shhhercommand.h

   1 #ifndef SHHHER_H
   2 #define SHHHER_H
   3
   4 /*
   5  *  shhher.h
   6  *  Mothur
   7  *
   8  *  Created by Pat Schloss on 12/27/10.
   9  *  Copyright 2010 Schloss Lab. All rights reserved.
  10  *
  11  */
  12
  13 #include "mothur.h"
  14 #include "command.hpp"
  15 #include "globaldata.hpp"
  16
  17 class ShhherCommand : public Command {
  18
  19 public:
  20         ShhherCommand(string);
  21         ShhherCommand();
  22         ~ShhherCommand();
  23         vector<string> getRequiredParameters();
  24         vector<string> getValidParameters();
  25         vector<string> getRequiredFiles();
  26         map<string, vector<string> > getOutputFiles() { return outputTypes; }
  27         int execute();
  28         void help();
  29
  30 private:
  31         GlobalData* globaldata;
  32
  33         int abort;
  34         map<string, vector<string> > outputTypes;
  35
  36         string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
  37
  38         int processors, maxIters;
  39         float cutoff, sigma, minDelta;
  40
  41         vector<int> nSeqsBreaks;
  42         vector<int> nOTUsBreaks;
  43         vector<double> flowDataPrI;
  44         vector<short> flowDataIntI;
  45         vector<int> lengths;
  46         vector<string> seqNameVector;
  47         vector<double> singleLookUp;
  48         vector<double> jointLookUp;
  49         map<string, int> nameMap;
  50         vector<int> otuData;
  51         vector<int> cumNumSeqs;
  52         vector<int> nSeqsPerOTU;
  53         vector<vector<int> > aaP;       //tMaster->aanP:        each row is a different otu / each col contains the sequence indices
  54         vector<int> seqNumber;          //tMaster->anP:         the sequence id number sorted by OTU
  55         vector<vector<int> > aaI;       //tMaster->aanI:        that are in each otu - can't differentiate between aaP and aaI
  56         vector<int> seqIndex;           //tMaster->anI;         the index that corresponds to seqNumber
  57         vector<double> dist;            //adDist - distance of sequences to centroids
  58         vector<short> change;           //did the centroid sequence change? 0 = no; 1 = yes
  59         vector<int> centroids;          //the representative flowgram for each cluster m
  60         vector<double> weight;
  61         vector<double> singleTau;       //tMaster->adTau:       1-D Tau vector (1xnumSeqs)
  62         vector<short> uniqueFlowgrams;
  63         vector<int> uniqueCount;
  64         vector<int> uniqueLengths;
  65         vector<int> mapSeqToUnique;
  66         vector<int> mapUniqueToSeq;
  67
  68         int numSeqs, numUniques, numOTUs, numFlowCells;
  69
  70         void getSingleLookUp();
  71         void getJointLookUp();
  72         void getFlowData();
  73         void getUniques();
  74         double getProbIntensity(int);
  75         float calcPairwiseDist(int, int);
  76         void flowDistParentFork(string, int, int);
  77
  78         string createDistFile(int);
  79         string createNamesFile();
  80         string cluster(string, string);
  81
  82         void getOTUData(string);
  83         void initPyroCluster();
  84         void fill();
  85         void calcCentroids();
  86         void calcCentroidsDriver(int, int);
  87         double getDistToCentroid(int, int, int);
  88         double getNewWeights();
  89         double getLikelihood();
  90         void checkCentroids();
  91         void calcNewDistances();
  92         void calcNewDistancesParent(int, int);
  93         void calcNewDistancesChild(int, int, vector<int>&, vector<int>&, vector<double>&);
  94
  95
  96         void setOTUs();
  97         void writeQualities(vector<int>);
  98         void writeSequences(vector<int>);
  99         void writeNames(vector<int>);
 100         void writeGroups();
 101         void writeClusters(vector<int>);
 102
 103
 104 #ifdef USE_MPI
 105         string flowDistMPI(int, int);
 106         void calcNewDistancesChildMPI(int, int, vector<int>&);
 107
 108         int pid, ncpus;
 109 #endif
 110
 111 };
 112
 113
 114 #endif
 115