X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimeraccodecommand.h;fp=chimeraccodecommand.h;h=0000000000000000000000000000000000000000;hp=5b8092b6f7075111c7fa8c5c58caf14ef3ebaeca;hb=4a877efa127e56e81a21f53cfdbbfd3bfbe8c4ff;hpb=a6cf29fa4dac0909c7582cb1094151d34093ee76

diff --git a/chimeraccodecommand.h b/chimeraccodecommand.h
deleted file mode 100644
index 5b8092b..0000000
--- a/chimeraccodecommand.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef CHIMERACCODECOMMAND_H
-#define CHIMERACCODECOMMAND_H
-
-/*
- *  chimeraccodecommand.h
- *  Mothur
- *
- *  Created by westcott on 3/30/10.
- *  Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "mothur.h"
-#include "command.hpp"
-#include "chimera.h"
-
-
-/***********************************************************/
-
-class ChimeraCcodeCommand : public Command {
-public:
-	ChimeraCcodeCommand(string);
-	ChimeraCcodeCommand();
-	~ChimeraCcodeCommand(){}
-	
-	vector<string> setParameters();
-	string getCommandName()			{ return "chimera.ccode";		}
-	string getCommandCategory()		{ return "Sequence Processing"; }
-	string getHelpString();	
-	string getCitation() { return "Gonzalez JM, Zimmermann J, Saiz-Jimenez C (2005). Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21: 333-7. \nhttp://www.mothur.org/wiki/Chimera.ccode"; }
-	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, string);
-	int createProcesses(string, string, string);
-	
-	#ifdef USE_MPI
-	int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&);
-	#endif
-
-	bool abort, filter, save;
-	string fastafile, templatefile, outputDir, maskfile;
-	int processors, window, numwanted, numSeqs, templateSeqsLength;
-	Chimera* chimera;
-	vector<string> fastaFileNames;
-	vector<string> outputNames;
-};
-
-/***********************************************************/
-
-#endif
-