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();
32 string getCitation() { return "Needleman SB, Wunsch CD (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-53. [ for needleman ]\nGotoh O (1982). An improved algorithm for matching biological sequences. J Mol Biol 162: 705-8. [ for gotoh ] \nhttp://www.mothur.org/wiki/Pairwise.seqs"; }
35 void help() { m->mothurOut(getHelpString()); }
43 vector<int> processIDS; //end line, processid
44 vector<distlinePair> lines;
50 void createProcesses(string);
51 int driver(int, int, string, float);
52 int driver(int, int, string, string);
55 int driverMPI(int, int, MPI_File&, float);
56 int driverMPI(int, int, string, unsigned long int&);
57 int driverMPI(int, int, string, unsigned long int&, string);
60 string fastaFileName, align, calc, outputDir, output;
61 float match, misMatch, gapOpen, gapExtend, cutoff;
63 vector<string> fastaFileNames, Estimators;
64 vector<string> outputNames;
66 bool abort, countends, compress;