X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.h;fp=chimeracheckcommand.h;h=0000000000000000000000000000000000000000;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hp=918b4e5e9bf8aa4a16a1e0ba0716e09753a29cea;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76;p=mothur.git

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
deleted file mode 100644
index 918b4e5..0000000
--- a/chimeracheckcommand.h
+++ /dev/null
@@ -1,69 +0,0 @@
-#ifndef CHIMERACHECKCOMMAND_H
-#define CHIMERACHECKCOMMAND_H
-
-/*
- *  chimeracheckcommand.h
- *  Mothur
- *
- *  Created by westcott on 3/31/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "chimera.h"
-#include "chimeracheckrdp.h"
-
-
-/***********************************************************/
-
-class ChimeraCheckCommand : public Command {
-public:
-	ChimeraCheckCommand(string);
-	ChimeraCheckCommand();
-	~ChimeraCheckCommand(){}
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "chimera.check";		}
-	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getHelpString();	
-	string getCitation() { return "CHIMERA_CHECK version 2.7 written by Niels Larsen (http://wdcm.nig.ac.jp/RDP/docs/chimera_doc.html) \nhttp://www.mothur.org/wiki/Chimera.check"; }
-	string getDescription()		{ return "detect chimeric sequences"; }
-	
-	int execute(); 
-	void help() { m->mothurOut(getHelpString()); }	
-	
-	
-private:
-
-	struct linePair {
-		unsigned long long start;
-		unsigned long long end;
-		linePair(unsigned long long i, unsigned long long j) : start(i), end(j) {}
-	};
-
-	vector<int> processIDS;   //processid
-	vector<linePair*> lines;
-	
-	int driver(linePair*, string, string);
-	int createProcesses(string, string);
-		
-	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, vector<unsigned long long>&);
-	#endif
-
-	bool abort, svg, save;
-	string fastafile, templatefile, namefile, outputDir;
-	int processors, increment, ksize, numSeqs, templateSeqsLength;
-	Chimera* chimera;
-	vector<string> fastaFileNames;
-	vector<string> nameFileNames;
-	vector<string> outputNames;
-};
-
-/***********************************************************/
-
-#endif
-
-