X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.h;h=979612f4aea3aa41187ea520483afadfa05b1782;hb=38029939675c5bf5e449eac90f801b35064b3a36;hp=7342b36584ce76b3b22a96d0e3ba885cb2ab172a;hpb=6c2b1e530a5c0bb87040e58a3e410097acdfcc3d;p=mothur.git

diff --git a/treegroupscommand.h b/treegroupscommand.h
index 7342b36..979612f 100644
--- a/treegroupscommand.h
+++ b/treegroupscommand.h
@@ -78,8 +78,9 @@ public:
 	vector<string> setParameters();
 	string getCommandName()			{ return "tree.shared";				}
 	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getOutputFileNameTag(string, string);
+	
 	string getHelpString();	
+    string getOutputPattern(string);	
 	string getCitation() { return "http://www.mothur.org/wiki/Tree.shared"; }
 	string getDescription()		{ return "generate a tree file that describes the dissimilarity among groups"; }
 
@@ -110,7 +111,7 @@ private:
 	vector<Calculator*> treeCalculators;
 	vector<SharedRAbundVector*> lookup;
 	string lastLabel;
-	string format, groupNames, filename, sharedfile, inputfile;
+	string format, groupNames, filename, sharedfile, countfile, inputfile;
 	int numGroups, subsampleSize, iters, processors;
 	ofstream out;
 	float precision, cutoff;