X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.h;h=9309c37378d8c08c0fc7e1c270f272a153e555f4;hb=db2df3a6a0e6354a666472ede1de74642cfeb06b;hp=dbdf31650235f5b0d5074923d8495591380ec30b;hpb=7597c66c08bac938fedcacc1f760186bc077b3f1;p=mothur.git

diff --git a/decalc.h b/decalc.h
index dbdf316..9309c37 100644
--- a/decalc.h
+++ b/decalc.h
@@ -27,16 +27,17 @@ class DeCalculator {
 		DeCalculator() {};
 		~DeCalculator() {};
 		
+		set<int> getPos() {  return h;  }
 		void setMask(string m); 
 		void runMask(Sequence*);
-		void trimSeqs(Sequence*, Sequence, map<int, int>&);
+		void trimSeqs(Sequence*, Sequence*, map<int, int>&);
 		vector<float> calcFreq(vector<Sequence*>, string);
 		vector<int> findWindows(Sequence*, int, int, int&, int);
-		vector<float> calcObserved(Sequence*, Sequence, vector<int>, int);
+		vector<float> calcObserved(Sequence*, Sequence*, vector<int>, int);
 		vector<float>  calcExpected(vector<float>, float);
 		vector<float>  findQav(vector<int>, int, vector<float>);  
 		float calcDE(vector<float>, vector<float>);
-		float calcDist(Sequence*, Sequence, int, int);
+		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);