pat's changes to seq.error command

[mothur.git] / slayer.h

diff --git a/slayer.h b/slayer.h
index ea79727561fbfad37dfaf1478276e529b79df22b..33ccc3fda70ad9e6dca595eb626c0bb9e5dedc1c 100644 (file)
--- 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;
                                
 };