X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=catchallcommand.h;fp=catchallcommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=238dfb608bb412a311f184d8df2f5dd4d4db9ab9;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/catchallcommand.h b/catchallcommand.h
deleted file mode 100644
index 238dfb6..0000000
--- a/catchallcommand.h
+++ /dev/null
@@ -1,58 +0,0 @@
-#ifndef CATCHALLCOMMAND_H
-#define CATCHALLCOMMAND_H
-
-/*
- *  catchallcommand.h
- *  Mothur
- *
- *  Created by westcott on 5/11/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "inputdata.h"
-#include "sabundvector.hpp"
-
-/* 
- citation goes here
- */ 
-
-/****************************************************************************/
-
-class CatchAllCommand : public Command {
-
-public:
-
-	CatchAllCommand(string);
-	CatchAllCommand();
-	~CatchAllCommand() {}
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "catchall";			}
-	string getCommandCategory()		{ return "OTU-Based Approaches";	}
-	string getHelpString();	
-	string getCitation() { return "Bunge, J. (2011). Estimating the number of species with CatchAll. Forthcoming in Proceedings of the Pacific Symposium on Biocomputing 2011.\nhttp://www.northeastern.edu/catchall/index.html http://www.mothur.org/wiki/Catchall"; }
-	string getDescription()		{ return "estimate number of species"; }
-	
-	int execute(); 
-	void help() { m->mothurOut(getHelpString()); }	
-	
-private:
-	string outputDir, sharedfile, sabundfile, format, path, savedOutputDir;
-	bool abort, allLines;
-	set<string> labels;
-	vector<string> outputNames;
-	vector<string> groups;
-	
-	string process(SAbundVector*, string);
-	int createSummaryFile(string, string, ofstream&); 
-	vector<string> parseSharedFile(string);
-	string combineSummmary(vector<string>&);
-};
-
-/****************************************************************************/
-
-#endif
-
-