X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slayer.h;h=107b02785fffb395662508dc8875e49013103b47;hb=47af4126c6ece121172cd486c1ca7eeb1ccae2de;hp=33ccc3fda70ad9e6dca595eb626c0bb9e5dedc1c;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/slayer.h b/slayer.h
index 33ccc3f..107b027 100644
--- a/slayer.h
+++ b/slayer.h
@@ -11,46 +11,11 @@
 
  
 #include "sequence.hpp"
+#include "chimera.h"
 
 /***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
-struct data_struct { //this is crazy big...but follow original.
-	float divr_qla_qrb;
-	float divr_qlb_qra;
-	float qla_qrb;
-	float qlb_qra;
-	float qla;
-	float qrb;
-	float ab; 
-	float qa;
-	float qb; 
-	float lab; 
-	float rab; 
-	float qra; 
-	float qlb; 
-	int winLStart;
-	int winLEnd; 
-	int winRStart; 
-	int winREnd; 
-	Sequence querySeq; 
-	Sequence parentA;
-	Sequence parentB;
-	float bsa;
-	float bsb;
-	float bsMax;
-	float chimeraMax;
-	
-};
-/***********************************************************************/
-//sorts lowest to highest first by bsMax, then if tie by chimeraMax
-inline bool compareDataStruct(data_struct left, data_struct right){
-	if (left.bsMax < right.bsMax) { return true; }
-	else if (left.bsMax == right.bsMax) {
-		return (left.chimeraMax < right.chimeraMax);
-	}else { return false;	}
-} 
-/***********************************************************************/
 struct snps { 
 	char queryChar;
 	char parentAChar;
@@ -64,7 +29,7 @@ class Slayer {
 
 	public:
 		
-		Slayer(int, int, int, float, int, int);
+		Slayer(int, int, int, float, int, int, int);
 		~Slayer() {};
 		
 		string getResults(Sequence*, vector<Sequence*>);
@@ -73,17 +38,18 @@ class Slayer {
 				
 	private:
 		
-		int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample;
+		int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample, minBS;
 		float divRThreshold; 
 		vector<data_struct>  outputResults;
 		vector< map<int, int> > baseSpots;
+		Sequence myQuery;
 		
 		map<int, int> verticalFilter(vector<Sequence*>);
 		float computePercentID(string, string, int, int);
 		
 		vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*, map<int, int>&);
 		vector<snps> getSNPS(string, string, string, int, int);
-		int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
+		int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&, int);
 		float snpQA(vector<snps>);
 		float snpQB(vector<snps>);
 		float snpAB(vector<snps>);