From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 27 Jul 2020 15:46:47 +0000 (+0100)
Subject: Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
X-Git-Tag: Release_2_11_1_1~22^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=6b56f0140b759b789da51aa4ed327d43297a3a5d;hp=-c;p=jalview.git

Merge branch 'bug/JAL-2983negativeSliderMin' into releases/Release_2_11_1_Branch
Conflict in way transparency slider was inited - followed HEAD's pattern here.
---

6b56f0140b759b789da51aa4ed327d43297a3a5d
diff --combined src/jalview/gui/FeatureSettings.java
index b87e4bf,3a04b88..aeac959
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@@ -20,13 -20,8 +20,13 @@@
   */
  package jalview.gui;
  
 +import jalview.api.AlignViewControllerGuiI;
 +import jalview.api.AlignViewportI;
  import jalview.api.FeatureColourI;
  import jalview.api.FeatureSettingsControllerI;
 +import jalview.api.SplitContainerI;
 +import jalview.api.ViewStyleI;
 +import jalview.controller.FeatureSettingsControllerGuiI;
  import jalview.datamodel.AlignmentI;
  import jalview.datamodel.SequenceI;
  import jalview.datamodel.features.FeatureMatcher;
@@@ -40,7 -35,6 +40,7 @@@ import jalview.schemes.FeatureColour
  import jalview.util.MessageManager;
  import jalview.util.Platform;
  import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean;
 +import jalview.viewmodel.styles.ViewStyle;
  import jalview.xml.binding.jalview.JalviewUserColours;
  import jalview.xml.binding.jalview.JalviewUserColours.Colour;
  import jalview.xml.binding.jalview.JalviewUserColours.Filter;
@@@ -50,7 -44,6 +50,7 @@@ import java.awt.BorderLayout
  import java.awt.Color;
  import java.awt.Component;
  import java.awt.Dimension;
 +import java.awt.FlowLayout;
  import java.awt.Font;
  import java.awt.Graphics;
  import java.awt.GridLayout;
@@@ -115,7 -108,7 +115,7 @@@ import javax.xml.stream.XMLInputFactory
  import javax.xml.stream.XMLStreamReader;
  
  public class FeatureSettings extends JPanel
 -        implements FeatureSettingsControllerI
 +        implements FeatureSettingsControllerI, FeatureSettingsControllerGuiI
  {
    private static final String SEQUENCE_FEATURE_COLOURS = MessageManager
            .getString("label.sequence_feature_colours");
@@@ -150,8 -143,6 +150,8 @@@
  
    private float originalTransparency;
  
 +  private ViewStyleI originalViewStyle;
 +
    private Map<String, FeatureMatcherSetI> originalFilters;
  
    final JInternalFrame frame;
@@@ -162,11 -153,7 +162,11 @@@
  
    JPanel groupPanel;
  
-   JSlider transparency = new JSlider();
 -  JSlider transparency;
++  JSlider transparency= new JSlider();
 +
 +  private JCheckBox showComplementOnTop;
 +
 +  private JCheckBox showComplement;
  
    /*
     * when true, constructor is still executing - so ignore UI events
@@@ -183,36 -170,10 +183,36 @@@
    private boolean handlingUpdate = false;
  
    /*
 +   * a change listener to ensure the dialog is updated if
 +   * FeatureRenderer discovers new features
 +   */
 +  private PropertyChangeListener change;
 +
 +  /*
     * holds {featureCount, totalExtent} for each feature type
     */
    Map<String, float[]> typeWidth = null;
  
 +  private void storeOriginalSettings()
 +  {
 +    // save transparency for restore on Cancel
 +    originalTransparency = fr.getTransparency();
 +
 +    updateTransparencySliderFromFR();
 +
 +    originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
 +    originalViewStyle = new ViewStyle(af.viewport.getViewStyle());
 +  }
 +
 +  private void updateTransparencySliderFromFR()
 +  {
 +    boolean incon = inConstruction;
 +    inConstruction = true;
 +
 +    int transparencyAsPercent = (int) (fr.getTransparency() * 100);
 +    transparency.setValue(100 - transparencyAsPercent);
 +    inConstruction = incon;
 +  }
    /**
     * Constructor
     * 
@@@ -223,7 -184,12 +223,7 @@@
      this.af = alignFrame;
      fr = af.getFeatureRenderer();
  
