X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=slayer.h;h=eeefc62392b64cdb0eb5797cba1c994b27058f50;hp=875e4a9d93c044339abfb71b8b3d0b009be0995a;hb=615301e57c25e241356a9c2380648d117709458d;hpb=7b80945ef716dd72d00563a5a4d692394f7f84c3

diff --git a/slayer.h b/slayer.h
index 875e4a9..eeefc62 100644
--- a/slayer.h
+++ b/slayer.h
@@ -29,26 +29,27 @@ class Slayer {
 
 	public:
 		
-		Slayer(int, int, int, float, int, int);
+		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, 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*>);
+		map<int, int> verticalFilter(Sequence&, Sequence&, Sequence&);
 		float computePercentID(string, string, int, int);
 		
-		vector<data_struct> runBellerophon(Sequence*, Sequence*, Sequence*, map<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>);