fixes while testing 1.33.0

[mothur.git] / removerarecommand.h

diff --git a/removerarecommand.h b/removerarecommand.h
index 388ec2d762e763ef1623d573eb90fa4074dbb039..6a9f2699c6d0a404403372e8ab081d11c9fa85d1 100644 (file)
--- a/removerarecommand.h
+++ b/removerarecommand.h
@@ -13,7 +13,7 @@
 
 #include "command.hpp"
 #include "listvector.hpp"
-#include "globaldata.hpp"
+
 
 class RemoveRareCommand : public Command {
        
@@ -22,27 +22,32 @@ 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(); 
+    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:
-       GlobalData* globaldata;
-       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;
        set<string> labels;
-       map<string, vector<string> > outputTypes;
        
        int processSabund();
        int processRabund();
        int processList();
        int processShared();
-       int processLookup(vector<SharedRAbundVector*>&, ofstream&);
+       int processLookup(vector<SharedRAbundVector*>&);
        
 };