 -    // save transparency for restore on Cancel
 -    originalTransparency = fr.getTransparency();
 -    int originalTransparencyAsPercent = (int) (originalTransparency * 100);
 -    transparency = new JSlider(0, 70, 100 - originalTransparencyAsPercent);
 -
 -    originalFilters = new HashMap<>(fr.getFeatureFilters()); // shallow copy
 +    storeOriginalSettings();
  
      try
      {
@@@ -309,8 -275,7 +309,8 @@@
        @Override
        public void mousePressed(MouseEvent evt)
        {
 -        selectedRow = table.rowAtPoint(evt.getPoint());
 +        Point pt = evt.getPoint();
 +        selectedRow = table.rowAtPoint(pt);
          String type = (String) table.getValueAt(selectedRow, TYPE_COLUMN);
          if (evt.isPopupTrigger())
          {
@@@ -318,15 -283,13 +318,15 @@@
            popupSort(selectedRow, type, colour, fr.getMinMax(), evt.getX(),
                    evt.getY());
          }
 -        else if (evt.getClickCount() == 2)
 +        else if (evt.getClickCount() == 2
 +                && table.columnAtPoint(pt) == TYPE_COLUMN)
          {
            boolean invertSelection = evt.isAltDown();
            boolean toggleSelection = Platform.isControlDown(evt);
            boolean extendSelection = evt.isShiftDown();
            fr.ap.alignFrame.avc.markColumnsContainingFeatures(
                    invertSelection, extendSelection, toggleSelection, type);
 +          fr.ap.av.sendSelection();
          }
        }
  
@@@ -383,6 -346,7 +383,6 @@@
      }
  
      discoverAllFeatureData();
 -    final PropertyChangeListener change;
      final FeatureSettings fs = this;
      fr.addPropertyChangeListener(change = new PropertyChangeListener()
      {
@@@ -399,115 -363,75 +399,115 @@@
        }
  
      });
 -
 -    frame = new JInternalFrame();
 -    frame.setContentPane(this);
 -    if (Platform.isAMac())
 +    SplitContainerI splitframe = af.getSplitViewContainer();
 +    if (splitframe != null)
      {
 -      Desktop.addInternalFrame(frame,
 -              MessageManager.getString("label.sequence_feature_settings"),
 -              600, 480);
 +      frame = null; // keeps eclipse happy
 +      splitframe.addFeatureSettingsUI(this);
      }
      else
      {
 -      Desktop.addInternalFrame(frame,
 -              MessageManager.getString("label.sequence_feature_settings"),
 -              600, 450);
 -    }
 -    frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
 +      frame = new JInternalFrame();
 +      frame.setContentPane(this);
 +      Rectangle bounds = af.getFeatureSettingsGeometry();
 +      String title;
 +      if (af.getAlignPanels().size() > 1 || Desktop.getAlignmentPanels(
 +              af.alignPanel.av.getSequenceSetId()).length > 1)
 +      {
 +        title = MessageManager.formatMessage(
 +                "label.sequence_feature_settings_for_view",
 +                af.alignPanel.getViewName());
 +      }
 +      else
 +      {
 +        title = MessageManager.getString("label.sequence_feature_settings");
 +      }
 +      if (bounds == null)
 +      {
 +        if (Platform.isAMac())
 +        {
 +          Desktop.addInternalFrame(frame, title, 600, 480);
 +        }
 +        else
 +        {
 +          Desktop.addInternalFrame(frame, title, 600, 450);
 +        }
 +      }
 +      else
 +      {
 +        Desktop.addInternalFrame(frame, title,
 +                false, bounds.width, bounds.height);
 +        frame.setBounds(bounds);
 +        frame.setVisible(true);
 +      }
 +      frame.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT));
  
