1 #ifndef SCREENSEQSCOMMAND_H
2 #define SCREENSEQSCOMMAND_H
8 * Created by Pat Schloss on 6/3/09.
9 * Copyright 2009 Patrick D. Schloss. All rights reserved.
13 #include "command.hpp"
15 class ScreenSeqsCommand : public Command {
18 ScreenSeqsCommand(string);
28 linePair(long int i, int j) : start(i), numSeqs(j) {}
30 vector<int> processIDS; //processid
31 vector<linePair*> lines;
33 int screenNameGroupFile(set<string>);
34 int screenGroupFile(set<string>);
35 int screenAlignReport(set<string>);
37 int driver(linePair*, string, string, string, string, set<string>&);
38 int createProcesses(string, string, string, string, set<string>&);
41 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<long>&, set<string>&);
45 string fastafile, namefile, groupfile, alignreport, outputDir;
46 int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
47 vector<string> outputNames;