Merge branch 'develop' into features/JAL-3187_uitweaks

diff --combined help/help/html/releases.html
index eac0445,d7f3ee1..2fa241c
--- 1/help/help/html/releases.html
--- 2/help/help/html/releases.html
+++ b/help/help/html/releases.html
@@@ -58,19 -58,21 +58,23 @@@ li:before 
      <tr>
        <td width="60" align="center" nowrap><strong><a
            name="Jalview.2.11.1">2.11.1</a><a name="Jalview.2.11.1.0">.0</a><br />
-           <em>16/2/2020</em></strong></td>
+           <em>25/2/2020</em></strong></td>
        <td align="left" valign="top">
          <ul>
 +          <li><!-- JAL-3121 -->Feature attributes from VCF files can be exported and re-imported as GFF3 files
 +          </li>
            <li>
-             <!-- JAL-3376 -->Record &quot;fixed column&quot; values POS, ID, QUAL, FILTER from VCF as Feature Attributes
+             <!-- JAL-3376 -->Record &quot;fixed column&quot; values POS,
+             ID, QUAL, FILTER from VCF as Feature Attributes
            </li>
            <li>
-             <!-- JAL-3375 -->More robust VCF numeric data field validation
-             while parsing (e.g. AF* attributes)
+             <!-- JAL-3375 -->More robust VCF numeric data field
+             validation while parsing (e.g. AF* attributes)
+           </li>
+           <li>
+             <!-- JAL-3538 -->Font anti-aliasing in alignment views
+             enabled by default
            </li>
-           
            <li>
            <!-- JAL -->
            </li>

diff --combined src/jalview/gui/AlignFrame.java
index de82fd8,9001015..7c0c55c
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -1479,13 -1479,9 +1479,13 @@@ public class AlignFrame extends GAlignF
            closeView(alignPanel);
          }
        }
 -
        if (closeAllTabs)
        {
 +        if (featureSettings != null && featureSettings.isOpen())
 +        {
 +          featureSettings.close();
 +          featureSettings = null;
 +        }
          /*
           * this will raise an INTERNAL_FRAME_CLOSED event and this method will
           * be called recursively, with the frame now in 'closed' state
@@@ -3191,15 -3187,9 +3191,15 @@@
    @Override
    public void featureSettings_actionPerformed(ActionEvent e)
    {
 +    showFeatureSettingsUI();
 +  }
 +
 +  @Override
 +  public FeatureSettingsControllerI showFeatureSettingsUI()
 +  {
      if (featureSettings != null)
      {
 -      featureSettings.close();
 +      featureSettings.closeOldSettings();
        featureSettings = null;
      }
      if (!showSeqFeatures.isSelected())
@@@ -3209,7 -3199,6 +3209,7 @@@
        showSeqFeatures_actionPerformed(null);
      }
      featureSettings = new FeatureSettings(this);
 +    return featureSettings;
    }
  
    /**
@@@ -4695,6 -4684,11 +4695,11 @@@
              if (parseFeaturesFile(file, sourceType))
              {
                alignPanel.paintAlignment(true, true);
+               SplitFrame splitFrame = (SplitFrame) getSplitViewContainer();
+               if (splitFrame != null)
+               {
+                 splitFrame.repaint();
+               }
              }
            }
            else
@@@ -4750,21 -4744,6 +4755,21 @@@
        viewport = alignPanel.av;
        avc.setViewportAndAlignmentPanel(viewport, alignPanel);
        setMenusFromViewport(viewport);
 +      if (featureSettings != null && featureSettings.isOpen()
 +              && featureSettings.fr.getViewport() != viewport)
 +      {
 +        if (viewport.isShowSequenceFeatures())
 +        {
 +          // refresh the featureSettings to reflect UI change
 +          showFeatureSettingsUI();
 +        }
 +        else
 +        {
 +          // close feature settings for this view.
 +          featureSettings.close();
 +        }
 +      }
 +
      }
  
      /*
@@@ -5684,19 -5663,6 +5689,19 @@@
      }
  
    }
 +
 +  private Rectangle lastFeatureSettingsBounds = null;
 +  @Override
 +  public void setFeatureSettingsGeometry(Rectangle bounds)
 +  {
 +    lastFeatureSettingsBounds = bounds;
 +  }
 +
 +  @Override
 +  public Rectangle getFeatureSettingsGeometry()
 +  {
 +    return lastFeatureSettingsBounds;
 +  }
  }
  
  class PrintThread extends Thread

diff --combined src/jalview/gui/AlignViewport.java
index c77d9e3,91af323..888ffcd
--- 1/src/jalview/gui/AlignViewport.java
--- 2/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@@ -79,9 -79,9 +79,9 @@@ public class AlignViewport extends Alig
  
    boolean antiAlias = false;
  
 -  private Rectangle explodedGeometry;
 +  private Rectangle explodedGeometry = null;
  
 -  private String viewName;
 +  private String viewName = null;
  
    /*
     * Flag set true on the view that should 'gather' multiple views of the same
@@@ -208,7 -208,7 +208,7 @@@
     */
    private void applyViewProperties()
    {
-     antiAlias = Cache.getDefault("ANTI_ALIAS", false);
+     antiAlias = Cache.getDefault("ANTI_ALIAS", true);
  
      viewStyle.setShowJVSuffix(Cache.getDefault("SHOW_JVSUFFIX", true));
      setShowAnnotation(Cache.getDefault("SHOW_ANNOTATIONS", true));