fixed some issues while testing 1.6

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 65a8f46038e53bc79fc24085e9c6a995f85fda6f..dca562a24e549a0a640006b97415e27b804c688a 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -44,7 +44,7 @@ class DeCalculator {
                void setAlignmentLength(int l) {  alignLength = l;  }
                void runMask(Sequence*);
                void trimSeqs(Sequence*, Sequence*, map<int, int>&);
-               vector< vector<float> > removeObviousOutliers(vector< vector<quanMember> >&, int);
+               void removeObviousOutliers(vector< vector<quanMember> >&, int);
                vector<float> calcFreq(vector<Sequence*>, string);
                vector<int> findWindows(Sequence*, int, int, int&, int);
                vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
@@ -53,18 +53,21 @@ class DeCalculator {
                float calcDE(vector<float>, vector<float>);
                float calcDist(Sequence*, Sequence*, int, int);
                float getCoef(vector<float>, vector<float>);
-               vector< vector<quanMember> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int, vector<float>&);
+               vector< vector<quanMember> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
                
                vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
                
+               map<int, int> getMaskMap() { return maskMap; }
+               
        private:
-               vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
+               //vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
                float findAverage(vector<float>);
-               int findLargestContrib(vector<int>);
-               void removeContrib(int, vector<quanMember>&);
+               //int findLargestContrib(vector<int>);
+               //void removeContrib(int, vector<quanMember>&);
                string seqMask;
                set<int> h;
                int alignLength;
+               map<int, int> maskMap;
 
 };