From 1a64eb3f07d8d54a605581c7e7338c55bcb3e70c Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Tue, 3 Sep 2024 22:37:05 +0100
Subject: [PATCH] JAL-34 JAL-4366 add a tolerance - 90% of one alignment
 should map to the other

---
 src/jalview/analysis/AlignmentUtils.java |    3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 020ffda..c7c618f 100644
--- 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;
-- 
1.7.10.2