Merge branch 'develop' into features/JAL-2068groovyAnnotationWorker

fun fact: Jalview.getCurrentAlignFrame() should be used in place of Desktop.getCurrentAlignFrame() now

diff --cc src/jalview/appletgui/FeatureRenderer.java
index 7ae333e,a93cdcb..d774131
--- 1/src/jalview/appletgui/FeatureRenderer.java
--- 2/src/jalview/appletgui/FeatureRenderer.java
+++ b/src/jalview/appletgui/FeatureRenderer.java
@@@ -61,10 -61,8 +61,8 @@@ public class FeatureRenderer extend
     */
    public FeatureRenderer(AlignmentViewport av)
    {
 -    super();
 -    this.av = av;
 +    super(av);
 +
-     setTransparencyAvailable(!System.getProperty("java.version")
-             .startsWith("1.1"));
    }
  
    static String lastFeatureAdded;

diff --cc src/jalview/gui/AnnotationLabels.java
Simple merge

diff --cc src/jalview/renderer/seqfeatures/FeatureRenderer.java
Simple merge

diff --cc src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
Simple merge

diff --cc src/jalview/workers/AlignmentAnnotationFactory.java
index ee48c73,520b232..f804a19
--- 1/src/jalview/workers/AlignmentAnnotationFactory.java
--- 2/src/jalview/workers/AlignmentAnnotationFactory.java
+++ b/src/jalview/workers/AlignmentAnnotationFactory.java
@@@ -1,7 -1,6 +1,8 @@@
  package jalview.workers;
  
 +import jalview.api.AlignViewportI;
 +import jalview.api.AlignmentViewPanel;
+ import jalview.bin.Jalview;
  import jalview.datamodel.AlignmentAnnotation;
  import jalview.datamodel.Annotation;
  import jalview.gui.AlignFrame;
@@@ -30,13 -28,9 +30,13 @@@ public class AlignmentAnnotationFactor
     */
    public static void newCalculator(FeatureCounterI counter)
    {
 -    if (Jalview.getCurrentAlignFrame() != null)
 +    // TODO need an interface for AlignFrame by which to access
 +    // its AlignViewportI and AlignmentViewPanel
-     AlignFrame currentAlignFrame = Desktop.getCurrentAlignFrame();
++    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame() ;
 +    if (currentAlignFrame != null)
      {
 -      newCalculator(Jalview.getCurrentAlignFrame(), counter);
 +      newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
 +              .getAlignPanels().get(0), counter);
      }
      else
      {
@@@ -67,13 -60,9 +67,13 @@@
     */
    public static void newCalculator(AnnotationProviderI calculator)
    {
 -    if (Jalview.getCurrentAlignFrame() != null)
 +    // TODO need an interface for AlignFrame by which to access
 +    // its AlignViewportI and AlignmentViewPanel
-     AlignFrame currentAlignFrame = Desktop.getCurrentAlignFrame();
++    AlignFrame currentAlignFrame = Jalview.getCurrentAlignFrame() ;
 +    if (currentAlignFrame != null)
      {
 -      newCalculator(Jalview.getCurrentAlignFrame(), calculator);
 +      newCalculator(currentAlignFrame.getViewport(), currentAlignFrame
 +              .getAlignPanels().get(0), calculator);
      }
      else
      {