JAL-1605 merge commit

diff --cc src/jalview/gui/AlignFrame.java
index 9f5b8f0,3180993..be8af7b
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -1230,17 -1227,12 +1230,18 @@@ public class AlignFrame extends GAlignF
    @Override
    protected void htmlMenuItem_actionPerformed(ActionEvent e)
    {
-     new HTMLOutput(alignPanel,
-             alignPanel.seqPanel.seqCanvas.getSequenceRenderer(),
-             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
+     // new HTMLOutput(alignPanel,
+     // alignPanel.getSeqPanel().seqCanvas.getSequenceRenderer(),
+     // alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
+     new HtmlSvgOutput(alignPanel);
    }
  
 +  @Override
 +  public void bioJSMenuItem_actionPerformed(ActionEvent e)
 +  {
 +    new BioJsHTMLOutput(alignPanel,
-             alignPanel.seqPanel.seqCanvas.getFeatureRenderer());
++            alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer());
 +  }
    public void createImageMap(File file, String image)
    {
      alignPanel.makePNGImageMap(file, image);

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

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

diff --cc src/jalview/gui/AnnotationExporter.java
index ecf4b8e,c68b2b1..e966c92
--- 1/src/jalview/gui/AnnotationExporter.java
--- 2/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@@ -20,16 -20,16 +20,32 @@@
   */
  package jalview.gui;
  
--import java.util.*;
++import jalview.datamodel.AlignmentAnnotation;
++import jalview.datamodel.SequenceGroup;
++import jalview.io.AnnotationFile;
++import jalview.io.FeaturesFile;
++import jalview.io.JalviewFileChooser;
++import jalview.io.JalviewFileView;
++import jalview.util.MessageManager;
++
++import java.awt.BorderLayout;
++import java.awt.Color;
++import java.awt.FlowLayout;
++import java.awt.event.ActionEvent;
++import java.awt.event.ActionListener;
++import java.util.Enumeration;
++import java.util.Hashtable;
  import java.util.List;
  
--import java.awt.*;
--import java.awt.event.*;
--import javax.swing.*;
--
--import jalview.datamodel.*;
--import jalview.io.*;
--import jalview.util.MessageManager;
++import javax.swing.BorderFactory;
++import javax.swing.ButtonGroup;
++import javax.swing.JButton;
++import javax.swing.JInternalFrame;
++import javax.swing.JLabel;
++import javax.swing.JLayeredPane;
++import javax.swing.JPanel;
++import javax.swing.JRadioButton;
++import javax.swing.SwingConstants;
  
  /**
   * 
@@@ -214,8 -214,8 +230,9 @@@ public class AnnotationExporter extend
      {
        return fcols;
      }
 -    Enumeration en = ap.av.featuresDisplayed.keys();
++
 +    Enumeration en = ap.av.getFeaturesDisplayed().keys();
-     FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
+     FeatureRenderer fr = ap.getSeqPanel().seqCanvas.getFeatureRenderer(); // consider
                                                                       // higher
                                                                       // level
                                                                       // method ?

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

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

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

diff --cc src/jalview/gui/Jalview2XML.java
index 08fd306,8ddd050..aa2ae7a
--- 1/src/jalview/gui/Jalview2XML.java
--- 2/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@@ -1180,9 -1180,9 +1180,9 @@@ public class Jalview2XM
                        .getColour(renderOrder[ro]).getRGB());
              }
  
 -            setting.setDisplay(av.featuresDisplayed
 +            setting.setDisplay(av.getFeaturesDisplayed()
                      .containsKey(renderOrder[ro]));
-             float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer()
+             float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
                      .getOrder(renderOrder[ro]);
              if (rorder > -1)
              {

diff --cc src/jalview/gui/Jalview2XML_V1.java
Simple merge

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

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