pintail.h

   1 #ifndef PINTAIL_H
   2 #define PINTAIL_H
   3
   4 /*
   5  *  pintail.h
   6  *  Mothur
   7  *
   8  *  Created by Sarah Westcott on 7/9/09.
   9  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
  10  *
  11  */
  12
  13 #include "chimera.h"
  14 #include "dist.h"
  15 #include "decalc.h"
  16
  17 /***********************************************************/
  18 //This class was created using the algorythms described in the
  19 // "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper
  20 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
  21
  22 /***********************************************************/
  23
  24 class Pintail : public Chimera {
  25
  26         public:
  27                 Pintail(string, string, bool, int, string, string, string, int, int, string); //fastafile, templatefile, filter, processors, mask, conservation, quantile, window, increment, outputDir)
  28                 ~Pintail();
  29
  30                 int getChimeras(Sequence*);
  31                 Sequence print(ostream&, ostream&);
  32
  33                 void setCons(string c)          { consfile = c;  }
  34                 void setQuantiles(string q) { quanfile = q;  }
  35
  36                 #ifdef USE_MPI
  37                 Sequence print(MPI_File&, MPI_File&);
  38                 #endif
  39
  40         private:
  41
  42                 Dist* distcalculator;
  43                 DeCalculator* decalc;
  44                 int iters, window, increment, processors;
  45                 string fastafile, quanfile, consfile;
  46
  47                 vector<linePair*> templateLines;
  48                 Sequence* querySeq;
  49
  50                 Sequence* bestfit;  //closest match to query in template
  51
  52                 vector<float>  obsDistance;  //obsDistance is the vector of observed distances for query
  53                 vector<float>  expectedDistance;  //expectedDistance is the vector of expected distances for query
  54                 float deviation;  //deviation is the percentage of mismatched pairs over the whole seq between query and its best match.
  55                 vector<int>  windowsForeachQuery;  // windowsForeachQuery is a vector containing the starting spot in query aligned sequence for each window.
  56                                                                                 //this is needed so you can move by bases and not just spots in the alignment
  57
  58                 int  windowSizes;                       //windowSizes = window size of query
  59                 vector<int> windowSizesTemplate;    //windowSizesTemplate[0] = window size of templateSeqs[0]
  60
  61                 map<int, int> trimmed;    //trimmed = start and stop of trimmed sequences for query
  62                 map<int, int>::iterator it;
  63
  64                 vector<float>  Qav;     //Qav is the vector of average variablility for query
  65                 float  seqCoef;         //seqCoef is the coeff for query
  66                 float DE;                       //DE is the deviaation for query
  67                 vector<float> probabilityProfile;
  68                 vector< vector<float> > quantiles;  //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...
  69                 vector< vector<float> > quantilesMembers;  //quantiles[0] is the vector of deviations with ceiling score of 1, quantiles[1] is the vector of deviations with ceiling score of 2...
  70                 set<int>  h;
  71                 string mergedFilterString;
  72
  73                 vector< vector<float> > readQuantiles();
  74                 vector<float> readFreq();
  75                 Sequence* findPairs(Sequence*);
  76
  77                 void createProcessesQuan();
  78                 int doPrep();
  79                 void printQuanFile(string, string);
  80
  81 };
  82
  83 /***********************************************************/
  84
  85 #endif
  86