X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pintail.h;h=92c399889c3be0aa0e552fe296612eb336bc8168;hp=7c0f81bca5659a0f3fa56357dd70fe5498570334;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=0f297d3c211acbdfd4d941ef193a6702c5046dd1

diff --git a/pintail.h b/pintail.h
index 7c0f81b..92c3998 100644
--- 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);
 		
 };