8 * Created by Sarah Westcott on 5/15/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "command.hpp"
15 #include "database.hpp"
16 #include "alignment.hpp"
17 #include "alignmentdb.h"
19 class AlignCommand : public Command {
31 linePair(long int i, int j) : start(i), numSeqs(j) {}
33 vector<int> processIDS; //processid
34 vector<linePair*> lines;
36 AlignmentDB* templateDB;
39 int driver(linePair*, string, string, string, string);
40 void createProcesses(string, string, string, string);
41 void appendAlignFiles(string, string);
42 void appendReportFiles(string, string);
44 string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
45 float match, misMatch, gapOpen, gapExtend, threshold;
46 int processors, kmerSize;
47 vector<string> candidateFileNames;