 -    frame.addInternalFrameListener(
 -            new javax.swing.event.InternalFrameAdapter()
 -            {
 -              @Override
 -              public void internalFrameClosed(
 -                      javax.swing.event.InternalFrameEvent evt)
 +      frame.addInternalFrameListener(
 +              new javax.swing.event.InternalFrameAdapter()
                {
 -                fr.removePropertyChangeListener(change);
 -              };
 -            });
 -    frame.setLayer(JLayeredPane.PALETTE_LAYER);
 +                @Override
 +                public void internalFrameClosed(
 +                        javax.swing.event.InternalFrameEvent evt)
 +                {
 +                  featureSettings_isClosed();
 +                };
 +              });
 +      frame.setLayer(JLayeredPane.PALETTE_LAYER);
 +    }
      inConstruction = false;
    }
  
 +  /**
 +   * Sets the state of buttons to show complement features from viewport
 +   * settings
 +   */
 +  private void updateComplementButtons()
 +  {
 +    showComplement.setSelected(af.getViewport().isShowComplementFeatures());
 +    showComplementOnTop
 +            .setSelected(af.getViewport().isShowComplementFeaturesOnTop());
 +  }
 +
 +  @Override
 +  public AlignViewControllerGuiI getAlignframe()
 +  {
 +    return af;
 +  }
 +
 +  @Override
 +  public void featureSettings_isClosed()
 +  {
 +    fr.removePropertyChangeListener(change);
 +    change = null;
 +  }
 +
    protected void popupSort(final int rowSelected, final String type,
            final Object typeCol, final Map<String, float[][]> minmax, int x,
            int y)
    {
 -    final FeatureColourI featureColour = (FeatureColourI) typeCol;
 -
      JPopupMenu men = new JPopupMenu(MessageManager
              .formatMessage("label.settings_for_param", new String[]
              { type }));
      JMenuItem scr = new JMenuItem(
              MessageManager.getString("label.sort_by_score"));
      men.add(scr);
 -    final FeatureSettings me = this;
      scr.addActionListener(new ActionListener()
      {
        @Override
        public void actionPerformed(ActionEvent e)
        {
 -        me.af.avc
 -                .sortAlignmentByFeatureScore(Arrays.asList(new String[]
 -                { type }));
 +        sortByScore(Arrays.asList(new String[] { type }));
        }
 -
      });
      JMenuItem dens = new JMenuItem(
              MessageManager.getString("label.sort_by_density"));
      dens.addActionListener(new ActionListener()
      {
        @Override
        public void actionPerformed(ActionEvent e)
        {
 -        me.af.avc
 -                .sortAlignmentByFeatureDensity(Arrays.asList(new String[]
 -                { type }));
 +        sortByDensity(Arrays.asList(new String[] { type }));
        }
 -
      });
      men.add(dens);
  
@@@ -520,7 -444,6 +520,7 @@@
        {
          fr.ap.alignFrame.avc.markColumnsContainingFeatures(false, false,
                  false, type);
 +        fr.ap.av.sendSelection();
        }
      });
      JMenuItem clearCols = new JMenuItem(MessageManager
@@@ -532,7 -455,6 +532,7 @@@
        {
          fr.ap.alignFrame.avc.markColumnsContainingFeatures(true, false,
                  false, type);
 +        fr.ap.av.sendSelection();
        }
      });
      JMenuItem hideCols = new JMenuItem(
@@@ -543,7 -465,6 +543,7 @@@
        public void actionPerformed(ActionEvent arg0)
        {
          fr.ap.alignFrame.hideFeatureColumns(type, true);
 +        fr.ap.av.sendSelection();
        }
      });
      JMenuItem hideOtherCols = new JMenuItem(
@@@ -554,7 -475,6 +554,7 @@@
        public void actionPerformed(ActionEvent arg0)
        {
          fr.ap.alignFrame.hideFeatureColumns(type, false);
 +        fr.ap.av.sendSelection();
        }
      });
      men.add(selCols);
@@@ -564,47 -484,6 +564,47 @@@
      men.show(table, x, y);
    }
  
