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"
18 class AlignCommand : public Command {
30 linePair(int i, int j) : start(i), numSeqs(j) {}
32 vector<int> processIDS; //processid
33 vector<linePair*> lines;
38 int driver(linePair*, string, string);
39 void createProcesses(string, string);
40 void appendAlignFiles(string, string);
41 void appendReportFiles(string, string);
43 string candidateFileName, templateFileName, distanceFileName, search, align;
44 float match, misMatch, gapOpen, gapExtend;
45 int processors, kmerSize;