X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=removegroupscommand.cpp;h=9b537281b4abef7ecb9f270e1438993fca198e22;hb=cd7040a22ae19c86a13c2c10ed90a64b77a0c482;hp=7034941e73e6a02ae07a02ab11631e8a7b752f3d;hpb=fc3a1319b64fd3638df074e4669a1fb0235d1b8d;p=mothur.git

diff --git a/removegroupscommand.cpp b/removegroupscommand.cpp
index 7034941..9b53728 100644
--- a/removegroupscommand.cpp
+++ b/removegroupscommand.cpp
@@ -166,14 +166,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 			accnosfile = validParameter.validFile(parameters, "accnos", true);
 			if (accnosfile == "not open") { abort = true; }
 			else if (accnosfile == "not found") {  accnosfile = ""; }	
+			else { m->setAccnosFile(accnosfile); }
 			
 			fastafile = validParameter.validFile(parameters, "fasta", true);
 			if (fastafile == "not open") { abort = true; }
 			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; }
@@ -182,15 +185,17 @@ RemoveGroupsCommand::RemoveGroupsCommand(string option)  {
 				groupfile = m->getGroupFile(); 
 				if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
 				else { 	m->mothurOut("You have no current groupfile and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
-			}	
+			}else { m->setGroupFile(groupfile); }	
 			
 			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); }
 			
 			groups = validParameter.validFile(parameters, "groups", false);			
 			if (groups == "not found") { groups = ""; }