 +  /**
 +   * Sort the sequences in the alignment by the number of features for the given
 +   * feature types (or all features if null)
 +   * 
 +   * @param featureTypes
 +   */
 +  protected void sortByDensity(List<String> featureTypes)
 +  {
 +    af.avc.sortAlignmentByFeatureDensity(featureTypes);
 +  }
 +
 +  /**
 +   * Sort the sequences in the alignment by average score for the given feature
 +   * types (or all features if null)
 +   * 
 +   * @param featureTypes
 +   */
 +  protected void sortByScore(List<String> featureTypes)
 +  {
 +    af.avc.sortAlignmentByFeatureScore(featureTypes);
 +  }
 +
 +  /**
 +   * Returns true if at least one feature type is visible. Else shows a warning
 +   * dialog and returns false.
 +   * 
 +   * @param title
 +   * @return
 +   */
 +  private boolean canSortBy(String title)
 +  {
 +    if (fr.getDisplayedFeatureTypes().isEmpty())
 +    {
 +      JvOptionPane.showMessageDialog(this,
 +              MessageManager.getString("label.no_features_to_sort_by"),
 +              title, JvOptionPane.OK_OPTION);
 +      return false;
 +    }
 +    return true;
 +  }
 +
    @Override
    synchronized public void discoverAllFeatureData()
    {
@@@ -659,7 -538,7 +659,7 @@@
        {
          fr.setGroupVisibility(check.getText(), check.isSelected());
          resetTable(new String[] { grp });
 -        af.alignPanel.paintAlignment(true, true);
 +        refreshDisplay();
        }
      });
      groupPanel.add(check);
@@@ -1188,38 -1067,11 +1188,38 @@@
      table.repaint();
    }
  
 +  /**
 +   * close ourselves but leave any existing UI handlers (e.g a CDS/Protein tabbed
 +   * feature settings dialog) intact
 +   */
 +  public void closeOldSettings()
 +  {
 +    closeDialog(false);
 +  }
 +
 +  /**
 +   * close the feature settings dialog (and any containing frame)
 +   */
    public void close()
    {
 +    closeDialog(true);
 +  }
 +
 +  private void closeDialog(boolean closeContainingFrame)
 +  {
      try
      {
 -      frame.setClosed(true);
 +      if (frame != null)
 +      {
 +        af.setFeatureSettingsGeometry(frame.getBounds());
 +        frame.setClosed(true);
 +      }
 +      else
 +      {
 +        SplitContainerI sc = af.getSplitViewContainer();
 +        sc.closeFeatureSettings(this, closeContainingFrame);
 +        af.featureSettings = null;
 +      }
      } catch (Exception exe)
      {
      }
@@@ -1244,7 -1096,7 +1244,7 @@@
  
      if (fr.setFeaturePriority(rowData, visibleNew))
      {
 -      af.alignPanel.paintAlignment(true, true);
 +      refreshDisplay();
      }
    }
  
@@@ -1270,9 -1122,6 +1270,9 @@@
    {
      this.setLayout(new BorderLayout());
  
 +    final boolean hasComplement = af.getViewport()
 +            .getCodingComplement() != null;
 +
      JPanel settingsPane = new JPanel();
      settingsPane.setLayout(new BorderLayout());
  
@@@ -1306,32 -1155,26 +1306,32 @@@
        }
      });
  
