From 254e3170f750a050d567158a94b26f7cb10d68c8 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 13 May 2024 11:23:23 +0100
Subject: [PATCH] JAL-4410 better logic for maximal mapped chains (I seem to
 remember coding this before...)

---
 src/jalview/structure/StructureSelectionManager.java |    9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index a8ee9fe..c9719b5 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -591,10 +591,15 @@ public class StructureSelectionManager
         }
         else
         {
-          if (as.maxscore >= max)
+          if (as.maxscore > max)
           {
-            maxChain.add(chain);
             max = as.maxscore;
+            maxChain.clear();
+            maxAlignSeqs.clear();
+          }
+          if (as.maxscore == max)
+          {
+            maxChain.add(chain);
             maxAlignSeqs.add(as);
           }
         }
-- 
1.7.10.2