FeatureDisplay.java

/* FeatureDisplay.java
 *
 * created: Fri Oct  9 1998
 *
 * This file is part of Artemis
 *
 * Copyright(C) 1998,1999,2000,2001,2002  Genome Research Limited
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or(at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.66 2009-06-12 13:50:35 tjc Exp $
 */

package uk.ac.sanger.artemis.components;

import uk.ac.sanger.artemis.components.filetree.*;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.util.RemoteFileDocument;
import uk.ac.sanger.artemis.util.ReadOnlyException;
import uk.ac.sanger.artemis.util.FileDocument;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.StringVector;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.GFFUtils;
import uk.ac.sanger.artemis.io.InvalidRelationException;
import uk.ac.sanger.artemis.io.Qualifier;
import uk.ac.sanger.artemis.io.Range;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.SimpleEntryInformation;
import uk.ac.sanger.artemis.io.Key;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.RawStreamSequence;
import uk.ac.sanger.artemis.io.FastaStreamSequence;
import uk.ac.sanger.artemis.io.Sequence;
import uk.ac.sanger.artemis.io.Location;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.components.genebuilder.*;

import java.io.IOException;
import java.io.File;
import java.awt.event.*;
import java.awt.*;
import java.lang.Math;
import java.util.Vector;
import java.util.Comparator;
import javax.swing.border.Border;
import javax.swing.border.BevelBorder;

import java.awt.datatransfer.*;
import java.awt.dnd.*;
import javax.swing.Box;
import javax.swing.JOptionPane;
import javax.swing.JScrollBar;
import javax.swing.JComponent;
import javax.swing.UIManager;
import javax.swing.ImageIcon;
import javax.swing.JFrame;

import org.apache.batik.svggen.SVGGraphics2D;

/**
 *  This component is used for displaying an Entry.
 *
 *  @author Kim Rutherford
 *  @version $Id: FeatureDisplay.java,v 1.66 2009-06-12 13:50:35 tjc Exp $
 **/

public class FeatureDisplay extends EntryGroupPanel
  implements EntryGroupChangeListener,
             EntryChangeListener, FeatureChangeListener,
             SelectionChangeListener, GotoListener, SequenceChangeListener,
             DisplayComponent, OptionChangeListener, DisplayAdjustmentListener,
             DragGestureListener, DropTargetListener,
             DragSourceListener
{

  /** */
  private static final long serialVersionUID = 1L;

  private int highlight_drop_base = -1;

  /** Key code for calling zoomToSelection(). */
  private final static int ZOOM_TO_SELECTION_KEY = KeyEvent.VK_Z;
  private final static int ARROW_LEFT = KeyEvent.VK_LEFT;
  private final static int ARROW_RIGHT = KeyEvent.VK_RIGHT;

  protected final static int SCROLLBAR_AT_TOP = 1;
  protected final static int SCROLLBAR_AT_BOTTOM = 2;

  private final static int FORWARD = Bases.FORWARD;
  private final static int REVERSE = Bases.REVERSE;

  private final static int NO_FRAME        = FeatureSegment.NO_FRAME;
  private final static int FORWARD_STRAND  = FeatureSegment.FORWARD_STRAND;
  private final static int REVERSE_STRAND  = FeatureSegment.REVERSE_STRAND;
  private final static int FORWARD_FRAME_1 = FeatureSegment.FORWARD_FRAME_1;
  private final static int FORWARD_FRAME_2 = FeatureSegment.FORWARD_FRAME_2;
  private final static int FORWARD_FRAME_3 = FeatureSegment.FORWARD_FRAME_3;
  private final static int REVERSE_FRAME_3 = FeatureSegment.REVERSE_FRAME_3;
  private final static int REVERSE_FRAME_2 = FeatureSegment.REVERSE_FRAME_2;
  private final static int REVERSE_FRAME_1 = FeatureSegment.REVERSE_FRAME_1;
  private final static int SCALE_LINE      = FeatureSegment.SCALE_LINE;


  /**
   *  The JScrollBar for this FeatureDisplay object.  We create the scrollbar
   *  as part of this object rather than in the EntryEdit component because we
   *  may need to change the parameters of the scrollbar later.
   **/
  private JScrollBar scrollbar = null;

