X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=slayer.h;h=eeefc62392b64cdb0eb5797cba1c994b27058f50;hp=e898989b17fa73020a367fef11fa1d3b0f688565;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=05a0195e07c42c996592ee1c8abb63adedb7f493

diff --git a/slayer.h b/slayer.h
index e898989..eeefc62 100644
--- a/slayer.h
+++ b/slayer.h
@@ -11,18 +11,17 @@
 
  
 #include "sequence.hpp"
+#include "chimera.h"
 
 /***********************************************************************/
 //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 snps { 
+	char queryChar;
+	char parentAChar;
+	char parentBChar;
 };
+
 /***********************************************************************/
 
 
@@ -30,24 +29,31 @@ class Slayer {
 
 	public:
 		
-		Slayer(int, int, int, float);
+		Slayer(int, int, int, float, int, 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, 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);
+		int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&, int);
+		float snpQA(vector<snps>);
+		float snpQB(vector<snps>);
+		float snpAB(vector<snps>);
+		MothurOut* m;
 				
 };