changes for chimera slayer

[mothur.git] / removerarecommand.h

diff --git a/removerarecommand.h b/removerarecommand.h
index 7db54b409672af8937c456d731fffecf91cbe6c2..fa22f7a53e6c5149af4c1c1a51504cfb77e9b04e 100644 (file)
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -14,6 +14,7 @@
 #include "command.hpp"
 #include "listvector.hpp"
 
+
 class RemoveRareCommand : public Command {
        
 public:
@@ -21,12 +22,14 @@ public:
        RemoveRareCommand(string);      
        RemoveRareCommand();
        ~RemoveRareCommand(){}
-       vector<string> getRequiredParameters();
-       vector<string> getValidParameters();
-       vector<string> getRequiredFiles();
-       map<string, vector<string> > getOutputFiles() { return outputTypes; }
-       int execute();
-       void help();    
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "remove.rare";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
 private:
        string sabundfile, rabundfile, sharedfile, groupfile, listfile, outputDir, groups, label;
@@ -34,12 +37,12 @@ private:
        bool abort, byGroup;
        vector<string> outputNames, Groups;
        set<string> labels;
-       map<string, vector<string> > outputTypes;
        
        int processSabund();
        int processRabund();
        int processList();
        int processShared();
+       int processLookup(vector<SharedRAbundVector*>&, ofstream&);
        
 };