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[mothur.git] / splitgroupscommand.h

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+#ifndef SPLITGROUPSCOMMAND_H
+#define SPLITGROUPSCOMMAND_H
+
+/*
+ *  splitgroupscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 9/20/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+/* split.groups - given a group file, split sequences and names files in to separate files *.group1.fasta and .group1.names. */
+
+
+#include "command.hpp"
+#include "groupmap.h"
+#include "sequence.hpp"
+
+/***************************************************************************************/
+
+class SplitGroupCommand : public Command {
+       
+public:
+       SplitGroupCommand(string);      
+       SplitGroupCommand();
+       ~SplitGroupCommand() {}
+       
+       vector<string> setParameters();
+       string getCommandName()                 { return "split.group";                         }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       string getHelpString(); 
+       string getCitation() { return "http://www.mothur.org/wiki/Split.group"; }
+       string getDescription()         { return "split a name or fasta file by group"; }
+
+       
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
+       
+private:
+       vector<string> outputNames;
+               
+       string outputDir, namefile, groupfile, groups, fastafile;
+       vector<string> Groups;
+       bool abort;
+};
+
+/***************************************************************************************/
+
+#endif
+
+
+