Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_R...

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 8aa2858..fff3b38 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -297,4 +297,11 @@ public interface FeatureRenderer
    * @return
    */
   MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence, int pos);
+
+  /**
+   * Sends a message to let any registered parties know that something about
+   * feature rendering has changed
+   */
+  void notifyFeaturesChanged();
+
 }

diff --git a/src/jalview/api/FeatureSettingsModelI.java b/src/jalview/api/FeatureSettingsModelI.java
index c0fc523..c8a835a 100644 (file)
--- a/src/jalview/api/FeatureSettingsModelI.java
+++ b/src/jalview/api/FeatureSettingsModelI.java
@@ -35,7 +35,8 @@ public interface FeatureSettingsModelI extends Comparator<String>
   // interface, simplifying instantiating classes
 
   /**
-   * Answers true if the specified feature type is displayed
+   * Answers true if the specified feature type is to be displayed, false if no
+   * preference
    * 
    * @param type
    * @return
@@ -43,6 +44,15 @@ public interface FeatureSettingsModelI extends Comparator<String>
   boolean isFeatureDisplayed(String type);
 
   /**
+   * Answers true if the specified feature type is to be hidden, false if no
+   * preference
+   * 
+   * @param type
+   * @return
+   */
+  boolean isFeatureHidden(String type);
+
+  /**
    * Answers true if the specified feature group is displayed
    * 
    * @param group

diff --git a/src/jalview/api/FeaturesDisplayedI.java b/src/jalview/api/FeaturesDisplayedI.java
index e69785f..9387e3f 100644 (file)
--- a/src/jalview/api/FeaturesDisplayedI.java
+++ b/src/jalview/api/FeaturesDisplayedI.java
@@ -39,6 +39,8 @@ public interface FeaturesDisplayedI
 
   void setVisible(String featureType);
 
+  void setHidden(String featureType);
+
   /**
    * Sets all the specified feature types to visible. Visibility of other
    * feature types is not changed.

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index 9c7ce63..461226b 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -629,10 +629,10 @@ public class EnsemblGene extends EnsemblSeqProxy
       SequenceOntologyI so = SequenceOntologyFactory.getInstance();
 
       @Override
-      public boolean isFeatureDisplayed(String type)
+      public boolean isFeatureHidden(String type)
       {
-        return (so.isA(type, SequenceOntologyI.EXON)
-                || so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
+        return (!so.isA(type, SequenceOntologyI.EXON)
+                && !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
       }
 
       @Override

diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 1ceabd1..b2224ab 100644 (file)
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -22,11 +22,13 @@ package jalview.ext.jmol;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AppJmol;
 import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
@@ -37,6 +39,7 @@ import jalview.structure.StructureMappingcommandSet;
 import jalview.structure.StructureSelectionManager;
 import jalview.structures.models.AAStructureBindingModel;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
 
 import java.awt.Color;
 import java.awt.Container;
@@ -1190,7 +1193,9 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
       FeatureRenderer fr = getFeatureRenderer(null);
       if (fr != null)
       {
-        fr.featuresAdded();
+        FeatureSettingsModelI colours = new Pdb().getFeatureColourScheme();
+        ((AppJmol) getViewer()).getAlignmentPanel().av
+                .applyFeaturesStyle(colours);
       }
       refreshGUI();
       loadNotifiesHandled++;

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index ba7aad4..8e12ff5 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -992,8 +992,8 @@ public class AlignViewport extends AlignmentViewport
     
     FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
             .getFeatureRenderer();
-    List<String> origRenderOrder = new ArrayList(),
-            origGroups = new ArrayList();
+    List<String> origRenderOrder = new ArrayList<>();
+    List<String> origGroups = new ArrayList<>();
     // preserve original render order - allows differentiation between user configured colours and autogenerated ones
     origRenderOrder.addAll(fr.getRenderOrder());
     origGroups.addAll(fr.getFeatureGroups());
@@ -1004,7 +1004,7 @@ public class AlignViewport extends AlignmentViewport
     if (!mergeOnly)
     {
       // only clear displayed features if we are mergeing
-      displayed.clear();
+      // displayed.clear();
     }
     // TODO this clears displayed.featuresRegistered - do we care?
     //
@@ -1036,6 +1036,10 @@ public class AlignViewport extends AlignmentViewport
         {
           displayed.setVisible(type);
         }
+        else if (featureSettings.isFeatureHidden(type))
+        {
+          displayed.setHidden(type);
+        }
       }
     }
 
