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 //KNN and Bayesian methods modeled from algorithms in
19 //Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences
20 //into the New Bacterial Taxonomy†
21 //Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1*
22 //Center for Microbial Ecology1 and Department of Microbiology and Molecular Genetics,2 Michigan State University,
23 //East Lansing, Michigan 48824
24 //Received 10 January 2007/Accepted 18 June 2007
28 class ClassifySeqsCommand : public Command {
31 ClassifySeqsCommand(string);
32 ~ClassifySeqsCommand();
40 linePair(int i, int j) : start(i), numSeqs(j) {}
42 vector<int> processIDS; //processid
43 vector<linePair*> lines;
44 vector<string> fastaFileNames;
45 vector<string> namefileNames;
46 map<string, int> nameMap;
47 map<string, int>::iterator itNames;
51 string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir;
52 int processors, kmerSize, numWanted, cutoff, iters;
53 float match, misMatch, gapOpen, gapExtend;
56 int driver(linePair*, string, string, string);
57 void appendTaxFiles(string, string);
58 void createProcesses(string, string, string);
59 string addUnclassifieds(string, int);