working on current change

[mothur.git] / splitabundcommand.cpp

diff --git a/splitabundcommand.cpp b/splitabundcommand.cpp
index ba59dfe66e1b333f88317542e3a17844ac6d558e..aa47940a030f968e02686b915d26e84c29584b8d 100644 (file)
--- a/splitabundcommand.cpp
+++ b/splitabundcommand.cpp
@@ -152,12 +152,12 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") { listfile = ""; }
-                       else{ inputFile = listfile; }   
+                       else{ inputFile = listfile; m->setListFile(listfile); } 
                        
                        namefile = validParameter.validFile(parameters, "name", true);
                        if (namefile == "not open") { abort = true; }
                        else if (namefile == "not found") { namefile = ""; }    
-                       else{ inputFile = namefile; }   
+                       else{ inputFile = namefile; m->setNameFile(namefile); } 
                
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
@@ -165,7 +165,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                fastafile = m->getFastaFile(); 
                                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 { m->setFastaFile(fastafile); }   
                        
                        groupfile = validParameter.validFile(parameters, "group", true);
                        if (groupfile == "not open") {  groupfile = ""; abort = true; } 
@@ -175,7 +175,7 @@ SplitAbundCommand::SplitAbundCommand(string option)  {
                                
                                int error = groupMap->readMap();
                                if (error == 1) { abort = true; }
-       
+                               m->setGroupFile(groupfile);
                        }
                        
                        groups = validParameter.validFile(parameters, "groups", false);