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);
26 unsigned long int start;
27 unsigned long int end;
28 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
31 vector<int> processIDS; //processid
32 vector<linePair*> lines;
34 int screenNameGroupFile(set<string>);
35 int screenGroupFile(set<string>);
36 int screenAlignReport(set<string>);
38 int driver(linePair*, string, string, string, set<string>&);
39 int createProcesses(string, string, string, set<string>&);
42 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&, set<string>&);
46 string fastafile, namefile, groupfile, alignreport, outputDir;
47 int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors;
48 vector<string> outputNames;