chimera.seqs pintail is working.

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 4ce45bf751915dd9e077ce478ae912358e789900..65a8f46038e53bc79fc24085e9c6a995f85fda6f 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -20,6 +20,18 @@
 
 /***********************************************************************/
 
+//this structure is necessary to determine the sequence that contributed to the outliers when we remove them
+//this way we can remove all scores that are contributed by outlier sequences.
+struct quanMember {
+       float score;
+       int member1;
+       int member2;
+       quanMember (float s, int m, int n) : score(s), member1(m),  member2(n) {}
+       quanMember() {}
+       
+};
+               
+//********************************************************************************************************************
 class DeCalculator {
 
        public:
@@ -32,7 +44,7 @@ class DeCalculator {
                void setAlignmentLength(int l) {  alignLength = l;  }
                void runMask(Sequence*);
                void trimSeqs(Sequence*, Sequence*, map<int, int>&);
-               void removeObviousOutliers(vector< vector<float> >&);
+               vector< vector<float> > 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);
@@ -41,10 +53,15 @@ class DeCalculator {
                float calcDE(vector<float>, vector<float>);
                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);
+               vector< vector<quanMember> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int, vector<float>&);
+               
+               vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
                
        private:
-               float findAverage(vector<float> myVector);
+               vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
+               float findAverage(vector<float>);
+               int findLargestContrib(vector<int>);
+               void removeContrib(int, vector<quanMember>&);
                string seqMask;
                set<int> h;
                int alignLength;