  /** A scroll bar for changing the viewing scale. */
  private ZoomScrollBar scale_changer = null;

  /** Used to colour the frames. */
  private Color light_grey = new Color(240, 240, 240);

  /** Used to colour sequence line. */
  private Color not_so_light_grey = new Color(200, 200, 200);

  /**
   *  The colour used for the active entry line when 
   *  one_line_per_entry is set.
   **/
  private Color active_entry_colour = new Color(255, 255, 140);

  /**
   *  This Vector containing the references of those features that are
   *  currently visible.
   **/
  private FeatureVector visible_features = new FeatureVector();

  /**
   *  If true updateVisibleFeatureVector() will be called by paint().
   *  updateVisibleFeatureVector() sets this to false,
   *  needVisibleFeatureVectorUpdate() sets this to true.
   **/
  private boolean update_visible_features = true;

  /** Contains those objects listening for adjustment events. */
  final private Vector<DisplayAdjustmentListener> adjustment_listener_list = 
      new Vector<DisplayAdjustmentListener>();

  /**
   *  The index of the first base that we are displaying.  
   *  Can be negative if hard_left_edge is true.
   **/
  private int left_edge_base = 1;

  /** See getScaleFactor(). */
  private int scale_factor = 3;

  /** See getScaleFactor(). */
  private float scale_value = 1;

  /** true if labels should be shown. */
  private boolean show_labels = true;

  /**
   *  This variable is true if the forward frame lines(or forward entry lines
   *  - see one_line_per_entry) should be drawn.
   **/
  private boolean show_forward_lines = true;

  /**
   *  This variable is true if the reverse frame lines(or reverse entry lines
   *  - see one_line_per_entry) should be drawn.
   **/
  private boolean show_reverse_lines = true;

  /**
   *  If true draw all features, sequence and scale lines reverse complemented.
   **/
  private boolean rev_comp_display = false;

  /**
   *  This variable is true if(for each strand) each entry should be on a
   *  separate line.
   **/
  private boolean one_line_per_entry = false;
  
  private boolean feature_stack_view = false;
  
  private short MAX_LINES_FEATURE_STACK = 10;
  
  /** expand / collapse stack view, 2 or 1 respectively */
  private int STACK_EXPAND_FACTOR = 1;
  
  /** visible features sorted by size */
  private FeatureVector visibleFeaturesSortBySize;
  /** visible features sorted by position */
  private FeatureVector visibleFeaturesSortByPosition;

  /**
   *  If true the there will never be a gap between the left edge of the
   *  screen and the first visible base.
   **/
  private boolean hard_left_edge = true;

  /** true if source features should be shown. */
  private boolean show_source_features = false;

  /** true if stop codons should be shown.     */
  private boolean show_stop_codons = true;

  /** true if start codons should be shown.    */
  private boolean show_start_codons = false;

  /** true if directional arrows should be shown on features. */
  private boolean show_feature_arrows;

  /** true a black border will be drawn around each feature.  */
  private boolean show_feature_borders;

  /**
   *  This variable is true if each base should be drawn in a different colour
   *  at scale feature 1.
   **/
  private boolean show_base_colours = false;

  /**
   *  All features(not just CDS features) will be drawn on the frame lines if
   *  and only if this variable is true.  See setFrameFeaturesFlag() and
   *  getFrameFeaturesFlag().
   **/
  private boolean frame_features_flag = false;

  /**
   *  The position(s) of the last mouse click on the dna line.  The
   *  MarkerRange contains a reference to the appropriate Strand and contains
   *  the base positions.  See getMarkerRangeFromPosition() to understand why
   *  one click can give multiple bases.
   **/
  private MarkerRange click_range = null;

  /**
   *  The last(FeatureSegment) Marker that the user clicked on.  This is used
   *  for dragging the ends of segments.
   **/
  private Marker click_segment_marker = null;

  /**
   *  This is true if click_segment_marker is the Marker at the start of
   *  segment false otherwise.  The value is only useful if
   *  click_segment_marker is set.
   **/
  private boolean click_segment_marker_is_start_marker = false;

  /**
   *  When a FeatureSegment Marker drag starts, this is set to the Marker at
   *  the other end of the segment.  This is used to check that the drag has
   *  not move the Marker too far(past the end of the segment).
   **/
  private Marker other_end_of_segment_marker = null;

