X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.cpp;fp=sensspeccommand.cpp;h=726c9045b20dfd7ac907b5e73f0692e3d0835c69;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=213a2ca99da988257a46ba8e91cb5e4123b5bb0e;hpb=220dc345e493cddc569521111ce32ac4d965ab7f;p=mothur.git

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 213a2ca..726c904 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -134,16 +134,17 @@ SensSpecCommand::SensSpecCommand(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") { abort = true; }	
+			else { m->setListFile(listFile); }
 			
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not found") { phylipfile = "";  }
 			else if (phylipfile == "not open") { abort = true; }	
-			else { distFile = phylipfile; format = "phylip";   }
+			else { distFile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile);  }
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not found") { columnfile = ""; }
 			else if (columnfile == "not open") { abort = true; }	
-			else { distFile = columnfile; format = "column";   }
+			else { distFile = columnfile; format = "column";   m->setColumnFile(columnfile); }
 			
 			if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
 				//give priority to column, then phylip