working on chimeras

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index dbdf31650235f5b0d5074923d8495591380ec30b..4ce45bf751915dd9e077ce478ae912358e789900 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -27,22 +27,27 @@ class DeCalculator {
                DeCalculator() {};
                ~DeCalculator() {};
                
-               void setMask(string m); 
+               set<int> getPos() {  return h;  }
+               void setMask(string); 
+               void setAlignmentLength(int l) {  alignLength = l;  }
                void runMask(Sequence*);
-               void trimSeqs(Sequence*, Sequence, map<int, int>&);
+               void trimSeqs(Sequence*, Sequence*, map<int, int>&);
+               void removeObviousOutliers(vector< vector<float> >&);
                vector<float> calcFreq(vector<Sequence*>, string);
                vector<int> findWindows(Sequence*, int, int, int&, int);
-               vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);
+               vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
                vector<float>  calcExpected(vector<float>, float);
                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:
+               float findAverage(vector<float> myVector);
                string seqMask;
                set<int> h;
+               int alignLength;
 
 };