  /**
   *  Features with a /score qualifier less than this value will not be shown.
   **/
  private int current_min_score = 0;

  /**
   *  Features with a /score qualifier greater than this value will not be
   *  shown.
   **/
  private int current_max_score = 100;

  private MouseEvent last_mouse_press_event;

  /**
   *  If set no DisplayAdjustment events will be sent.  This is set by
   *  displayAdjustmentValueChanged() to prevent an event we send from
   *  returning to us(a FeatureDisplay can listen for DisplayAdjustment
   *  events from another FeatureDisplay).
   **/
  private boolean disable_display_events = false;

  /**
   *  Set to true by selectionChanged() to tell updateVisibleFeatureVector()
   *  to raise the contents of the select before updating.
   **/
  private boolean raise_selection_flag = false;
 
  /** the minimum distance in pixels between the labels. */
  private final static int MINIMUM_LABEL_SPACING = 80;
 
  /** colour used for A. */
  private static Color dark_green = new Color(0, 150, 0);

  private final int scrollbar_style;
  
  private static Vector<String> contigKeys;
  private static Vector<String> allPossibleContigKeys;

  private Object[] protein_keys = { "CDS", 
                                    "BLASTCDS",
                                    "polypeptide",
                                    "pseudogenic_exon"};

  /**
   *  Create a new FeatureDisplay object with the horizontal scrollbar at the
   *  bottom of the component.
   *  @param entry_group The EntryGroup that this component will display.
   *  @param selection The Selection object for this component.  Selected
   *    objects will be highlighted.
   *  @param goto_event_source The object to use when we need to call
   *    gotoBase().
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   **/
  public FeatureDisplay(final EntryGroup entry_group,
                        final Selection selection,
                        final GotoEventSource goto_event_source,
                        final BasePlotGroup base_plot_group) 
  {
    this(entry_group, selection, goto_event_source,
         base_plot_group, SCROLLBAR_AT_BOTTOM);
  }

  /**
   *  Create a new FeatureDisplay object.
   *  @param entry_group The EntryGroup that this component will display.
   *  @param owning_component The EntryEdit object that contains the selection
   *    that this component uses.
   *  @param scrollbar_at_top If true the horizontal scrollbar will be at the
   *    top of component.
   *  @param base_plot_group The BasePlotGroup associated with this JMenu -
   *    needed to call getCodonUsageAlgorithm()
   *  @param scrollbar_style Controls the type of horizontal scrollbar.  Must
   *    be one of SCROLLBAR_AT_TOP, SCROLLBAR_AT_BOTTOM or NO_SCROLLBAR.
   **/
  public FeatureDisplay(final EntryGroup entry_group,
                        final Selection selection,
                        final GotoEventSource goto_event_source,
                        final BasePlotGroup base_plot_group,
                        final int scrollbar_style) 
  {
    super(entry_group, selection, goto_event_source, base_plot_group);

    this.scrollbar_style = scrollbar_style;

    show_feature_arrows =
      Options.getOptions().getPropertyTruthValue("draw_feature_arrows");

    show_feature_borders =
      Options.getOptions().getPropertyTruthValue("draw_feature_borders");

    frame_features_flag =
      Options.getOptions().getPropertyTruthValue("features_on_frame_lines");

    one_line_per_entry =
      Options.getOptions().getPropertyTruthValue("one_line_per_entry");
    
    feature_stack_view =
      Options.getOptions().getPropertyTruthValue("feature_stack_view");

    show_labels =
      Options.getOptions().getPropertyTruthValue("feature_labels");

    show_reverse_lines =
      Options.getOptions().getPropertyTruthValue("show_reverse_lines");
    
    show_forward_lines =
      Options.getOptions().getPropertyTruthValue("show_forward_lines");
    
    final StringVector frame_line_features = 
      Options.getOptions().getOptionValues("frame_line_features");
    if(frame_line_features != null)
      protein_keys = frame_line_features.toArray();
    
    addComponentListener(new ComponentAdapter()
    {
      public void componentResized(ComponentEvent e) 
      {
        // update the scroll bar as soon as we know the size of the canvas
        fixScrollbar();
        needVisibleFeatureVectorUpdate();
        fireAdjustmentEvent(DisplayAdjustmentEvent.ALL_CHANGE_ADJUST_EVENT);
      }

