added modify names parameter to set.dir

[mothur.git] / summarytaxcommand.h

diff --git a/summarytaxcommand.h b/summarytaxcommand.h
index 5f0630f66a03ba9f08a2dd4d2098808a513f0a3c..5f61d13849fbfb332c8927445825bc5447b4ce8f 100644 (file)
--- 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"; }
                
@@ -33,7 +35,7 @@ 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;
 };