X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summarytaxcommand.h;h=7716ad0ca41b4dee22f993c95c8955c94e5b4852;hb=f6a58db15cdc7b90a601f8bf9c9d3b69d642f85d;hp=5f0630f66a03ba9f08a2dd4d2098808a513f0a3c;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/summarytaxcommand.h b/summarytaxcommand.h
index 5f0630f..7716ad0 100644
--- a/summarytaxcommand.h
+++ b/summarytaxcommand.h
@@ -11,6 +11,7 @@
  */
 
 #include "command.hpp"
+#include "counttable.h"
 
 /**************************************************************************************************/
 
@@ -23,8 +24,9 @@ class SummaryTaxCommand : public Command {
 		vector<string> setParameters();
 		string getCommandName()			{ return "summary.tax";			}
 		string getCommandCategory()		{ return "Phylotype Analysis";		}
-		string getOutputFileNameTag(string, string);
+		
 	string getHelpString();	
+    string getOutputPattern(string);	
 		string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
 		string getDescription()		{ return "summarize the taxonomies of a set of sequences"; }
 		
@@ -32,8 +34,8 @@ class SummaryTaxCommand : public Command {
 		void help() { m->mothurOut(getHelpString()); }	
 		
 	private:
-		bool abort;
-		string taxfile, outputDir, namefile, groupfile, refTaxonomy;
+		bool abort, relabund;
+		string taxfile, outputDir, namefile, groupfile, refTaxonomy, countfile;
 		vector<string> outputNames;
 		map<string, int> nameMap;
 };