changed added group output to indicator command. a few changes to work with the guy

[mothur.git] / summarytaxcommand.h

diff --git a/summarytaxcommand.h b/summarytaxcommand.h
index b5bdab15ab977b97b1d1a813869ff0dbe38d8deb..e8033e23c76837809aa7828389b9cbae13b9c639 100644 (file)
--- a/summarytaxcommand.h
+++ b/summarytaxcommand.h
@@ -11,6 +11,7 @@
  */
 
 #include "command.hpp"
+#include "counttable.h"
 
 /**************************************************************************************************/
 
@@ -23,7 +24,8 @@ class SummaryTaxCommand : public Command {
                vector<string> setParameters();
                string getCommandName()                 { return "summary.tax";                 }
                string getCommandCategory()             { return "Phylotype Analysis";          }
-               string getHelpString(); 
+               string getOutputFileNameTag(string, string);
+       string getHelpString(); 
                string getCitation() { return "http://www.mothur.org/wiki/Summary.tax"; }
                string getDescription()         { return "summarize the taxonomies of a set of sequences"; }
                
@@ -32,7 +34,7 @@ class SummaryTaxCommand : public Command {
                
        private:
                bool abort;
-               string taxfile, outputDir, namefile, groupfile, refTaxonomy;
+               string taxfile, outputDir, namefile, groupfile, refTaxonomy, countfile;
                vector<string> outputNames;
                map<string, int> nameMap;
 };