working on current change

[mothur.git] / subsamplecommand.cpp

diff --git a/subsamplecommand.cpp b/subsamplecommand.cpp
index 0f7bdec57cc94e1b721c8cee65c57eb01a5e6124..95a0442d6c970bd74a383c1e13765af305eeac57 100644 (file)
--- a/subsamplecommand.cpp
+++ b/subsamplecommand.cpp
@@ -182,32 +182,38 @@ SubSampleCommand::SubSampleCommand(string option) {
                        //check for required parameters
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { listfile = ""; abort = true; }
-                       else if (listfile == "not found") { listfile = ""; }    
+                       else if (listfile == "not found") { listfile = ""; }
+                       else { m->setListFile(listfile); }
                        
                        sabundfile = validParameter.validFile(parameters, "sabund", true);
                        if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
                        else if (sabundfile == "not found") { sabundfile = ""; }
+                       else { m->setSabundFile(sabundfile); }
                        
                        rabundfile = validParameter.validFile(parameters, "rabund", true);
                        if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
                        else if (rabundfile == "not found") { rabundfile = ""; }
+                       else { m->setRabundFile(rabundfile); }
                        
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { fastafile = ""; abort = true; }  
                        else if (fastafile == "not found") { fastafile = ""; }
+                       else { m->setFastaFile(fastafile); }
                        
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { sharedfile = ""; abort = true; }        
                        else if (sharedfile == "not found") { sharedfile = ""; }
+                       else { m->setSharedFile(sharedfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }    
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { groupfile = ""; abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
-                       
+                       else { m->setGroupFile(groupfile); }
                        
                        //check for optional parameter and set defaults
                        // ...at some point should added some additional type checking...