Merge branch 'features/JAL-1553_select-columns-by-annotation' into develop

diff --combined src/jalview/gui/AlignFrame.java
index 699f707,34ccf9c..4c45aad
--- 1/src/jalview/gui/AlignFrame.java
--- 2/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@@ -768,7 -768,7 +768,7 @@@ public class AlignFrame extends GAlignF
      setColourSelected(ColourSchemeProperty.getColourName(av
              .getGlobalColourScheme()));
  
 -    showSeqFeatures.setSelected(av.showSequenceFeatures);
 +    showSeqFeatures.setSelected(av.isShowSequenceFeatures());
      hiddenMarkers.setState(av.showHiddenMarkers);
      applyToAllGroups.setState(av.getColourAppliesToAllGroups());
      showNpFeatsMenuitem.setSelected(av.isShowNpFeats());
@@@ -3092,7 -3092,7 +3092,7 @@@
    {
      viewport.setShowSequenceFeaturesHeight(showSeqFeaturesHeight
              .isSelected());
 -    if (viewport.getShowSequenceFeaturesHeight())
 +    if (viewport.isShowSequenceFeaturesHeight())
      {
        // ensure we're actually displaying features
        viewport.setShowSequenceFeatures(true);
@@@ -3327,7 -3327,7 +3327,7 @@@
    @Override
    public void annotationColumn_actionPerformed(ActionEvent e)
    {
-     new AnnotationColumnSelection(viewport, alignPanel);
+     new AnnotationColumnChooser(viewport, alignPanel);
    }
  
    @Override
@@@ -4888,7 -4888,7 +4888,7 @@@
      {
        featuresFile = new FeaturesFile(file, type).parse(viewport
                .getAlignment().getDataset(), alignPanel.getSeqPanel().seqCanvas
 -              .getFeatureRenderer().featureColours, false,
 +              .getFeatureRenderer().getFeatureColours(), false,
                jalview.bin.Cache.getDefault("RELAXEDSEQIDMATCHING", false));
      } catch (Exception ex)
      {
@@@ -4897,7 -4897,7 +4897,7 @@@
  
      if (featuresFile)
      {
 -      viewport.showSequenceFeatures = true;
 +      viewport.setShowSequenceFeatures(true);
        showSeqFeatures.setSelected(true);
        if (alignPanel.getSeqPanel().seqCanvas.fr != null)
        {

diff --combined src/jalview/gui/AlignViewport.java
index dd61c79,cff9e94..29d936f
--- 1/src/jalview/gui/AlignViewport.java
--- 2/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@@ -95,6 -95,10 +95,6 @@@ public class AlignViewport extends Alig
  
    boolean renderGaps = true;
  
 -  boolean showSequenceFeatures = false;
 -
 -  private boolean showAnnotation = true;
 -
    SequenceAnnotationOrder sortAnnotationsBy = null;
  
    int charHeight;
@@@ -121,6 -125,12 +121,6 @@@
  
    boolean cursorMode = false;
  
 -  /**
 -   * Keys are the feature types which are currently visible. Note: Values are
 -   * not used!
 -   */
 -  private Hashtable featuresDisplayed = null;
 -
    boolean antiAlias = false;
  
    Rectangle explodedPosition;
@@@ -138,9 -148,10 +138,9 @@@
    Color textColour = Color.black;
  
    Color textColour2 = Color.white;
 -
    private boolean rightAlignIds = false;
  
-   private AnnotationColumnSelection currentAnnotationColumnSelectionState;
+   private AnnotationColumnChooser currentAnnotationColumnSelectionState;
    /**
     * Creates a new AlignViewport object.
     * 
@@@ -358,6 -369,22 +358,6 @@@
    }
  
    /**
 -   * set the flag
 -   * 
 -   * @param b
 -   *          features are displayed if true
 -   */
 -  public void setShowSequenceFeatures(boolean b)
 -  {
 -    showSequenceFeatures = b;
 -  }
 -
 -  public boolean getShowSequenceFeatures()
 -  {
 -    return showSequenceFeatures;
 -  }
 -
 -  /**
     * centre columnar annotation labels in displayed alignment annotation TODO:
     * add to jalviewXML and annotation display settings
     */
@@@ -811,6 -838,27 +811,6 @@@
     * 
     * @return DOCUMENT ME!
     */
 -  public boolean getShowAnnotation()
 -  {
 -    return isShowAnnotation();
 -  }
 -
 -  /**
 -   * DOCUMENT ME!
 -   * 
 -   * @param b
 -   *          DOCUMENT ME!
 -   */
 -  public void setShowAnnotation(boolean b)
 -  {
 -    showAnnotation = b;
 -  }
 -
 -  /**
 -   * DOCUMENT ME!
 -   * 
 -   * @return DOCUMENT ME!
 -   */
    public boolean getScaleAboveWrapped()
    {
      return scaleAboveWrapped;
@@@ -1054,6 -1102,8 +1054,6 @@@
      return followSelection;
    }
  
 -  boolean showSeqFeaturesHeight;
 -
    public void sendSelection()
    {
      jalview.structure.StructureSelectionManager
@@@ -1062,6 -1112,16 +1062,6 @@@
                      new ColumnSelection(getColumnSelection()), this);
    }
  
 -  public void setShowSequenceFeaturesHeight(boolean selected)
 -  {
 -    showSeqFeaturesHeight = selected;
 -  }
 -
 -  public boolean getShowSequenceFeaturesHeight()
 -  {
 -    return showSeqFeaturesHeight;
 -  }
 -
    /**
     * return the alignPanel containing the given viewport. Use this to get the
     * components currently handling the given viewport.
@@@ -1215,6 -1275,16 +1215,6 @@@
      }
    }
  
 -
 -  public Hashtable getFeaturesDisplayed()
 -  {
 -    return featuresDisplayed;
 -  }
 -
 -  public void setFeaturesDisplayed(Hashtable featuresDisplayed)
 -  {
 -    this.featuresDisplayed = featuresDisplayed;
 -  }
    protected SequenceAnnotationOrder getSortAnnotationsBy()
    {
      return sortAnnotationsBy;
@@@ -1235,10 -1305,9 +1235,10 @@@
      this.showAutocalculatedAbove = showAutocalculatedAbove;
    }
  
 +
    public boolean isShowAnnotation()
    {
 -    return showAnnotation;
 +    return super.isShowAnnotation();
    }
  
    public boolean isRightAlignIds()
@@@ -1251,13 -1320,13 +1251,13 @@@
      this.rightAlignIds = rightAlignIds;
    }
  
-   public AnnotationColumnSelection getCurrentAnnotationColumnSelectionState()
+   public AnnotationColumnChooser getCurrentAnnotationColumnSelectionState()
    {
      return currentAnnotationColumnSelectionState;
    }
  
    public void setCurrentAnnotationColumnSelectionState(
-           AnnotationColumnSelection currentAnnotationColumnSelectionState)
+           AnnotationColumnChooser currentAnnotationColumnSelectionState)
    {
      this.currentAnnotationColumnSelectionState = currentAnnotationColumnSelectionState;
    }