@@ -1064,6 +1068,8 @@ public class AlignViewport extends AlignmentViewport
       fr.orderFeatures(featureSettings);
     }
     fr.setTransparency(featureSettings.getTransparency());
+
+    fr.notifyFeaturesChanged();
   }
 
   public String getViewName()

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 724cec1..3432911 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -208,11 +208,6 @@ public class AppJmolBinding extends JalviewJmolBinding
     AlignmentPanel ap = (alignment == null)
             ? appJmolWindow.getAlignmentPanel()
             : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
-    }
-
-    return null;
+    return ap.av.getAlignPanel().getFeatureRenderer();
   }
 }

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index a7349b8..47bad81 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -575,7 +575,8 @@ public class ChimeraViewFrame extends StructureViewerBase
 
       /*
        * ensure that any newly discovered features (e.g. RESNUM)
-       * are added to any open feature settings dialog
+       * are notified to the FeatureRenderer (and added to any 
+       * open feature settings dialog)
        */
       FeatureRenderer fr = getBinding().getFeatureRenderer(null);
       if (fr != null)

diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java
index b3bff0d..279d89f 100644 (file)
--- a/src/jalview/gui/CutAndPasteTransfer.java
+++ b/src/jalview/gui/CutAndPasteTransfer.java
@@ -272,11 +272,8 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer
        */
       if (viewport != null && viewport.getAlignment() != null)
       {
-        if (proxyColourScheme != null)
-        {
-          viewport.applyFeaturesStyle(proxyColourScheme);
-        }
         ((AlignViewport) viewport).addAlignment(al, title);
+        viewport.applyFeaturesStyle(proxyColourScheme);
       }
       else
       {

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 1c4e6a6..7451646 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -1023,10 +1023,7 @@ public class SequenceFetcher extends JPanel implements Runnable
           }
         }
 
-        if (preferredFeatureColours != null)
-        {
-          af.getViewport().applyFeaturesStyle(preferredFeatureColours);
-        }
+        af.getViewport().applyFeaturesStyle(preferredFeatureColours);
         if (Cache.getDefault("HIDE_INTRONS", true))
         {
           af.hideFeatureColumns(SequenceOntologyI.EXON, false);

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3afbaad..20db946 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -391,12 +391,9 @@ public class FileLoader implements Runnable
                   .getFeatureColourScheme();
           if (viewport != null)
           {
-            if (proxyColourScheme != null)
-            {
-              viewport.applyFeaturesStyle(proxyColourScheme);
-            }
             // append to existing alignment
             viewport.addAlignment(al, title);
+            viewport.applyFeaturesStyle(proxyColourScheme);
           }
           else
           {

diff --git a/src/jalview/io/PDBFeatureSettings.java b/src/jalview/io/PDBFeatureSettings.java
index 0f2b0ac..ee82418 100644 (file)
--- a/src/jalview/io/PDBFeatureSettings.java
+++ b/src/jalview/io/PDBFeatureSettings.java
@@ -36,10 +36,9 @@ public class PDBFeatureSettings extends FeatureSettingsAdapter
   private static final String FEATURE_RES_NUM = PDBChain.RESNUM_FEATURE;
 
   @Override
-  public boolean isFeatureDisplayed(String type)
+  public boolean isFeatureHidden(String type)
   {
-    return type.equalsIgnoreCase(FEATURE_INSERTION)
-            || type.equalsIgnoreCase(FEATURE_RES_NUM);
+    return type.equalsIgnoreCase(FEATURE_RES_NUM);
   }
 
   @Override

diff --git a/src/jalview/schemes/FeatureSettingsAdapter.java b/src/jalview/schemes/FeatureSettingsAdapter.java
index b15e4cf..6e8554f 100644 (file)
--- a/src/jalview/schemes/FeatureSettingsAdapter.java
+++ b/src/jalview/schemes/FeatureSettingsAdapter.java
@@ -36,6 +36,12 @@ public class FeatureSettingsAdapter implements FeatureSettingsModelI
   }
 
