X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pintail.h;h=516c682da3d9123cc07f9e6e143dd7fdc7d519c4;hb=a5afca18544555fba2d9c3670ad1f8574916b0a0;hp=2e841475c79f9382fff32314a3a46577696ddfc3;hpb=db2df3a6a0e6354a666472ede1de74642cfeb06b;p=mothur.git

diff --git a/pintail.h b/pintail.h
index 2e84147..516c682 100644
--- a/pintail.h
+++ b/pintail.h
@@ -14,6 +14,7 @@
 #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.
@@ -26,7 +27,7 @@ class Pintail : public Chimera {
 		Pintail(string, string);	
 		~Pintail();
 		
-		void getChimeras();
+		int getChimeras();
 		void print(ostream&);
 		
 		void setCons(string c)		{ consfile = c;  }
@@ -35,17 +36,10 @@ class Pintail : public Chimera {
 		
 	private:
 	
-		struct linePair {
-			int start;
-			int end;
-			linePair(int i, int j) : start(i), end(j) {}
-			linePair(){}
-		};
-
 		Dist* distcalculator;
 		DeCalculator* decalc;
 		int iters;
-		string fastafile, templateFile, consfile, quanfile;
+		string fastafile, templateFile, consfile;
 		
 		
 		vector<linePair*> lines;
@@ -72,11 +66,11 @@ class Pintail : public Chimera {
 		vector<float> DE;					//DE[0] is the deviaation for queryseqs[0]...
 		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<quanMember> > 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...
 		vector< set<int> > h;
 		
 		
 		vector<float> readFreq();
-		vector< vector<float> > readQuantiles();
 		vector<Sequence*> findPairs(int, int);
 			
 		void createProcessesSpots();
@@ -84,8 +78,6 @@ class Pintail : public Chimera {
 		void createProcesses();
 		void createProcessesQuan();
 		
-		
-		
 };
 
 /***********************************************************/