Merge branch 'develop' into bug/JAL-4125_flatlaf_quithandler_warning_doesnt_display_p...

[jalview.git] / src / jalview / project / Jalview2XML.java

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index c8f9be6..c900c06 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -5094,7 +5094,10 @@ public class Jalview2XML
               + annotationId);
       return null;
     }
-    if (matchedAnnotation.getThreshold() == null)
+    // belt-and-braces create a threshold line if the 
+    // colourscheme needs one but the matchedAnnotation doesn't have one
+    if (safeInt(viewAnnColour.getAboveThreshold()) != 0
+            && matchedAnnotation.getThreshold() == null)
     {
       matchedAnnotation.setThreshold(
               new GraphLine(safeFloat(viewAnnColour.getThreshold()),