X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=decalc.h;h=4ce45bf751915dd9e077ce478ae912358e789900;hb=fe346922fe0af5b1a025beacb211078d37598fd4;hp=1579d86cb8950c2cbbc857407233e1014283344f;hpb=143ce9d26deb936202317b52f6af473542c7df78;p=mothur.git

diff --git a/decalc.h b/decalc.h
index 1579d86..4ce45bf 100644
--- a/decalc.h
+++ b/decalc.h
@@ -28,7 +28,8 @@ class DeCalculator {
 		~DeCalculator() {};
 		
 		set<int> getPos() {  return h;  }
-		void setMask(string m); 
+		void setMask(string); 
+		void setAlignmentLength(int l) {  alignLength = l;  }
 		void runMask(Sequence*);
 		void trimSeqs(Sequence*, Sequence*, map<int, int>&);
 		void removeObviousOutliers(vector< vector<float> >&);
@@ -46,6 +47,7 @@ class DeCalculator {
 		float findAverage(vector<float> myVector);
 		string seqMask;
 		set<int> h;
+		int alignLength;
 
 };