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();
38 unsigned long int start;
39 unsigned long int end;
40 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
43 vector<int> processIDS; //processid
44 vector<linePair*> lines;
45 vector<string> fastaFileNames;
46 vector<string> namefileNames;
47 vector<string> groupfileNames;
48 map<string, vector<string> > nameMap;
49 map<string, vector<string> >::iterator itNames;
53 string fastaFileName, templateFileName, distanceFileName, namefile, search, method, taxonomyFileName, outputDir, groupfile;
54 int processors, kmerSize, numWanted, cutoff, iters;
55 float match, misMatch, gapOpen, gapExtend;
58 int driver(linePair*, string, string, string);
59 void appendTaxFiles(string, string);
60 int createProcesses(string, string, string);
61 string addUnclassifieds(string, int);
63 int MPIReadNamesFile(string);
65 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);