X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=pintail.h;h=516c682da3d9123cc07f9e6e143dd7fdc7d519c4;hb=a5afca18544555fba2d9c3670ad1f8574916b0a0;hp=181be2ca4410c32a4ab0222adbe8e5e2c138e1de;hpb=8c3489da5da7fb7274f34bfa091c54aa496e75bd;p=mothur.git

diff --git a/pintail.h b/pintail.h
index 181be2c..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;
@@ -77,7 +71,6 @@ class Pintail : public Chimera {
 		
 		
 		vector<float> readFreq();
-		vector< vector<float> > readQuantiles();
 		vector<Sequence*> findPairs(int, int);
 			
 		void createProcessesSpots();
@@ -85,8 +78,6 @@ class Pintail : public Chimera {
 		void createProcesses();
 		void createProcessesQuan();
 		
-		vector<float> makeCompliant;  //used by decalc->getQuantiles so pintail and mallard can use same function, it contains the highest de value for each seq in the template
-		
 };
 
 /***********************************************************/