      public void componentShown(ComponentEvent e) 
      {
        // update the scroll bar as soon as we know the size of the canvas
        fixScrollbar();
        needVisibleFeatureVectorUpdate();
        fireAdjustmentEvent(DisplayAdjustmentEvent.ALL_CHANGE_ADJUST_EVENT);
      }
    });

    setScaleValue();

    if(scrollbar_style == SCROLLBAR_AT_TOP) 
      createScrollbar(true);
    else if(scrollbar_style == SCROLLBAR_AT_BOTTOM)
      createScrollbar(false);

    createScaleScrollbar();
    addListeners();

    needVisibleFeatureVectorUpdate();

    getSelection().addSelectionChangeListener(this);
    getGotoEventSource().addGotoListener(this);

    getEntryGroup().addEntryGroupChangeListener(this);
    getEntryGroup().addEntryChangeListener(this);
    getEntryGroup().addFeatureChangeListener(this);

    getBases().addSequenceChangeListener(this, Bases.MIN_PRIORITY);

    Options.getOptions().addOptionChangeListener(this);
    setBackground(Color.white);

    DragSource dragSource = DragSource.getDefaultDragSource();

    dragSource.createDefaultDragGestureRecognizer(
       this,                             // component where drag originates
       DnDConstants.ACTION_COPY_OR_MOVE, // actions
       this);                            // drag gesture recognizer

    setDropTarget(new DropTarget(this,this));
  }


  /**
   *  Overriden to call fixCanvasSize()
   **/
  public void setVisible(final boolean visible) 
  {
    super.setVisible(visible);
    fixCanvasSize();
  }

  /**
   *  Set value of the show label flag.
   *  @param show_label Show labels if and only if this argument is true.
   **/
  protected void setShowLabels(boolean show_labels) 
  {
    if(this.show_labels != show_labels) 
    {
      this.show_labels = show_labels;
      fixCanvasSize();
    } 
  }

  /**
   *  Get the value of the "show label" flag.
   **/
  protected boolean getShowLabels() 
  {
    return show_labels;
  }

  /**
   *  Set value of the "show forward frame lines" flag.
   *  @param show_forward_lines Show forward frame lines if and only if
   *    this argument is true.
   **/
  protected void setShowForwardFrameLines(boolean show_forward_lines) 
  {
    if(this.show_forward_lines != show_forward_lines) 
    {
      this.show_forward_lines = show_forward_lines;
      fixCanvasSize();
    } 
  }

  /**
   *  Get the value of the "show forward frame lines" flag.
   **/
  protected boolean getShowForwardFrameLines() 
  {
    return show_forward_lines;
  }

  /**
   *  Set value of the "show reverse frame lines" flag.
   *  @param show_reverse_lines Show frame lines if and only if this
   *    argument is true.
   **/
  protected void setShowReverseFrameLines(boolean show_reverse_lines) 
  {
    if(this.show_reverse_lines != show_reverse_lines) 
    {
      this.show_reverse_lines = show_reverse_lines;
      fixCanvasSize();
    }
  }

  /**
   *  Get the value of the "show source features" flag.
   **/
  protected boolean getShowSourceFeatures() 
  {
    return show_source_features;
  }

  /**
   *  Set value of the "show source features" flag.
   *  @param show_source_features Show features with a "source" key if and
   *    only if this argument is true.
   **/
  protected void setShowSourceFeatures(boolean show_source_features) 
  {
    if(this.show_source_features != show_source_features) 
    {
      this.show_source_features = show_source_features;
      needVisibleFeatureVectorUpdate();
      repaint();
    } 
  }

  /**
   *  Get the value of the "show frame lines" flag.
   **/
  protected boolean getShowReverseFrameLines()
  {
    return show_reverse_lines;
  }

  /**
   *  Set value of the show base colours flag.
   *  @param show_base_colours At scale_factor less than two show each base in
   *    a different colour if and only if this argument is true.
   **/
  protected void setShowBaseColours(boolean show_base_colours) 
  {
    if(this.show_base_colours != show_base_colours) 
    {
      this.show_base_colours = show_base_colours;
      if(getScaleFactor() > 1) 
        setScaleFactor(1);
      repaint();
    } 
  }

