working on current change

[mothur.git] / screenseqscommand.cpp

diff --git a/screenseqscommand.cpp b/screenseqscommand.cpp
index b68a8cc8ea0042d53222da781770627c58ff3966..9f7aa40b3cc6786388a4e9eb8e47326661460e2d 100644 (file)
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -173,20 +173,24 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
                                if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
                        }
-                       else if (fastafile == "not open") { abort = true; }     
+                       else if (fastafile == "not open") { abort = true; }
+                       else { m->setFastaFile(fastafile); }
        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") { abort = true; }  
                        else if (groupfile == "not found") { groupfile = ""; }
+                       else { m->setGroupFile(groupfile); }
                        
                        qualfile = validParameter.validFile(parameters, "qfile", true);
                        if (qualfile == "not open") { abort = true; }   
                        else if (qualfile == "not found") { qualfile = ""; }
+                       else { m->setQualFile(qualfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
-
+                       else { m->setNameFile(namefile); }
+                       
                        alignreport = validParameter.validFile(parameters, "alignreport", true);
                        if (alignreport == "not open") { abort = true; }
                        else if (alignreport == "not found") { alignreport = ""; }