X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=splitgroupscommand.h;fp=splitgroupscommand.h;h=a6b8854752f406a2bcaf82d5094c9abe023c2a46;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/splitgroupscommand.h b/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
+
+
+