JAL-34 JAL-4366 add a tolerance - 90% of one alignment should map to the other

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 020ffda..c7c618f 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1416,8 +1416,9 @@ public class AlignmentUtils
         mappable++;
       }
     }
-    if (mappable == al1.getHeight())
+    if (mappable>0 && mappable >= (al1.getHeight()*9/10))
     {
+      // TODO allow optional if mappable > a few
       return true;
     }
     return false;