added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / chimerapintailcommand.h

diff --git a/chimerapintailcommand.h b/chimerapintailcommand.h
new file mode 100644 (file)
index 0000000..0ddfc1c
--- /dev/null
+++ b/chimerapintailcommand.h
@@ -0,0 +1,58 @@
+#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
+
+