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[mothur.git] / removerarecommand.h

diff --git a/removerarecommand.h b/removerarecommand.h
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+#ifndef REMOVERARECOMMAND_H
+#define REMOVERARECOMMAND_H
+
+/*
+ *  removerarecommand.h
+ *  mothur
+ *
+ *  Created by westcott on 1/21/11.
+ *  Copyright 2011 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "listvector.hpp"
+
+
+class RemoveRareCommand : public Command {
+       
+public:
+       
+       RemoveRareCommand(string);      
+       RemoveRareCommand();
+       ~RemoveRareCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "remove.rare";                         }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       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;
+       int nseqs, allLines;
+       bool abort, byGroup;
+       vector<string> outputNames, Groups;
+       set<string> labels;
+       
+       int processSabund();
+       int processRabund();
+       int processList();
+       int processShared();
+       int processLookup(vector<SharedRAbundVector*>&, ofstream&);
+       
+};
+
+#endif
+
+
+
+