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#ifndef CLASSIFYSEQSCOMMAND_H
#define CLASSIFYSEQSCOMMAND_H
/*
* classifyseqscommand.h
* Mothur
*
* Created by westcott on 11/2/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "classify.h"
#include "sequence.hpp"
#include "bayesian.h"
#include "phylotree.h"
#include "phylosummary.h"
#include "knn.h"
#include "kmertree.h"
#include "aligntree.h"
//KNN and Wang methods modeled from algorithms in
//Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences
//into the New Bacterial Taxonomy†
//Qiong Wang,1 George M. Garrity,1,2 James M. Tiedje,1,2 and James R. Cole1*
//Center for Microbial Ecology1 and Department of Microbiology and Molecular Genetics,2 Michigan State University,
//East Lansing, Michigan 48824
//Received 10 January 2007/Accepted 18 June 2007
class ClassifySeqsCommand : public Command {
public:
ClassifySeqsCommand(string);
~ClassifySeqsCommand();
vector<string> setParameters();
string getCommandName() { return "classify.seqs"; }
string getCommandCategory() { return "Phylotype Analysis"; }
string getCommonQuestions();
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Wang Q, Garrity GM, Tiedje JM, Cole JR (2007). Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73: 5261-7. [ for Bayesian classifier ] \nAltschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402. [ for BLAST ] \nDeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006). Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72: 5069-72. [ for kmer ] \nhttp://www.mothur.org/wiki/Classify.seqs"; }
string getDescription() { return "classify sequences"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
vector<string> outputNames;
Classify* classify;
string fastafile, templateFileName, countfile, distanceFileName, namefile, search, method, taxonomyFileName, groupfile, output;
int processors, kmerSize, numWanted, cutoff, iters, printlevel;
float match, misMatch, gapOpen, gapExtend;
bool abort, probs, save, flip, hasName, hasCount, writeShortcuts, relabund;
int createProcesses(string, string, string, string);
};
/**************************************************************************************************/
#endif
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