working on current change

[mothur.git] / listseqscommand.cpp

diff --git a/listseqscommand.cpp b/listseqscommand.cpp
index 902ac87286e302977d2fe555754a632487e6e43b..3fe8360e3241477b869c26f5b1892541e28d84a4 100644 (file)
--- a/listseqscommand.cpp
+++ b/listseqscommand.cpp
@@ -150,15 +150,18 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        //check for required parameters
                        fastafile = validParameter.validFile(parameters, "fasta", true);
                        if (fastafile == "not open") { abort = true; }
-                       else if (fastafile == "not found") {  fastafile = "";  }        
+                       else if (fastafile == "not found") {  fastafile = "";  }
+                       else { m->setFastaFile(fastafile); }
                        
                        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); }
                        
                        alignfile = validParameter.validFile(parameters, "alignreport", true);
                        if (alignfile == "not open") { abort = true; }
@@ -167,10 +170,12 @@ ListSeqsCommand::ListSeqsCommand(string option)  {
                        listfile = validParameter.validFile(parameters, "list", true);
                        if (listfile == "not open") { abort = true; }
                        else if (listfile == "not found") {  listfile = "";  }
-
+                       else { m->setListFile(listfile); }
+                       
                        taxfile = validParameter.validFile(parameters, "taxonomy", true);
                        if (taxfile == "not open") { abort = true; }
                        else if (taxfile == "not found") {  taxfile = "";  }
+                       else { m->setTaxonomyFile(taxfile); }
                        
                        if ((fastafile == "") && (namefile == "") && (listfile == "") && (groupfile == "") && (alignfile == "") && (taxfile == ""))  { m->mothurOut("You must provide a file."); m->mothurOutEndLine(); abort = true; }