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#ifndef SHHHER_H
#define SHHHER_H
/*
* shhher.h
* Mothur
*
* Created by Pat Schloss on 12/27/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "mothur.h"
#include "command.hpp"
#include "readcolumn.h"
#include "readmatrix.hpp"
#include "rabundvector.hpp"
#include "sabundvector.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
#include "inputdata.h"
#include <cfloat>
//**********************************************************************************************************************
#define NUMBINS 1000
#define HOMOPS 10
#define MIN_COUNT 0.1
#define MIN_WEIGHT 0.1
#define MIN_TAU 0.0001
#define MIN_ITER 10
//**********************************************************************************************************************
class ShhherCommand : public Command {
public:
ShhherCommand(string);
~ShhherCommand() = default;
vector<string> setParameters();
string getCommandName() { return "shhh.flows"; }
string getCommandCategory() { return "Sequence Processing"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "Schloss PD, Gevers D, Westcott SL (2011). Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies. PLoS ONE. 6:e27310.\nQuince C, Lanzen A, Davenport RJ, Turnbaugh PJ (2011). Removing noise from pyrosequenced amplicons. BMC Bioinformatics 12:38.\nQuince C, Lanzén A, Curtis TP, Davenport RJ, Hall N, Head IM, Read LF, Sloan WT (2009). Accurate determination of microbial diversity from 454 pyrosequencing data. Nat. Methods 6:639.\nhttp://www.mothur.org/wiki/Shhh.flows"; }
string getDescription() { return "shhh.flows"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort, large;
string flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName, compositeNamesFileName;
int maxIters, largeSize;
float cutoff, sigma, minDelta;
string flowOrder;
vector<string> outputNames;
vector<double> singleLookUp;
vector<double> jointLookUp;
vector<string> flowFileVector;
vector<string> parseFlowFiles(string);
int driver(vector<string>, string, string);
int getFlowData(string, vector<string>&, vector<int>&, vector<short>&, map<string, int>&, int&);
int getUniques(int, int, vector<short>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<double>&, vector<short>&);
int flowDistParentFork(int, string, int, vector<int>&, vector<int>&, vector<int>&, vector<double>&, vector<short>&);
float calcPairwiseDist(int, int, int, vector<int>&, vector<int>&, vector<double>&, vector<short>&);
int createNamesFile(int, int, string, vector<string>&, vector<int>&, vector<int>&);
int cluster(string, string, string);
int getOTUData(int numSeqs, string, vector<int>&, vector<int>&, vector<int>&, vector<vector<int> >&, vector<vector<int> >&, vector<int>&, vector<int>&,map<string, int>&);
int calcCentroidsDriver(int numOTUs, vector<int>&, vector<int>&, vector<int>&, vector<short>&, vector<int>&, vector<double>&, vector<int>&, vector<short>&, vector<short>&, vector<int>&, int, vector<int>&);
double getDistToCentroid(int, int, int, vector<short>&, vector<short>&, int);
double getNewWeights(int, vector<int>&, vector<int>&, vector<double>&, vector<int>&, vector<double>&);
double getLikelihood(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<double>&, vector<double>&);
int checkCentroids(int, vector<int>&, vector<double>&);
void calcNewDistances(int, int, vector<int>& , vector<double>&,vector<double>& , vector<short>& change, vector<int>&,vector<vector<int> >&, vector<double>&, vector<vector<int> >&, vector<int>&, vector<int>&, vector<short>&, vector<short>&, int, vector<int>&);
int fill(int, vector<int>&, vector<int>&, vector<int>&, vector<int>&, vector<vector<int> >&, vector<vector<int> >&);
void setOTUs(int, int, vector<int>&, vector<int>&, vector<int>&, vector<int>&,
vector<int>&, vector<double>&, vector<double>&, vector<vector<int> >&, vector<vector<int> >&);
void writeQualities(int, int, string, vector<int>, vector<int>&, vector<int>&, vector<double>&, vector<short>&, vector<short>&, vector<int>&, vector<int>&, vector<string>&, vector<int>&, vector<vector<int> >&);
void writeSequences(string, int, int, string, vector<int>, vector<short>&, vector<string>&, vector<vector<int> >&, vector<int>&);
void writeNames(string, int, string, vector<int>, vector<string>&, vector<vector<int> >&, vector<int>&);
void writeGroups(string, string, int, vector<string>&);
void writeClusters(string, int, int, vector<int>, vector<int>&, vector<short>&, vector<string>&, vector<vector<int> >&, vector<int>&, vector<int>&, vector<short>&);
void getSingleLookUp();
void getJointLookUp();
double getProbIntensity(int);
};
//**********************************************************************************************************************
#endif
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