X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.h;fp=getgroupscommand.h;h=7c4c92fff02ae6f577ca92a736fb7b14711cb302;hb=e3e0858c684c4608d679840024e5095ddc8e2719;hp=0000000000000000000000000000000000000000;hpb=3a13eff5c26d6fc156a299c9fa7f5497bded94a0;p=mothur.git

diff --git a/getgroupscommand.h b/getgroupscommand.h
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+#ifndef GETGROUPSCOMMAND_H
+#define GETGROUPSCOMMAND_H
+
+/*
+ *  getgroupscommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 11/10/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+
+#include "command.hpp"
+#include "groupmap.h"
+
+class GetGroupsCommand : public Command {
+	
+public:
+	
+	GetGroupsCommand(string);	
+	GetGroupsCommand();
+	~GetGroupsCommand(){}
+	vector<string> getRequiredParameters();
+	vector<string> getValidParameters();
+	vector<string> getRequiredFiles();
+	map<string, vector<string> > getOutputFiles() { return outputTypes; }
+	int execute();
+	void help();	
+	
+private:
+	set<string> names;
+	string accnosfile, fastafile, namefile, groupfile, listfile, taxfile, outputDir, groups;
+	bool abort;
+	vector<string> outputNames, Groups;
+	map<string, vector<string> > outputTypes;
+	GroupMap* groupMap;
+	
+	int readFasta();
+	int readName();
+	int readGroup();
+	void readAccnos();
+	int readList();
+	int readTax();
+	int fillNames();
+	
+};
+
+#endif
+
+
+