X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerapintailcommand.h;fp=chimerapintailcommand.h;h=0ddfc1c6229758991e74b0def36a778182a74da6;hb=fdc1f6eaf544f695fc1511f24bddd7e6069c33ba;hp=0000000000000000000000000000000000000000;hpb=aba5f8811829037b0a3004ef33f0ad4ed5e5fcf8;p=mothur.git

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
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+++ b/chimerapintailcommand.h
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+#ifndef CHIMERAPINTAILCOMMAND_H
+#define CHIMERAPINTAILCOMMAND_H
+
+/*
+ *  chimerapintailcommand.h
+ *  Mothur
+ *
+ *  Created by westcott on 4/1/10.
+ *  Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "mothur.h"
+#include "command.hpp"
+#include "chimera.h"
+
+
+/***********************************************************/
+
+class ChimeraPintailCommand : public Command {
+
+public:
+
+	ChimeraPintailCommand(string);
+	~ChimeraPintailCommand();
+	int execute();
+	void help();
+	
+private:
+
+	struct linePair {
+		int start;
+		int numSeqs;
+		linePair(long int i, int j) : start(i), numSeqs(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<long>&);
+	#endif
+
+	bool abort, filter, MPIWroteAccnos;
+	string fastafile, templatefile, consfile, quanfile, maskfile, outputDir;
+	int processors, window, increment, numSeqs, templateSeqsLength;
+	Chimera* chimera;
+	
+	
+};
+
+/***********************************************************/
+
+#endif
+
+