changes while testing

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 011993652618dc38294ade4638ad0657238b9377..d6cca182e81937dd5a494d57c2c8221b6039ad45 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -36,17 +36,18 @@ class DeCalculator {
 
        public:
                
-               DeCalculator() {};
+               DeCalculator() { m = MothurOut::getInstance(); }
                ~DeCalculator() {};
                
-               vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int);  //takes querySeq, a reference db and numWanted - returns indexes to closest seqs in db
+               vector<Sequence> findClosest(Sequence, vector<Sequence*>&, vector<Sequence*>&, int, int);  //takes querySeq, a reference db, filteredRefDB, numWanted, minSim 
+               Sequence* findClosest(Sequence*, vector<Sequence*>);
                set<int> getPos() {  return h;  }
                void setMask(string); 
                void setAlignmentLength(int l) {  alignLength = l;  }
                void runMask(Sequence*);
                void trimSeqs(Sequence*, Sequence*, map<int, int>&);
-               map<int, int> trimSeqs(Sequence*, vector<Sequence*>);
-               void removeObviousOutliers(vector< vector<quanMember> >&, int);
+               map<int, int> trimSeqs(Sequence&, vector<Sequence>&);
+               void removeObviousOutliers(vector< vector<float> >&, int);
                vector<float> calcFreq(vector<Sequence*>, string);
                vector<int> findWindows(Sequence*, int, int, int&, int);
                vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
@@ -55,7 +56,7 @@ 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< vector<float> > getQuantiles(vector<Sequence*>, vector<int>, int, vector<float>, int, int, int);
                
                vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
                
@@ -70,6 +71,7 @@ class DeCalculator {
                set<int> h;
                int alignLength;
                map<int, int> maskMap;
+               MothurOut* m;
 
 };