  /**
   *  Get the value of the "show base colours" flag.
   **/
  protected boolean getShowBaseColours() 
  {
    return show_base_colours;
  }

  /**
   *  Set value of the "one line per entry" flag.
   *  @param one_line_per_entry If true then each entry will be shown on a
   *    different line, instead of showing frame lines.
   **/
  protected void setOneLinePerEntry(final boolean one_line_per_entry)
  {
    if(this.one_line_per_entry != one_line_per_entry) 
    {
      this.one_line_per_entry = one_line_per_entry;
      fixCanvasSize();
    }
  }

  /**
   *  Get the value of the "one line per entry" flag.
   **/
  protected boolean getOneLinePerEntryFlag() 
  {
    return one_line_per_entry;
  }
  
  
  /**
   *  Set value of the feature stack view flag.
   *  @param feature_stack_view If true then each CDS will be shown on a
   *    different line, instead of showing frame lines.
   **/
  protected void setFeatureStackViewFlag(final boolean feature_stack_view)
  {
    if(this.feature_stack_view != feature_stack_view) 
    {
      this.feature_stack_view = feature_stack_view;
      fixCanvasSize();
    }
  }

  /**
   *  Get the value of the "one line per entry" flag.
   **/
  protected boolean getFeatureStackViewFlag() 
  {
    return feature_stack_view;
  }

  /**
   *  Set value of the "hard left edge" flag.
   *  @param hard_left_edge If true the there will never be a gap between the
   *    left edge of the screen and the first visible base.  If false base one
   *    can be moved to the centre of the display.
   **/
  protected void setHardLeftEdge(final boolean hard_left_edge) 
  {
    if(this.hard_left_edge != hard_left_edge) 
    {
      this.hard_left_edge = hard_left_edge;
      if(hard_left_edge && getForwardBaseAtLeftEdge() < 1) 
        setFirstVisibleForwardBase(1);
      
      fixScrollbar();
    } 
  }

  /**
   *  Set value of the show stop codons flag.
   *  @param show_stop_codons Show stop codons if and only if this argument is
   *    true.
   **/
  protected void setShowStopCodons(boolean show_stop_codons) 
  {
    if(this.show_stop_codons != show_stop_codons) 
    {
      this.show_stop_codons = show_stop_codons;
      repaint();
    } 
  }

  /**
   *  Return the value of the "show stop codons" flag.
   **/
  protected boolean getShowStopCodons() 
  { 
    return show_stop_codons;
  }

  /**
   *  Set value of the show start codons flag.
   *  @param show_start_codons Show start codons if and only if this argument
   *    is true.
   **/
  protected void setShowStartCodons(boolean show_start_codons) 
  {
    if(this.show_start_codons != show_start_codons) 
    {
      this.show_start_codons = show_start_codons;
      repaint();
    } 
  }

  /**
   *  Return the value of the "show start codons" flag.
   **/
  protected boolean getShowStartCodons() 
  {
    return show_start_codons;
  }

  /**
   *  Set value of the reverse complement display flag.
   *  @param show_start_codons Draw all features and sequence reverse
   *    complemented if and only if this argument is true.
   **/
  protected void setRevCompDisplay(boolean rev_comp_display) 
  {
    if(this.rev_comp_display != rev_comp_display) 
    {
      this.rev_comp_display = rev_comp_display;
      int remember_position = getCentreForwardBase();

      // we want to keep the selection visible after the flip, so
      // that will override the centre position
      final Marker first_base_marker =
        getSelection().getStartBaseOfSelection();

      if(first_base_marker != null && baseVisible(first_base_marker)) 
        remember_position = first_base_marker.getRawPosition();

      final Marker last_base_marker =
        getSelection().getStartBaseOfSelection();

      if(last_base_marker != null && baseVisible(last_base_marker)) 
        remember_position = last_base_marker.getRawPosition();

      fireAdjustmentEvent(DisplayAdjustmentEvent.REV_COMP_EVENT);

      makeBaseVisibleInternal(remember_position, isRevCompDisplay(), true);

      needVisibleFeatureVectorUpdate();
      fixScrollbar();
      repaint();
    }
  }

  /**
   *  Return the value of the "reverse complement display" flag.
   **/
  protected boolean isRevCompDisplay() 
  {
    return rev_comp_display;
  }

