working on chimeras

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 5818539dd8db0c94f19c62bfa942eb499368149b..9309c37378d8c08c0fc7e1c270f272a153e555f4 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -23,22 +23,27 @@
 class DeCalculator {
 
        public:
-       
-               void trimSeqs(Sequence*, Sequence, map<int, int>&);
-               vector<float> readFreq();
-               vector<float> calcFreq(vector<Sequence*>);
                
-               vector<Sequence> findPairs(int, int);
-               vector<int> findWindows(Sequence*, int, int, int&);
-               vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);
+               DeCalculator() {};
+               ~DeCalculator() {};
+               
+               set<int> getPos() {  return h;  }
+               void setMask(string m); 
+               void runMask(Sequence*);
+               void trimSeqs(Sequence*, Sequence*, map<int, int>&);
+               vector<float> calcFreq(vector<Sequence*>, string);
+               vector<int> findWindows(Sequence*, int, int, int&, int);
+               vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
                vector<float>  calcExpected(vector<float>, float);
-               vector<float>  findQav(vector<int>, int);  
+               vector<float>  findQav(vector<int>, int, vector<float>);  
                float calcDE(vector<float>, vector<float>);
-               float calcDist(Sequence*, Sequence, int, int);
+               float calcDist(Sequence*, Sequence*, int, int);
                float getCoef(vector<float>, vector<float>);
+               vector< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
                
        private:
-
+               string seqMask;
+               set<int> h;
 
 };