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[mothur.git] / chimeracheckcommand.h

diff --git a/chimeracheckcommand.h 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
+
+