started adding chimeraslayer method and fixed minor bug in treegroupscommand deconstr...

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index da0f96cd72b69acf3350a1565f66e7586644ff12..5f0a82025c557a75c3adc4715526fa17bd5fe5a5 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -39,11 +39,13 @@ class DeCalculator {
                DeCalculator() {};
                ~DeCalculator() {};
                
+               vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int);  //takes querySeq, a reference db and numWanted - returns indexes to closest seqs in db
                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*, vector<Sequence*>);
                void removeObviousOutliers(vector< vector<quanMember> >&, int);
                vector<float> calcFreq(vector<Sequence*>, string);
                vector<int> findWindows(Sequence*, int, int, int&, int);
@@ -57,6 +59,8 @@ class DeCalculator {
                
                vector<int> returnObviousOutliers(vector< vector<quanMember> >, int);
                
+               map<int, int> getMaskMap() { return maskMap; }
+               
        private:
                //vector<quanMember> sortContrib(map<quanMember*, float>);  //used by mallard
                float findAverage(vector<float>);
@@ -65,6 +69,7 @@ class DeCalculator {
                string seqMask;
                set<int> h;
                int alignLength;
+               map<int, int> maskMap;
 
 };