X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getotuscommand.h;fp=getotuscommand.h;h=ec69acb4c0381c6b2b5190abf1a88ae214751647;hb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da;hp=0000000000000000000000000000000000000000;hpb=e3e0858c684c4608d679840024e5095ddc8e2719;p=mothur.git

diff --git a/getotuscommand.h b/getotuscommand.h
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+++ 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> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute();
+	void help();	
+	
+private:
+	string accnosfile, groupfile, listfile, outputDir, groups, label;
+	bool abort;
+	vector<string> outputNames, Groups;
+	map<string, vector<string> > outputTypes;
+	GroupMap* groupMap;
+	
+	void readAccnos();
+	int readListGroup();
+	int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
+	
+};
+
+#endif
+
+
+