 -    JButton sortByScore = new JButton(
 -            MessageManager.getString("label.seq_sort_by_score"));
 +    final String byScoreLabel = MessageManager.getString("label.seq_sort_by_score");
 +    JButton sortByScore = new JButton(byScoreLabel);
      sortByScore.setFont(JvSwingUtils.getLabelFont());
      sortByScore.addActionListener(new ActionListener()
      {
        @Override
        public void actionPerformed(ActionEvent e)
        {
 -        af.avc.sortAlignmentByFeatureScore(null);
 +        if (canSortBy(byScoreLabel))
 +        {
 +          sortByScore(null);
 +        }
        }
      });
 -    JButton sortByDens = new JButton(
 -            MessageManager.getString("label.sequence_sort_by_density"));
 +    final String byDensityLabel = MessageManager.getString("label.sequence_sort_by_density");
 +    JButton sortByDens = new JButton(byDensityLabel);
      sortByDens.setFont(JvSwingUtils.getLabelFont());
      sortByDens.addActionListener(new ActionListener()
      {
        @Override
        public void actionPerformed(ActionEvent e)
        {
 -        af.avc.sortAlignmentByFeatureDensity(null);
 +        if (canSortBy(byDensityLabel))
 +        {
 +          sortByDensity(null);
 +        }
        }
      });
  
@@@ -1351,48 -1194,29 +1351,48 @@@
          }
        }
      });
 -
 -    JButton cancel = new JButton(MessageManager.getString("action.cancel"));
 +    // Cancel for a SplitFrame should just revert changes to the currently displayed
 +    // settings. May want to do this for either or both - so need a splitview
 +    // feature settings cancel/OK.
 +    JButton cancel = new JButton(MessageManager
 +            .getString(hasComplement ? "action.revert" : "action.cancel"));
 +    cancel.setToolTipText(MessageManager.getString(hasComplement
 +            ? "action.undo_changes_to_feature_settings"
 +            : "action.undo_changes_to_feature_settings_and_close_the_dialog"));
      cancel.setFont(JvSwingUtils.getLabelFont());
 +    // TODO: disable cancel (and apply!) until current settings are different
      cancel.addActionListener(new ActionListener()
      {
        @Override
        public void actionPerformed(ActionEvent e)
        {
 -        fr.setTransparency(originalTransparency);
 -        fr.setFeatureFilters(originalFilters);
 -        updateFeatureRenderer(originalData);
 -        close();
 +        revert();
 +        refreshDisplay();
 +        if (!hasComplement)
 +        {
 +          close();
 +        }
        }
      });
 -
 -    JButton ok = new JButton(MessageManager.getString("action.ok"));
 +    // Cancel for the whole dialog should cancel both CDS and Protein.
 +    // OK for an individual feature settings just applies changes, but dialog
 +    // remains open
 +    JButton ok = new JButton(MessageManager
 +            .getString(hasComplement ? "action.apply" : "action.ok"));
      ok.setFont(JvSwingUtils.getLabelFont());
      ok.addActionListener(new ActionListener()
      {
        @Override
        public void actionPerformed(ActionEvent e)
        {
 -        close();
 +        if (!hasComplement)
 +        {
 +          close();
 +        }
 +        else
 +        {
 +          storeOriginalSettings();
 +        }
        }
      });
  
@@@ -1431,50 -1255,16 +1431,50 @@@
          if (!inConstruction)
          {
            fr.setTransparency((100 - transparency.getValue()) / 100f);
 -          af.alignPanel.paintAlignment(true, true);
 +          refreshDisplay();
          }
        }
      });
  
 +    transparency.setMaximum(70);
      transparency.setToolTipText(
              MessageManager.getString("label.transparency_tip"));
  
 -    JPanel transPanel = new JPanel(new GridLayout(1, 2));
 -    bigPanel.add(transPanel, BorderLayout.SOUTH);
 +    boolean nucleotide = af.getViewport().getAlignment().isNucleotide();
 +    String text = MessageManager.formatMessage("label.show_linked_features",
 +            nucleotide
 +                    ? MessageManager.getString("label.protein")
 +                            .toLowerCase()
 +                    : "CDS");
 +    showComplement = new JCheckBox(text);
 +    showComplement.addActionListener(new ActionListener()
 +    {
 +      @Override
 +      public void actionPerformed(ActionEvent e)
 +      {
 +        af.getViewport()
 +                .setShowComplementFeatures(showComplement.isSelected());
 +        refreshDisplay();
 +      }
 +    });
 +
 +    showComplementOnTop = new JCheckBox(
 +            MessageManager.getString("label.on_top"));
 +    showComplementOnTop.addActionListener(new ActionListener()
 +    {
 +      @Override
 +      public void actionPerformed(ActionEvent e)
 +      {
 +        af.getViewport().setShowComplementFeaturesOnTop(
 +                showComplementOnTop.isSelected());
 +        refreshDisplay();
 +      }
 +    });
 +
 +    updateComplementButtons();
 +
 +    JPanel lowerPanel = new JPanel(new GridLayout(1, 2));
 +    bigPanel.add(lowerPanel, BorderLayout.SOUTH);
  
