1 #ifndef PAIRWISESEQSCOMMAND_H
2 #define PAIRWISESEQSCOMMAND_H
5 * pairwiseseqscommand.h
8 * Created by westcott on 10/20/10.
9 * Copyright 2010 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "database.hpp"
16 #include "alignment.hpp"
17 #include "validcalculator.h"
19 #include "sequencedb.h"
21 class PairwiseSeqsCommand : public Command {
24 PairwiseSeqsCommand(string);
25 PairwiseSeqsCommand();
26 ~PairwiseSeqsCommand() {}
28 vector<string> setParameters();
29 string getCommandName() { return "pairwise.seqs"; }
30 string getCommandCategory() { return "Sequence Processing"; }
31 string getHelpString();
34 void help() { m->mothurOut(getHelpString()); }
42 vector<int> processIDS; //end line, processid
43 vector<distlinePair> lines;
49 void createProcesses(string);
50 int driver(int, int, string, float);
51 int driver(int, int, string, string);
54 int driverMPI(int, int, MPI_File&, float);
55 int driverMPI(int, int, string, unsigned long int&);
56 int driverMPI(int, int, string, unsigned long int&, string);
59 string fastaFileName, align, calc, outputDir, output;
60 float match, misMatch, gapOpen, gapExtend, cutoff;
62 vector<string> fastaFileNames, Estimators;
63 vector<string> outputNames;
65 bool abort, countends, compress;