabund"; inputfile = sabundfile; }
+                       else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
                        
                        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); }
                        
                        if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
                                //is there are current file available for any of these?