X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.h;h=da663e80f786d1a98b646fe856bbe32522dd2c42;hb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;hp=da0f96cd72b69acf3350a1565f66e7586644ff12;hpb=f7fbd74ffedcf62217109c22e828453eaefa1458;p=mothur.git

diff --git a/decalc.h b/decalc.h
index da0f96c..da663e8 100644
--- a/decalc.h
+++ b/decalc.h
@@ -36,14 +36,17 @@ class DeCalculator {
 
 	public:
 		
-		DeCalculator() {};
+		DeCalculator() { m = MothurOut::getInstance(); }
 		~DeCalculator() {};
 		
+		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>&);
+		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);
@@ -57,6 +60,8 @@ 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 +70,8 @@ class DeCalculator {
 		string seqMask;
 		set<int> h;
 		int alignLength;
+		map<int, int> maskMap;
+		MothurOut* m;
 
 };