Merge branch 'develop' into features/JAL-653_gffalignments

update for incoming changes and finessing against JAL-1641

diff --cc src/jalview/appletgui/AlignFrame.java
index 77747d1,1510a14..a14da77
--- 1/src/jalview/appletgui/AlignFrame.java
--- 2/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@@ -4179,35 -4207,4 +4208,36 @@@ public class AlignFrame extends Embmenu
    {
      this.splitFrame = sf;
    }
++
 +    // may not need this
 +  @Override
 +  public void setShowSeqFeatures(boolean b)
 +  {
 +    // showSeqFeatures.setSelected(b);
 +    viewport.setShowSequenceFeatures(b);
 +
 +  }
 +
 +  @Override
 +  public void setMenusForViewport()
 +  {
 +    // setMenusFromViewport(viewport);
 +
 +  }
 +  @Override
 +  public void refreshFeatureUI(boolean enableIfNecessary)
 +  {
 +    if (enableIfNecessary)
 +    {
 +      sequenceFeatures.setState(true);
 +      alignPanel.av.setShowSequenceFeatures(true);
 +    }
 +  }
 +
 +  @Override
 +  public FeatureSettingsControllerI getFeatureSettingsUI()
 +  {
 +    return alignPanel.av.featureSettings;
 +  }
 +
  }

diff --cc src/jalview/datamodel/Sequence.java
Simple merge

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

diff --cc src/jalview/io/AppletFormatAdapter.java
Simple merge

diff --cc src/jalview/io/FileLoader.java
Simple merge