working on pam

[mothur.git] / removerarecommand.h

diff --git a/removerarecommand.h b/removerarecommand.h
index 2ab1272efbef88fdb008f903cf02a7d66ed3215a..6a9f2699c6d0a404403372e8ab081d11c9fa85d1 100644 (file)
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -26,14 +26,18 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "remove.rare";                         }
        string getCommandCategory()             { return "OTU-Based Approaches";        }
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Remove.rare"; }
+       string getDescription()         { return "removes rare sequences from a sabund, rabund, shared or list and group file"; }
+
        
        int execute(); 
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
+       string sabundfile, rabundfile, sharedfile, groupfile, countfile, listfile, outputDir, groups, label;
        int nseqs, allLines;
        bool abort, byGroup;
        vector<string> outputNames, Groups;
@@ -43,7 +47,7 @@ private:
        int processRabund();
        int processList();
        int processShared();
-       int processLookup(vector<SharedRAbundVector*>&, ofstream&);
+       int processLookup(vector<SharedRAbundVector*>&);
        
 };