working on current change

[mothur.git] / classifyotucommand.cpp

diff --git a/classifyotucommand.cpp b/classifyotucommand.cpp
index eaf8cc206cebfe6eb1a60b40ff7042ede86ef6bd..d065b3a37c5ac41f9c6c3b59eb9ca3832f8697a9 100644 (file)
--- a/classifyotucommand.cpp
+++ b/classifyotucommand.cpp
@@ -166,6 +166,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                else {  m->mothurOut("You have no current listfile and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (listfile == "not open") { abort = true; }      
+                       else { m->setListFile(listfile); }
                        
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not found") {  //if there is a current list file, use it
@@ -174,6 +175,7 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                                else {  m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
                        else if (taxfile == "not open") { abort = true; }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        refTaxonomy = validParameter.validFile(parameters, "reftaxonomy", true);
                        if (refTaxonomy == "not found") { refTaxonomy = ""; m->mothurOut("reftaxonomy is not required, but if given will keep the rankIDs in the summary file static."); m->mothurOutEndLine(); }
@@ -182,10 +184,12 @@ ClassifyOtuCommand::ClassifyOtuCommand(string option)  {
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }   
                        else if (namefile == "not found") { namefile = ""; }
+                       else { m->setNameFile(namefile); }
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { 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...