X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getotuscommand.h;fp=getotuscommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=1a784935c476c22c798f8dfda33008606cc43439;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/getotuscommand.h b/getotuscommand.h
deleted file mode 100644
index 1a78493..0000000
--- a/getotuscommand.h
+++ /dev/null
@@ -1,54 +0,0 @@
-#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
-
-
-