      JPanel transbuttons = new JPanel(new GridLayout(5, 1));
      transbuttons.add(optimizeOrder);
@@@ -1482,20 -1272,8 +1482,20 @@@
      transbuttons.add(sortByScore);
      transbuttons.add(sortByDens);
      transbuttons.add(help);
 -    transPanel.add(transparency);
 -    transPanel.add(transbuttons);
 +
 +    JPanel transPanelLeft = new JPanel(
 +            new GridLayout(hasComplement ? 4 : 2, 1));
 +    transPanelLeft.add(new JLabel(" Colour transparency" + ":"));
 +    transPanelLeft.add(transparency);
 +    if (hasComplement)
 +    {
 +      JPanel cp = new JPanel(new FlowLayout(FlowLayout.LEFT));
 +      cp.add(showComplement);
 +      cp.add(showComplementOnTop);
 +      transPanelLeft.add(cp);
 +    }
 +    lowerPanel.add(transPanelLeft);
 +    lowerPanel.add(transbuttons);
  
      JPanel buttonPanel = new JPanel();
      buttonPanel.add(ok);
@@@ -1509,27 -1287,11 +1509,27 @@@
    }
  
    /**
 +   * Repaints alignment, structure and overview (if shown). If there is a
 +   * complementary view which is showing this view's features, then also
 +   * repaints that.
 +   */
 +  void refreshDisplay()
 +  {
 +    af.alignPanel.paintAlignment(true, true);
 +    AlignViewportI complement = af.getViewport().getCodingComplement();
 +    if (complement != null && complement.isShowComplementFeatures())
 +    {
 +      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
 +      af2.alignPanel.paintAlignment(true, true);
 +    }
 +  }
 +
 +  /**
     * Answers a suitable tooltip to show on the colour cell of the table
     * 
     * @param fcol
     * @param withHint
 -   *          if true include 'click to edit' and similar text
 +   *                   if true include 'click to edit' and similar text
     * @return
     */
    public static String getColorTooltip(FeatureColourI fcol,
@@@ -1666,22 -1428,13 +1666,22 @@@
      }
  
      /**
 -     * Answers the class of the object in column c of the first row of the table
 +     * Answers the class of column c of the table
       */
      @Override
      public Class<?> getColumnClass(int c)
      {
 -      Object v = getValueAt(0, c);
 -      return v == null ? null : v.getClass();
 +      switch (c)
 +      {
 +      case TYPE_COLUMN:
 +        return String.class;
 +      case COLOUR_COLUMN:
 +        return FeatureColour.class;
 +      case FILTER_COLUMN:
 +        return FeatureMatcherSet.class;
 +      default:
 +        return Boolean.class;
 +      }
      }
  
      @Override
@@@ -2064,27 -1817,6 +2064,27 @@@
        return button;
      }
    }
 +
 +  public boolean isOpen()
 +  {
 +    if (af.getSplitViewContainer() != null)
 +    {
 +      return af.getSplitViewContainer().isFeatureSettingsOpen();
 +    }
 +    return frame != null && !frame.isClosed();
 +  }
 +
 +  @Override
 +  public void revert()
 +  {
 +    fr.setTransparency(originalTransparency);
 +    fr.setFeatureFilters(originalFilters);
 +    updateFeatureRenderer(originalData);
 +    af.getViewport().setViewStyle(originalViewStyle);
 +    updateTransparencySliderFromFR();
 +    updateComplementButtons();
 +    refreshDisplay();
 +  }
  }
  
  class FeatureIcon implements Icon
diff --combined src/jalview/gui/FeatureTypeSettings.java
index 5b77dfc,92918d4..512cf06
--- a/src/jalview/gui/FeatureTypeSettings.java
+++ b/src/jalview/gui/FeatureTypeSettings.java
@@@ -20,7 -20,6 +20,7 @@@
   */
  package jalview.gui;
  
