JAL-2483 JAL-2481 fixed findAllFeatures to handle null group correctly

[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 5d817c7..5bbdbec 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -339,15 +339,22 @@ public abstract class FeatureRendererModel implements
       SequenceI asq = alignment.getSequenceAt(i);
       for (String group : asq.getFeatures().getFeatureGroups(true))
       {
-        if (group == null)
+        /*
+         * features in null group are always displayed; other groups
+         * keep their current visibility; new groups as 'newMadeVisible'
+         */
+        boolean groupDisplayed = true;
+        if (group != null)
         {
-          continue;
-        }
-        Boolean groupDisplayed = featureGroups.get(group);
-        if (groupDisplayed == null)
-        {
-          groupDisplayed = Boolean.valueOf(newMadeVisible);
-          featureGroups.put(group, groupDisplayed);
+          if (featureGroups.containsKey(group))
+          {
+            groupDisplayed = featureGroups.get(group);
+          }
+          else
+          {
+            groupDisplayed = newMadeVisible;
+            featureGroups.put(group, groupDisplayed);
+          }
         }
         if (groupDisplayed)
         {