X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.h;fp=chimeracheckcommand.h;h=918b4e5e9bf8aa4a16a1e0ba0716e09753a29cea;hb=0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc;hp=0000000000000000000000000000000000000000;hpb=1b73ff67c83892a025e597dabd9df6fe7b58206a;p=mothur.git

diff --git a/chimeracheckcommand.h b/chimeracheckcommand.h
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+++ b/chimeracheckcommand.h
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+#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
+
+