X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=pintail.h;h=92c399889c3be0aa0e552fe296612eb336bc8168;hp=797c99e1543ace2df4a142015a17fe56eaf4f033;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=3abb236c602eb168ee112f080b563ebe2c705029

diff --git a/pintail.h b/pintail.h
index 797c99e..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.
@@ -22,64 +24,59 @@
 class Pintail : public Chimera {
 	
 	public:
-		Pintail(string, 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 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;
-		int iters;
-		string fastafile, templateFile, consfile;
-		vector<linePair*> lines;
-		vector<Sequence*> querySeqs;
-		vector<Sequence*> templateSeqs;
+		DeCalculator* decalc;
+		int iters, window, increment, processors;
+		string fastafile, quanfile, consfile;
 		
-		vector<Sequence> bestfit;  //bestfit[0] matches queryseqs[0]...
+		vector<linePair*> templateLines;
+		Sequence* querySeq;
+				
+		Sequence* bestfit;  //closest match to query in template
 		
-		vector< vector<float> > obsDistance;  //obsDistance[0] is the vector of observed distances for queryseqs[0]... 
-		vector< vector<float> > expectedDistance;  //expectedDistance[0] is the vector of expected distances for queryseqs[0]... 
-		vector<float> deviation;  //deviation[0] is the percentage of mismatched pairs over the whole seq between querySeqs[0] and its best match.
-		vector< vector<int> > windows;  // windows[0] is a vector containing the starting spot in queryseqs[0] aligned sequence for each window.
+		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
-		vector< map<int, int> >  trim;  //trim[0] is the start and end position of trimmed querySeqs[0].  Used to find the variability over each sequence window.
 										
-		vector<int> windowSizes;    //windowSizes[0] = window size of querySeqs[0]
+		int  windowSizes;			//windowSizes = window size of query
+		vector<int> windowSizesTemplate;    //windowSizesTemplate[0] = window size of templateSeqs[0]
 		
-		vector< vector<float> > Qav;	//Qav[0] is the vector of average variablility for queryseqs[0]... 
-		vector<float>  seqCoef;				//seqCoef[0] is the coeff for queryseqs[0]...
-		vector<float> DE;					//DE[0] is the deviaation for queryseqs[0]...
+		map<int, int> trimmed;    //trimmed = start and stop of trimmed sequences for query
+		map<int, int>::iterator it;
+		
+		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;
 		
-		vector<Sequence*> readSeqs(string);
-		void trimSeqs(Sequence*, Sequence&, int);
+		vector< vector<float> > readQuantiles();
 		vector<float> readFreq();
-		vector< vector<float> > findQav(int, int);  
-		vector<float> calcFreq(vector<Sequence*>);
-		vector<float> getCoef(int, int);
-		
-		vector<Sequence> findPairs(int, int);
-		vector< vector<int> > findWindows(int, int);
-		vector< vector<float> > calcObserved(int, int);
-		vector< vector<float> > calcExpected(int, int);
-		vector<float> calcDE(int, int);
-		vector<float> calcDist(int, int);
-	
-		void createProcessesSpots();
-		void createProcesses();
-		
-		
+		Sequence* findPairs(Sequence*);
+			
+		void createProcessesQuan();
+		int doPrep();
+		void printQuanFile(string, string);
 		
 };