X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getseqscommand.cpp;fp=getseqscommand.cpp;h=71a2db9723c32a39ea8e158074fbfac8a29de1ca;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=a4697ca3fded8c34ec5320630a588e243601373d;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/getseqscommand.cpp b/getseqscommand.cpp
index a4697ca..71a2db9 100644
--- a/getseqscommand.cpp
+++ b/getseqscommand.cpp
@@ -201,21 +201,24 @@ GetSeqsCommand::GetSeqsCommand(string option)  {
 					m->mothurOut("You have no valid accnos file and accnos is required."); m->mothurOutEndLine(); 
 					abort = true;
 				} 
-			}	
+			}else { m->setAccnosFile(accnosfile); }	
 			
 			if (accnosfile2 == "not found") { accnosfile2 = ""; }
 			
 			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; }
@@ -224,14 +227,17 @@ GetSeqsCommand::GetSeqsCommand(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); }
 			
 			qualfile = validParameter.validFile(parameters, "qfile", true);
 			if (qualfile == "not open") { abort = true; }
 			else if (qualfile == "not found") {  qualfile = "";  }
+			else { m->setQualFile(qualfile); }
 			
 			accnosfile2 = validParameter.validFile(parameters, "accnos2", true);
 			if (accnosfile2 == "not open") { abort = true; }