 +import jalview.api.AlignViewportI;
  import jalview.api.AlignmentViewPanel;
  import jalview.api.FeatureColourI;
  import jalview.bin.Cache;
@@@ -49,6 -48,8 +49,8 @@@ import java.awt.event.ItemEvent
  import java.awt.event.ItemListener;
  import java.awt.event.MouseAdapter;
  import java.awt.event.MouseEvent;
+ import java.math.BigDecimal;
+ import java.math.MathContext;
  import java.text.DecimalFormat;
  import java.util.ArrayList;
  import java.util.List;
@@@ -63,7 -64,6 +65,6 @@@ import javax.swing.JComboBox
  import javax.swing.JLabel;
  import javax.swing.JPanel;
  import javax.swing.JRadioButton;
- import javax.swing.JSlider;
  import javax.swing.JTextField;
  import javax.swing.border.EmptyBorder;
  import javax.swing.border.LineBorder;
@@@ -79,6 -79,8 +80,8 @@@ import javax.swing.event.ChangeListener
   */
  public class FeatureTypeSettings extends JalviewDialog
  {
+   private final static MathContext FOUR_SIG_FIG = new MathContext(4);
+ 
    private final static String LABEL_18N = MessageManager
            .getString("label.label");
  
@@@ -142,11 -144,6 +145,6 @@@
    private float max;
  
    /*
-    * scale factor for conversion between absolute min-max and slider
-    */
-   private float scaleFactor;
- 
-   /*
     * radio button group, to select what to colour by:
     * simple colour, by category (text), or graduated
     */
@@@ -169,7 -166,7 +167,7 @@@
  
    private JComboBox<Object> threshold = new JComboBox<>();
  
-   private JSlider slider = new JSlider();
+   private Slider slider;
  
    private JTextField thresholdValue = new JTextField(20);
  
@@@ -348,12 -345,11 +346,11 @@@
         * update min-max scaling if there is a range to work with,
         * else disable the widgets (this shouldn't happen if only 
         * valid options are offered in the combo box)
+        * offset slider to have only non-negative values if necessary (JAL-2983)
         */
-       scaleFactor = (max == min) ? 1f : 100f / (max - min);
-       float range = (max - min) * scaleFactor;
-       slider.setMinimum((int) (min * scaleFactor));
-       slider.setMaximum((int) (max * scaleFactor));
-       slider.setMajorTickSpacing((int) (range / 10f));
+       slider.setSliderModel(min, max, min);
+       slider.setMajorTickSpacing(
+               (int) ((slider.getMaximum() - slider.getMinimum()) / 10f));
  
        threshline = new GraphLine((max - min) / 2f, "Threshold",
                Color.black);
@@@ -365,8 -361,8 +362,8 @@@
                  fc.isAboveThreshold() ? ABOVE_THRESHOLD_OPTION
                          : BELOW_THRESHOLD_OPTION);
          slider.setEnabled(true);
-         slider.setValue((int) (fc.getThreshold() * scaleFactor));
-         thresholdValue.setText(String.valueOf(fc.getThreshold()));
+         slider.setSliderValue(fc.getThreshold());
+         setThresholdValueText(fc.getThreshold());
          thresholdValue.setEnabled(true);
          thresholdIsMin.setEnabled(true);
        }
@@@ -641,6 -637,7 +638,7 @@@
          thresholdValue_actionPerformed();
        }
      });
+     slider = new Slider(0f, 100f, 50f);
      slider.setPaintLabels(false);
      slider.setPaintTicks(true);
      slider.setBackground(Color.white);
@@@ -657,8 -654,7 +655,7 @@@
        {
          if (!adjusting)
          {
-           thresholdValue
-                   .setText(String.valueOf(slider.getValue() / scaleFactor));
+           setThresholdValueText(slider.getSliderValue());
            thresholdValue.setBackground(Color.white); // to reset red for invalid
            sliderValueChanged();
          }
@@@ -675,7 -671,7 +672,7 @@@
           */
          if (ap != null)
          {
 -          ap.paintAlignment(true, true);
 +          refreshDisplay(true);
          }
        }
      });
@@@ -876,7 -872,7 +873,7 @@@
       * save the colour, and repaint stuff
       */
      fr.setColour(featureType, acg);
 -    ap.paintAlignment(updateStructsAndOverview, updateStructsAndOverview);
 +    refreshDisplay(updateStructsAndOverview);
  
