working on chimeras

[mothur.git] / decalc.h

diff --git a/decalc.h b/decalc.h
index 1579d86cb8950c2cbbc857407233e1014283344f..4ce45bf751915dd9e077ce478ae912358e789900 100644 (file)
--- 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;
 
 };