1 #ifndef CLASSIFYSEQSCOMMAND_H
2 #define CLASSIFYSEQSCOMMAND_H
5 * classifyseqscommand.h
8 * Created by westcott on 11/2/09.
9 * Copyright 2009 Schloss Lab. All rights reserved.
14 #include "command.hpp"
15 #include "alignment.hpp"
18 class ClassifySeqsCommand : public Command {
21 ClassifySeqsCommand(string);
22 ~ClassifySeqsCommand();
30 linePair(int i, int j) : start(i), numSeqs(j) {}
32 vector<int> processIDS; //processid
33 vector<linePair*> lines;
37 string fastaFileName, templateFileName, distanceFileName, search, method, taxonomyFileName;
38 int processors, kmerSize, numWanted;
39 float match, misMatch, gapOpen, gapExtend;
42 int driver(linePair*, string);
43 void appendTaxFiles(string, string);
44 void createProcesses(string);