Merge branch 'bug/JAL-2510amendFeatures' into develop

[jalview.git] / src / jalview / viewmodel / seqfeatures / FeatureRendererModel.java

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 84c9477..f6addb8 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -36,6 +36,7 @@ import java.beans.PropertyChangeSupport;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
@@ -344,6 +345,8 @@ public abstract class FeatureRendererModel implements
     {
       minmax = new Hashtable<String, float[][]>();
     }
+
+    Set<String> oldGroups = new HashSet<String>(featureGroups.keySet());
     AlignmentI alignment = av.getAlignment();
     for (int i = 0; i < alignment.getHeight(); i++)
     {
@@ -358,9 +361,10 @@ public abstract class FeatureRendererModel implements
       int index = 0;
       while (index < features.length)
       {
+        String fgrp = features[index].getFeatureGroup();
+        oldGroups.remove(fgrp);
         if (!featuresDisplayed.isRegistered(features[index].getType()))
         {
-          String fgrp = features[index].getFeatureGroup();
           if (fgrp != null)
           {
             Boolean groupDisplayed = featureGroups.get(fgrp);
@@ -424,6 +428,16 @@ public abstract class FeatureRendererModel implements
         index++;
       }
     }
+
+    /*
+     * oldGroups now consists of groups that no longer 
+     * have any feature in them - remove these
+     */
+    for (String grp : oldGroups)
+    {
+      featureGroups.remove(grp);
+    }
+
     updateRenderOrder(allfeatures);
     findingFeatures = false;
   }