  /**
   *  Set value of the show feature arrows flag.
   *  @param show_feature_arrows Show directional arrows if and only if this
   *    argument is true.
   **/
  protected void setShowFeatureArrows(boolean show_feature_arrows)
  {
    if(this.show_feature_arrows != show_feature_arrows)
    {
      this.show_feature_arrows = show_feature_arrows;
      repaint();
    } 
  }

  /**
   *  Return the value of the "show feature arrows" flag.
   **/
  protected boolean getShowFeatureArrows() 
  {
    return show_feature_arrows;
  }

  /**
   *  Set value of the show feature borders flag.
   *  @param show_feature_borders Draw a border around each feature if and
   *    only if this argument is true.
   **/
  protected void setShowFeatureBorders(boolean show_feature_borders) 
  {
    if(this.show_feature_borders != show_feature_borders) 
    {
      this.show_feature_borders = show_feature_borders;
      repaint();
    } 
  }

  /**
   *  Return the value of the "show feature borders" flag.
   **/
  protected boolean getShowFeatureBorders() 
  {
    return show_feature_borders;
  }

  /**
   *  Set value of the show frame features flag.
   *  @param frame_features_flag All features(not just CDS features) will be
   *    drawn on the frame lines if and only if this argument is true.
   **/
  protected void setFrameFeaturesFlag(boolean frame_features_flag) 
  {
    if(this.frame_features_flag != frame_features_flag) 
    {
      this.frame_features_flag = frame_features_flag;
      repaint();
    } 
  }

  /**
   *  Return the value of the "show frame features" flag.
   **/
  protected boolean getFrameFeaturesFlag() 
  {
    return frame_features_flag;
  }

  /**
   *  Set the value of the minimum score for this FeatureDisplay - features
   *  that have a /score lower than this value are never shown.
   **/
  protected void setMinimumScore(final int minimum_score) 
  {
    current_min_score = minimum_score;
    needVisibleFeatureVectorUpdate();
    repaint();
  }

  /**
   *  Return the value of the minimum score for this FeatureDisplay - see
   *  setMinimumScore().
   **/
  private int getMinimumScore() 
  {
    return current_min_score;
  }

  /**
   *  Set the value of the maximum score for this FeatureDisplay - features
   *  that have a /score higher than this value are never shown.
   **/
  protected void setMaximumScore(final int maximum_score) 
  {
    current_max_score = maximum_score;
    needVisibleFeatureVectorUpdate();
    repaint();
  }

  /**
   *  Return the value of the maximum score for this FeatureDisplay - see
   *  setMaximumScore().
   **/
  private int getMaximumScore() 
  {
    return current_max_score;
  }

  /**
   *  Adds the specified event adjustment listener to receive adjustment
   *  change events from this object.
   *  @param l the event change listener.
   **/
  public void addDisplayAdjustmentListener(DisplayAdjustmentListener l) 
  {
    adjustment_listener_list.addElement(l);
  }

  /**
   *  Removes the specified event listener so that it no longer receives
   *  adjustment change events from this object.
   *  @param l the event change listener.
   **/
  public void removeDisplayAdjustmentListener(DisplayAdjustmentListener l) 
  {
    adjustment_listener_list.removeElement(l);
  }

  /**
   *  Handle key press events.  This is static because making it non-static
   *  triggered a java.lang.VerifyError
   **/
  private static void handleKeyPress(final FeatureDisplay feature_display,
                                      final KeyEvent event) 
  {
    // this is done so that menu shortcuts don't cause each action to be
    // performed twice
    if(event.getModifiers() != 0) 
      return;

    switch(event.getKeyCode()) 
    {
      case ZOOM_TO_SELECTION_KEY:
        FeaturePopup.zoomToSelection(feature_display);
        break;
      case ARROW_LEFT:
        feature_display.setFirstBase(
            feature_display.getFirstVisibleForwardBase()-
            feature_display.scrollbar.getUnitIncrement());
        break;
      case ARROW_RIGHT:
        feature_display.setFirstBase(
            feature_display.getFirstVisibleForwardBase()+
            feature_display.scrollbar.getUnitIncrement());
        break;
      default:
        break;
    }
  }

