From aa666651e7f6934500f8cde2ac75483f67e394c9 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 6 Jul 2023 14:49:36 +0100
Subject: [PATCH] JAL-4220 if a threshold is defined, use it to show - for
 symbols present below assigned threshold

---
 src/jalview/analysis/AAFrequency.java |    7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index b1505d6..aa0deed 100755
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -252,6 +252,11 @@ public class AAFrequency
       return;
     }
 
+    float threshhold = 100;
+    if (consensus.getThreshold()!=null)
+    {
+      threshhold =  consensus.getThreshold().value;
+    }
     for (int i = startCol; i < endCol; i++)
     {
       ProfileI profile = profiles.get(i);
@@ -273,7 +278,7 @@ public class AAFrequency
               ignoreGaps, dp);
 
       String modalResidue = profile.getModalResidue();
-      if ("".equals(modalResidue))
+      if ("".equals(modalResidue) || threshhold>value)
       {
         modalResidue = "-";
       }
-- 
1.7.10.2