X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=slayer.h;h=33ccc3fda70ad9e6dca595eb626c0bb9e5dedc1c;hb=9013e13ecfb2fda3c2664a76f76cc99b8c7fa74c;hp=ea79727561fbfad37dfaf1478276e529b79df22b;hpb=58cc09a375d1e1afceef3b036574ff21394ccc4d;p=mothur.git

diff --git a/slayer.h b/slayer.h
index ea79727..33ccc3f 100644
--- a/slayer.h
+++ b/slayer.h
@@ -64,7 +64,7 @@ class Slayer {
 
 	public:
 		
-		Slayer(int, int, int, float);
+		Slayer(int, int, int, float, int, int);
 		~Slayer() {};
 		
 		string getResults(Sequence*, vector<Sequence*>);
@@ -73,19 +73,21 @@ class Slayer {
 				
 	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);
-		void bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
+		int bootstrapSNPS(vector<snps>, vector<snps>, float&, float&);
 		float snpQA(vector<snps>);
 		float snpQB(vector<snps>);
 		float snpAB(vector<snps>);
+		MothurOut* m;
 				
 };