working on chimeras

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
index dc13e6daa3f1e4ce9e2340da2cf201c9881a3083..099cb208f1e69ee9f943ea81ee395aba9bbc4efc 100644 (file)
--- a/slayer.h
+++ b/slayer.h
@@ -64,7 +64,7 @@ class Slayer {
 
        public:
                
-               Slayer(int, int, int, float, int);
+               Slayer(int, int, int, float, int, int);
                ~Slayer() {};
                
                string getResults(Sequence*, vector<Sequence*>);
@@ -73,14 +73,15 @@ class Slayer {
                                
        private:
                
-               int windowSize, windowStep, parentFragmentThreshold, iters;
+               int windowSize, windowStep, parentFragmentThreshold, iters, percentSNPSample;
                float divRThreshold; 
                vector<data_struct>  outputResults;
+               vector< map<int, int> > baseSpots;
                
                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&);
                float snpQA(vector<snps>);