changing command name classify.shared to classifyrf.shared

[mothur.git] / getlabelcommand.cpp

diff --git a/getlabelcommand.cpp b/getlabelcommand.cpp
index aba8e8a128f6299feabfee18a8118384974fa206..03bf7ad991829e2afc693db3d15560d66e597a91 100644 (file)
--- a/getlabelcommand.cpp
+++ b/getlabelcommand.cpp
@@ -13,11 +13,11 @@
 //**********************************************************************************************************************
 vector<string> GetlabelCommand::setParameters(){       
        try {
-               CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
-               CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
-               CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(plist);
+               CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
+               CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -113,17 +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?