changes while testing

[mothur.git] / pintail.h

diff --git a/pintail.h b/pintail.h
index bae39d7e3d7cb5654ca5e4fd1bfb09119a994758..92c399889c3be0aa0e552fe296612eb336bc8168 100644 (file)
--- a/pintail.h
+++ b/pintail.h
@@ -12,7 +12,9 @@
 
 #include "chimera.h"
 #include "dist.h"
+#include "decalc.h"
 
+/***********************************************************/
 //This class was created using the algorythms described in the 
 // "At Least 1 in 20 16S rRNA Sequence Records Currently Held in the Public Repositories is Estimated To Contain Substantial Anomalies" paper 
 //by Kevin E. Ashelford 1, Nadia A. Chuzhanova 3, John C. Fry 1, Antonia J. Jones 2 and Andrew J. Weightman 1.
@@ -22,56 +24,59 @@
 class Pintail : public Chimera {
        
        public:
-               Pintail(string);        
+               Pintail(string, string, bool, int, string, string, string, int, int, string); //fastafile, templatefile, filter, processors, mask, conservation, quantile, window, increment, outputDir)        
                ~Pintail();
                
-               void getChimeras();
-               void print(ostream&);
+               int getChimeras(Sequence*);
+               Sequence print(ostream&, ostream&);
+               
+               void setCons(string c)          { consfile = c;  }
+               void setQuantiles(string q) { quanfile = q;  }
                
+               #ifdef USE_MPI
+               Sequence print(MPI_File&, MPI_File&);
+               #endif
                
        private:
        
-               struct linePair {
-                       int start;
-                       int end;
-                       linePair(int i, int j) : start(i), end(j) {}
-               };
-
-       
-               Dist* distCalculator;
-               string fastafile;
-               int iters;
-               vector<linePair*> lines;
-               vector<Sequence*> querySeqs;
-               vector<Sequence*> templateSeqs;
+               Dist* distcalculator;
+               DeCalculator* decalc;
+               int iters, window, increment, processors;
+               string fastafile, quanfile, consfile;
                
-               map<Sequence*, Sequence*> bestfit;  //maps a query sequence to its most similiar sequence in the template
-               map<Sequence*, Sequence*>::iterator itBest;
+               vector<linePair*> templateLines;
+               Sequence* querySeq;
+                               
+               Sequence* bestfit;  //closest match to query in template
                
-               map<Sequence*, vector<float> > obsDistance;  //maps a query sequence to its observed distance at each window
-               map<Sequence*, vector<float> > expectedDistance;  //maps a query sequence to its expected distance at each window
-               map<Sequence*, vector<float> >::iterator itObsDist;
-               map<Sequence*, vector<float> >::iterator itExpDist;
+               vector<float>  obsDistance;  //obsDistance is the vector of observed distances for query 
+               vector<float>  expectedDistance;  //expectedDistance is the vector of expected distances for query
+               float deviation;  //deviation is the percentage of mismatched pairs over the whole seq between query and its best match.
+               vector<int>  windowsForeachQuery;  // windowsForeachQuery is a vector containing the starting spot in query aligned sequence for each window.
+                                                                               //this is needed so you can move by bases and not just spots in the alignment
+                                                                               
+               int  windowSizes;                       //windowSizes = window size of query
+               vector<int> windowSizesTemplate;    //windowSizesTemplate[0] = window size of templateSeqs[0]
                
-               vector<float> averageProbability;                       //Qav
-               map<Sequence*, float> seqCoef;                          //maps a sequence to its coefficient
-               map<Sequence*, float> DE;                                       //maps a sequence to its deviation
-               map<Sequence*, float>::iterator itCoef;         
+               map<int, int> trimmed;    //trimmed = start and stop of trimmed sequences for query
+               map<int, int>::iterator it;
                
-               vector<Sequence*> readSeqs(string);
-               vector<float> findQav(vector<float>);
-               vector<float> calcFreq(vector<Sequence*>);
-               map<Sequence*, float> getCoef(vector<float>);
+               vector<float>  Qav;     //Qav is the vector of average variablility for query
+               float  seqCoef;         //seqCoef is the coeff for query
+               float DE;                       //DE is the deviaation for query
+               vector<float> probabilityProfile;
+               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...
+               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...
+               set<int>  h;
+               string mergedFilterString;
                
-               void findPairs(int, int);
-               void calcObserved(int, int);
-               void calcExpected(int, int);
-               void calcDE(int, int);
-       
-               void createProcessesPairs();
-               void createProcessesObserved();
-               void createProcessesExpected();
-               void createProcessesDE();
+               vector< vector<float> > readQuantiles();
+               vector<float> readFreq();
+               Sequence* findPairs(Sequence*);
+                       
+               void createProcessesQuan();
+               int doPrep();
+               void printQuanFile(string, string);
                
 };