added parse.list command

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 5f0a82025c557a75c3adc4715526fa17bd5fe5a5..48a72bb9cc10f6387694bee21d5265c6f12e043d 100644 (file)
--- a/decalc.h
+++ b/decalc.h
@@ -39,13 +39,14 @@ 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
+               vector<Sequence*> findClosest(Sequence*, vector<Sequence*>, int&, vector<int>&);  //takes querySeq, a reference db, numWanted and indexes 
+               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>&);
-               void trimSeqs(Sequence*, vector<Sequence*>);
+               map<int, int> trimSeqs(Sequence*, vector<Sequence*>);
                void removeObviousOutliers(vector< vector<quanMember> >&, int);
                vector<float> calcFreq(vector<Sequence*>, string);
                vector<int> findWindows(Sequence*, int, int, int&, int);