Revert to previous commit

[mothur.git] / getotuscommand.h

diff --git a/getotuscommand.h b/getotuscommand.h
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+#ifndef GETOTUSCOMMAND_H
+#define GETOTUSCOMMAND_H
+
+/*
+ *  getotuscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/10/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+
+#include "command.hpp"
+#include "groupmap.h"
+#include "listvector.hpp"
+
+class GetOtusCommand : public Command {
+       
+public:
+       
+       GetOtusCommand(string); 
+       GetOtusCommand();
+       ~GetOtusCommand(){}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "get.otus";                            }
+       string getCommandCategory()             { return "OTU-Based Approaches";        }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
+       string getDescription()         { return "outputs a new list file containing the otus containing sequences from the groups specified"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+       
+private:
+       string accnosfile, groupfile, listfile, outputDir, groups, label;
+       bool abort;
+       vector<string> outputNames, Groups;
+       GroupMap* groupMap;
+       
+       void readAccnos();
+       int readListGroup();
+       int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
+       
+};
+
+#endif
+
+
+