X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getdistscommand.h;fp=getdistscommand.h;h=8767067695190655cc311dc3942bdc02884feca3;hb=1f0e54b53b714781f3f2fee7d01177fade98a625;hp=0000000000000000000000000000000000000000;hpb=14cddf859d97118481161bf3e85a647976020758;p=mothur.git

diff --git a/getdistscommand.h b/getdistscommand.h
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+//
+//  getdistscommand.h
+//  Mothur
+//
+//  Created by Sarah Westcott on 1/28/13.
+//  Copyright (c) 2013 Schloss Lab. All rights reserved.
+//
+
+#ifndef Mothur_getdistscommand_h
+#define Mothur_getdistscommand_h
+
+#include "command.hpp"
+
+class GetDistsCommand : public Command {
+	
+public:
+	
+	GetDistsCommand(string);	
+	GetDistsCommand();
+	~GetDistsCommand(){}
+	
+	vector<string> setParameters();
+	string getCommandName()			{ return "get.dists";				}
+	string getCommandCategory()		{ return "General";                 }
+	
+	string getHelpString();	
+    string getOutputPattern(string);	
+	string getCitation() { return "http://www.mothur.org/wiki/Get.dists"; }
+	string getDescription()		{ return "gets distances from a phylip or column file related to groups or sequences listed in an accnos file"; }
+    
+	
+	int execute(); 
+	void help() { m->mothurOut(getHelpString()); }	
+	
+	
+private:
+	set<string> names;
+	string accnosfile, phylipfile, columnfile, outputDir;
+	bool abort;
+	vector<string> outputNames;
+	
+	int readPhylip();
+	int readColumn();
+	
+};
+
+
+#endif