X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getotuscommand.h;fp=getotuscommand.h;h=1a784935c476c22c798f8dfda33008606cc43439;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

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
+
+
+