X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=getgroupscommand.h;fp=getgroupscommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=224f4f07ea1c45d3e734d8f6406e8a17f40fd1fd;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/getgroupscommand.h b/getgroupscommand.h
deleted file mode 100644
index 224f4f0..0000000
--- a/getgroupscommand.h
+++ /dev/null
@@ -1,62 +0,0 @@
-#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> setParameters();
-	string getCommandName()			{ return "get.groups";				}
-	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getHelpString();	
-	string getCitation() { return "http://www.mothur.org/wiki/Get.groups"; }
-	string getDescription()		{ return "gets sequences from a list, fasta, name, group, shared, design or taxonomy file from a given group or set of groups"; }
-
-	
-	int execute(); 
-	void help() { m->mothurOut(getHelpString()); }	
-	
-	
-private:
-	set<string> names;
-	map<string, string> uniqueToRedundant; //if a namefile is given and the first column name is not selected
-										   //then the other files need to change the unique name in their file to match.
-										   //only add the names that need to be changed to keep the map search quick
-	string accnosfile, fastafile, namefile, groupfile, listfile, designfile, taxfile, outputDir, groups, sharedfile;
-	bool abort;
-	vector<string> outputNames, Groups;
-	GroupMap* groupMap;
-	
-	int readFasta();
-	int readName();
-	int readGroup();
-	void readAccnos();
-	int readList();
-	int readTax();
-	int fillNames();
-	int readShared();
-    int readDesign();
-	
-};
-
-#endif
-
-
-