  /**
   *  Set the scale factor and update the display if the scale factor has
   *  changed.  A factor of zero means the full translation will be visible.
   *  At higher scale factors only stop codons are visible, and a bigger
   *  number will mean more bases are visible.
   **/
  protected void setScaleFactor(int scale_factor) 
  {
    if(this.scale_factor != scale_factor) 
    {
      // we will try to keep the base in the centre of the view to stay where
      // it is, so we save it's position in remember_position.
      int remember_position = getCentreForwardBase();

      // if the first base is visible then keep it visible
      if(hard_left_edge && getFirstVisibleForwardBase() == 1) 
        remember_position = 1;

      if(!getSelection().isEmpty()) 
      {
        // but, we want to keep the selection visible after a scale change, so
        // that will override the centre position
        final Marker first_base_marker =
          getSelection().getStartBaseOfSelection();

        final int first_base_marker_raw_position =
                  first_base_marker.getRawPosition();
        final int first_base_marker_position;

        if(isRevCompDisplay()) 
          first_base_marker_position =
              getBases().getComplementPosition(first_base_marker_raw_position);
        else 
          first_base_marker_position = first_base_marker_raw_position;

        final Marker last_base_marker =
                                   getSelection().getEndBaseOfSelection();

        final int last_base_marker_raw_position =
                                   last_base_marker.getRawPosition();

        final int last_base_marker_position;

        if(isRevCompDisplay()) 
          last_base_marker_position =
            getBases().getComplementPosition(last_base_marker_raw_position);
        else 
          last_base_marker_position = last_base_marker_raw_position;

        final int lowest_visible_base = getFirstVisibleForwardBase();
        final int highest_visible_base = getLastVisibleForwardBase();

        // first selected base or first visible base, whichever is greater
        int restricted_first_selected_base = lowest_visible_base;

        // last selected base or last visible base, whichever is smaller
        int restricted_last_selected_base = highest_visible_base;

        if(first_base_marker != null) 
        {
          if(first_base_marker_position > lowest_visible_base &&
              first_base_marker_position < highest_visible_base) 
            restricted_first_selected_base = first_base_marker_position;
        }

        if(last_base_marker != null) 
        {
          if(last_base_marker_position < highest_visible_base &&
              last_base_marker_position > lowest_visible_base) 
            restricted_last_selected_base = last_base_marker_position;
        }

        if(getSelection().getMarkerRange() == null) 
          remember_position = restricted_first_selected_base;
        else 
        {
          // keep the centre of the selection in the middle of the display if
          // a range of bases is selected
          remember_position = restricted_first_selected_base +
                             (restricted_last_selected_base -
                               restricted_first_selected_base) / 2;
        }
      }

      this.scale_factor = scale_factor;

      setScaleValue();
      
      if(scale_changer != null)
        scale_changer.setValue(scale_factor);
      setCentreVisibleForwardBase(remember_position);
      fixScrollbar();
      fireAdjustmentEvent(DisplayAdjustmentEvent.SCALE_ADJUST_EVENT);
      needVisibleFeatureVectorUpdate();

      repaint();
    }
  }

  /**
   *  Implementation of the FeatureChangeListener interface.  We listen to
   *  FeatureChange events so that we can update the display if qualifiers
   *  change.
   **/
  public void featureChanged(final FeatureChangeEvent event) 
  {
    final Feature event_feature = event.getFeature();

    if( event.getType() ==  FeatureChangeEvent.LOCATION_CHANGED &&
        event_feature.getEmblFeature() instanceof GFFStreamFeature &&
        !GeneUtils.isDatabaseEntry(event_feature.getEmblFeature()))
    {
      try
      {
        GFFUtils.updateSegmentRangeStore((GFFStreamFeature)event_feature.getEmblFeature(),
          event.getOldLocation(), event.getNewLocation());
      } catch(Exception e) {}
    }

    // the feature isn't in an active entry
    if(!getEntryGroup().contains(event_feature)) 
      return;
    
    // if the feature is visible now or is in the list of visible features
    //(ie. it was visible previously) then redisplay.
    if(featureVisible(event_feature) ||
       getVisibleFeatures().contains(event_feature)) 
    {
      // update the visible_features vector
      if(getVisibleFeatures().contains(event_feature) &&
         !featureVisible(event_feature)) 
        getVisibleFeatures().remove(event_feature);
      else 
      {