changing command name classify.shared to classifyrf.shared

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
index 875e4a9d93c044339abfb71b8b3d0b009be0995a..eeefc62392b64cdb0eb5797cba1c994b27058f50 100644 (file)
--- 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>);