X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slayer.h;h=33ccc3fda70ad9e6dca595eb626c0bb9e5dedc1c;hb=3b137af694d322b7162e97275c070c41b42597a3;hp=e898989b17fa73020a367fef11fa1d3b0f688565;hpb=05a0195e07c42c996592ee1c8abb63adedb7f493;p=mothur.git

diff --git a/slayer.h b/slayer.h
index e898989..33ccc3f 100644
--- a/slayer.h
+++ b/slayer.h
@@ -15,39 +15,79 @@
 /***********************************************************************/
 //This class was modeled after the chimeraSlayer written by the Broad Institute
 /***********************************************************************/
-struct data_struct { //not right needs work...
-	int regionStart;
-	int regionEnd;
-	string parent;
-	float queryToParent;
-	float queryToParentLocal;
-	float divR;
+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;
+	char parentBChar;
+};
+
+/***********************************************************************/
 
 
 class Slayer {
 
 	public:
 		
-		Slayer(int, int, int, float);
+		Slayer(int, int, int, float, int, int);
 		~Slayer() {};
 		
-		void getResults(Sequence*, vector<Sequence*>);
-		//float getPercentID() {	return percentIdenticalQueryChimera;	}
-		//vector<results> getOutput()  {	return outputResults;			}
+		string getResults(Sequence*, vector<Sequence*>);
+		vector<data_struct> getOutput()  {	return outputResults;			}
 		
 				
 	private:
 		
-		int windowSize, windowStep, parentFragmentThreshold;
+		int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample;
 		float divRThreshold; 
+		vector<data_struct>  outputResults;
+		vector< map<int, int> > baseSpots;
 		
-		void verticalFilter(vector<Sequence*>);
+		map<int, int> verticalFilter(vector<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);
+		int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
+		float snpQA(vector<snps>);
+		float snpQB(vector<snps>);
+		float snpAB(vector<snps>);
+		MothurOut* m;
 				
 };