X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=hclustercommand.cpp;h=d98f5c69926f795cb75510853184197676647ab9;hb=7bf9a81bba76538ecaf351ae208de3da4bf1b6dd;hp=12f1f9e0b33904639cca446f0b0d698e9f64f625;hpb=e51cb7e261265800fa2d2831b6516e33ebc7d78b;p=mothur.git

diff --git a/hclustercommand.cpp b/hclustercommand.cpp
index 12f1f9e..d98f5c6 100644
--- a/hclustercommand.cpp
+++ b/hclustercommand.cpp
@@ -74,6 +74,7 @@ HClusterCommand::HClusterCommand(string option)  {
 		
 		//allow user to run help
 		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
 			vector<string> myArray = setParameters();
@@ -134,16 +135,17 @@ HClusterCommand::HClusterCommand(string option)  {
 			phylipfile = validParameter.validFile(parameters, "phylip", true);
 			if (phylipfile == "not open") { abort = true; }
 			else if (phylipfile == "not found") { phylipfile = ""; }	
-			else {  distfile = phylipfile;  format = "phylip"; 	}
+			else {  distfile = phylipfile;  format = "phylip"; 	m->setPhylipFile(phylipfile); }
 			
 			columnfile = validParameter.validFile(parameters, "column", true);
 			if (columnfile == "not open") { abort = true; }	
 			else if (columnfile == "not found") { columnfile = ""; }
-			else {  distfile = columnfile; format = "column";	}
+			else {  distfile = columnfile; format = "column";	m->setColumnFile(columnfile); }
 			
 			namefile = validParameter.validFile(parameters, "name", true);
 			if (namefile == "not open") { abort = true; }	
 			else if (namefile == "not found") { namefile = ""; }
+			else { m->setNameFile(namefile); }
 			
 			if ((phylipfile == "") && (columnfile == "")) { 
 				//is there are current file available for either of these?