From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 4 Sep 2023 11:56:33 +0000 (+0100)
Subject: JAL-3088 check for validEnd when working out whether arrow should point to left when... 
X-Git-Tag: Release_2_11_4_0~106^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c956ba7ae40dd7f269aa372044ed4ed5f28fb042;p=jalview.git

JAL-3088 check for validEnd when working out whether arrow should point to left when last base is paired
---

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 3f0c9fa..cba36d2 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -185,7 +185,7 @@ public class AnnotationRenderer
             : row_annotations[column - 1].secondaryStructure;
 
     boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
-            || dc != row_annotations[sCol - 1].secondaryStructure;
+            || dc != row_annotations[sCol - 1].secondaryStructure || !validEnd;
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || dc != row_annotations[column].secondaryStructure;
@@ -251,7 +251,7 @@ public class AnnotationRenderer
             : row_annotations[column - 1].displayCharacter;
 
     boolean diffupstream = sCol == 0 || row_annotations[sCol - 1] == null
-            || !dc.equals(row_annotations[sCol - 1].displayCharacter);
+            || !dc.equals(row_annotations[sCol - 1].displayCharacter) || !validEnd;
     boolean diffdownstream = !validRes || !validEnd
             || row_annotations[column] == null
             || !dc.equals(row_annotations[column].displayCharacter);