   @Override
+  public boolean isFeatureHidden(String type)
+  {
+    return false;
+  }
+
+  @Override
   public boolean isGroupDisplayed(String group)
   {
     return true;

diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index 426ec1f..b348766 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -102,11 +102,11 @@ public abstract class FeatureRendererModel
 
   Map<String, Float> featureOrder = null;
 
-  protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
-          this);
-
   protected AlignViewportI av;
 
+  private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+          this);
+
   @Override
   public AlignViewportI getViewport()
   {
@@ -299,13 +299,19 @@ public abstract class FeatureRendererModel
       {
         firing = Boolean.TRUE;
         findAllFeatures(true); // add all new features as visible
-        changeSupport.firePropertyChange("changeSupport", null, null);
+        notifyFeaturesChanged();
         firing = Boolean.FALSE;
       }
     }
   }
 
   @Override
+  public void notifyFeaturesChanged()
+  {
+    changeSupport.firePropertyChange("changeSupport", null, null);
+  }
+
+  @Override
   public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
   {
     /*

diff --git a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
index f44a2d1..d7da519 100644 (file)
--- a/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
+++ b/src/jalview/viewmodel/seqfeatures/FeaturesDisplayed.java
@@ -29,9 +29,9 @@ import java.util.Set;
 
 public class FeaturesDisplayed implements FeaturesDisplayedI
 {
-  private Set<String> featuresDisplayed = new HashSet<String>();
+  private Set<String> featuresDisplayed = new HashSet<>();
 
-  private Set<String> featuresRegistered = new HashSet<String>();
+  private Set<String> featuresRegistered = new HashSet<>();
 
   public FeaturesDisplayed(FeaturesDisplayedI featuresDisplayed2)
   {
@@ -93,6 +93,13 @@ public class FeaturesDisplayed implements FeaturesDisplayedI
   }
 
   @Override
+  public void setHidden(String featureType)
+  {
+    featuresDisplayed.remove(featureType);
+    featuresRegistered.add(featureType);
+  }
+
+  @Override
   public boolean isRegistered(String type)
   {
     return featuresRegistered.contains(type);

diff --git a/test/jalview/ext/ensembl/EnsemblGeneTest.java b/test/jalview/ext/ensembl/EnsemblGeneTest.java
index 8b1e840..ef12ed4 100644 (file)
--- a/test/jalview/ext/ensembl/EnsemblGeneTest.java
+++ b/test/jalview/ext/ensembl/EnsemblGeneTest.java
@@ -271,18 +271,24 @@ public class EnsemblGeneTest
 
   /**
    * Check behaviour of feature colour scheme for EnsemblGene sequences.
-   * Currently coded to display exon and sequence_variant (or sub-types) only,
-   * with sequence_variant in red above exon coloured by label.
+   * Currently coded to hide all except exon and sequence_variant (or sub-types)
+   * only, with sequence_variant in red above exon coloured by label.
    */
   @Test(groups = "Functional")
   public void testGetFeatureColourScheme()
   {
     FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
-    assertTrue(fc.isFeatureDisplayed("exon"));
-    assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
-    assertTrue(fc.isFeatureDisplayed("sequence_variant"));
-    assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
-    assertFalse(fc.isFeatureDisplayed("transcript"));
+    assertFalse(fc.isFeatureDisplayed("exon"));
+    assertFalse(fc.isFeatureHidden("exon"));
+    assertFalse(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureHidden("coding_exon")); // subtype of exon
+    assertFalse(fc.isFeatureDisplayed("sequence_variant"));
+    assertFalse(fc.isFeatureHidden("sequence_variant"));
+    assertFalse(fc.isFeatureDisplayed("feature_variant")); // subtype
+    assertFalse(fc.isFeatureHidden("feature_variant")); // subtype
+    assertTrue(fc.isFeatureHidden("transcript"));
+    assertTrue(fc.isFeatureHidden("CDS"));
+
     assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
             .getColour());
     assertEquals(Color.RED, fc.getFeatureColour("feature_variant")