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#ifndef MGCLUSTERCOMMAND_H
#define MGCLUSTERCOMMAND_H
/*
* mgclustercommand.h
* Mothur
*
* Created by westcott on 12/11/09.
* Copyright 2009 Schloss Lab. All rights reserved.
*
*/
#include "command.hpp"
#include "readblast.h"
#include "nameassignment.hpp"
#include "cluster.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "counttable.h"
#include "opticluster.h"
#include "optiblastmatrix.hpp"
/**********************************************************************/
class MGClusterCommand : public Command {
public:
MGClusterCommand(string);
~MGClusterCommand(){}
vector<string> setParameters();
string getCommandName() { return "mgcluster"; }
string getCommandCategory() { return "Clustering"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Handelsman J (2008). A statistical toolbox for metagenomics. BMC Bioinformatics 9: 34. \nhttp://www.mothur.org/wiki/Mgcluster"; }
string getDescription() { return "cluster your sequences into OTUs using a blast file"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
ReadBlast* read;
NameAssignment* nameMap;
Cluster* cluster;
ListVector* list;
ListVector oldList;
CountTable* ct;
RAbundVector rav;
vector<seqDist> overlapMatrix;
vector<string> outputNames;
string blastfile, method, namefile, countfile, overlapFile, distFile, sabundFileName, rabundFileName, listFileName, metric, initialize, tag, fileroot;
ofstream sabundFile, rabundFile, listFile;
double cutoff;
float penalty, adjust, stableMetric;
int precision, length, precisionLength, maxIters;
bool abort, minWanted, hclusterWanted, merge, cutoffSet;
void printData(ListVector*, map<string, int>&, bool&);
ListVector* mergeOPFs(map<string, int>, float);
vector<seqDist> getSeqs(ifstream&);
void createRabund(CountTable*&, ListVector*&, RAbundVector*&);
int runOptiCluster();
int runMothurCluster();
};
/**********************************************************************/
#endif
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