X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=binsequencecommand.cpp;fp=binsequencecommand.cpp;h=8e8ec2bc51362d8b8876d6e3cbb10ef9ff5e167e;hb=220dc345e493cddc569521111ce32ac4d965ab7f;hp=c4ef741f80c22bc784df4e6916f4a214fb2feacd;hpb=23e60689fa4306234b3d05b116f25d198316d1ae;p=mothur.git

diff --git a/binsequencecommand.cpp b/binsequencecommand.cpp
index c4ef741..8e8ec2b 100644
--- a/binsequencecommand.cpp
+++ b/binsequencecommand.cpp
@@ -138,6 +138,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 				else { 	m->mothurOut("You have no current fasta file and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (fastafile == "not open") { abort = true; }	
+			else { m->setFastaFile(fastafile); }
 			
 			listfile = validParameter.validFile(parameters, "list", true);
 			if (listfile == "not found") { 			
@@ -146,6 +147,7 @@ BinSeqCommand::BinSeqCommand(string option) {
 				else { 	m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
 			}
 			else if (listfile == "not open") { listfile = ""; abort = true; }	
+			else { m->setListFile(listfile); }
 			
 			//if the user changes the output directory command factory will send this info to us in the output parameter 
 			outputDir = validParameter.validFile(parameters, "outputdir", false);		if (outputDir == "not found"){	
@@ -167,10 +169,12 @@ BinSeqCommand::BinSeqCommand(string option) {
 			namesfile = validParameter.validFile(parameters, "name", true);
 			if (namesfile == "not open") { abort = true; }	
 			else if (namesfile == "not found") { namesfile = ""; }
+			else {  m->setNameFile(namesfile); }
 
 			groupfile = validParameter.validFile(parameters, "group", true);
 			if (groupfile == "not open") { abort = true; }
 			else if (groupfile == "not found") { groupfile = ""; }
+			else { m->setGroupFile(groupfile); }
 			
 		}
 	}