X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=slayer.h;h=eeefc62392b64cdb0eb5797cba1c994b27058f50;hp=ea79727561fbfad37dfaf1478276e529b79df22b;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=58cc09a375d1e1afceef3b036574ff21394ccc4d

diff --git a/slayer.h b/slayer.h
index ea79727..eeefc62 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;
@@ -64,28 +29,31 @@ class Slayer {
 
 	public:
 		
-		Slayer(int, int, int, float);
+		Slayer(int, int, int, float, int, int, int);
 		~Slayer() {};
 		
-		string getResults(Sequence*, vector<Sequence*>);
+		string getResults(Sequence, vector<Sequence>);
 		vector<data_struct> getOutput()  {	return outputResults;			}
 		
 				
 	private:
 		
-		int windowSize, windowStep, parentFragmentThreshold;
+		int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample, minBS;
 		float divRThreshold; 
 		vector<data_struct>  outputResults;
+		vector< map<int, int> > baseSpots;
+		Sequence myQuery;
 		
-		void verticalFilter(vector<Sequence*>);
+		map<int, int> verticalFilter(Sequence&, Sequence&, Sequence&);
 		float computePercentID(string, string, int, int);
 		
-		vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*);
+		vector<data_struct> runBellerophon(Sequence, Sequence, Sequence, map<int, int>&);
 		vector<snps> getSNPS(string, string, string, int, int);
-		void 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>);
+		MothurOut* m;
 				
 };