      updateColoursTab();
    }
@@@ -1015,7 -1011,7 +1012,7 @@@
    {
      fr.setColour(featureType, originalColour);
      fr.setFeatureFilter(featureType, originalFilter);
 -    ap.paintAlignment(true, true);
 +    refreshDisplay(true);
    }
  
    /**
@@@ -1033,8 -1029,8 +1030,8 @@@
        float f = Float.parseFloat(thresholdValue.getText());
        f = Float.max(f,  this.min);
        f = Float.min(f, this.max);
-       thresholdValue.setText(String.valueOf(f));
-       slider.setValue((int) (f * scaleFactor));
+       setThresholdValueText(f);
+       slider.setSliderValue(f);
        threshline.value = f;
        thresholdValue.setBackground(Color.white); // ok
        adjusting = false;
@@@ -1047,13 -1043,25 +1044,25 @@@
    }
  
    /**
+    * Sets the text field for threshold value, rounded to four significant figures
+    * 
+    * @param f
+    */
+   void setThresholdValueText(float f)
+   {
+     BigDecimal formatted = new BigDecimal(f).round(FOUR_SIG_FIG)
+             .stripTrailingZeros();
+     thresholdValue.setText(formatted.toPlainString());
+   }
+ 
+   /**
     * Action on change of threshold slider value. This may be done interactively
     * (by moving the slider), or programmatically (to update the slider after
     * manual input of a threshold value).
     */
    protected void sliderValueChanged()
    {
-     threshline.value = getRoundedSliderValue();
+     threshline.value = slider.getSliderValue();
  
      /*
       * repaint alignment, but not Overview or structure,
@@@ -1062,21 -1070,6 +1071,6 @@@
      colourChanged(false);
    }
  
-   /**
-    * Converts the slider value to its absolute value by dividing by the
-    * scaleFactor. Rounding errors are squashed by forcing min/max of slider
-    * range to the actual min/max of feature score range
-    * 
-    * @return
-    */
-   private float getRoundedSliderValue()
-   {
-     int value = slider.getValue();
-     float f = value == slider.getMaximum() ? max
-             : (value == slider.getMinimum() ? min : value / scaleFactor);
-     return f;
-   }
- 
    void addActionListener(ActionListener listener)
    {
      if (featureSettings != null)
@@@ -1754,26 -1747,8 +1748,26 @@@
       * (note this might now be an empty filter with no conditions)
       */
      fr.setFeatureFilter(featureType, combined.isEmpty() ? null : combined);
 -    ap.paintAlignment(true, true);
 +    refreshDisplay(true);
  
      updateFiltersTab();
    }
 +
 +  /**
 +   * Repaints alignment, structure and overview (if shown). If there is a
 +   * complementary view which is showing this view's features, then also
 +   * repaints that.
 +   * 
 +   * @param updateStructsAndOverview
 +   */
 +  void refreshDisplay(boolean updateStructsAndOverview)
 +  {
 +    ap.paintAlignment(true, updateStructsAndOverview);
 +    AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
 +    if (complement != null && complement.isShowComplementFeatures())
 +    {
 +      AlignFrame af2 = Desktop.getAlignFrameFor(complement);
 +      af2.alignPanel.paintAlignment(true, updateStructsAndOverview);
 +    }
 +  }
  }