From e69db6fc850b0e89328bb2dbc3d371930fa6c595 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@dundee.ac.uk>
Date: Mon, 19 Aug 2024 17:13:24 +0100
Subject: [PATCH] JAL-789 limit applicable score models to substitution matrix
 based ones

---
 src/jalview/gui/CalculationChooser.java |    2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index bd3c960..8e5cc9e 100644
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -593,7 +593,7 @@ public class CalculationChooser extends JPanel
             .isSecondaryStructurePresent(alignmentAnnotations);
 
     List<ScoreModelI> models = getApplicableScoreModels(nucleotide,
-            pca.isSelected(), ssPresent, pasimap.isSelected());
+            pca.isSelected(), ssPresent, (pasimap.isSelected() || pairwise.isSelected()));
 
     /*
      * now we can actually add entries to the combobox,
-- 
1.7.10.2