X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=adfb520c2236b045384a6b70417e7de2a207ebe9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=60a075984eadec2b3808ae11f834be3093df0d25;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 60a0759..adfb520 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,66 +1,83 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-import javax.swing.event.*;
-
-import net.miginfocom.swing.MigLayout;
-
 import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.schemes.*;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
 import jalview.util.MessageManager;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
 import java.awt.Dimension;
+import java.awt.FlowLayout;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.util.Hashtable;
+
+import javax.swing.BorderFactory;
+import javax.swing.JButton;
+import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.JPanel;
 
-public class AnnotationColourChooser extends JPanel
-{
-  JInternalFrame frame;
-
-  AlignViewport av;
+import net.miginfocom.swing.MigLayout;
 
-  AlignmentPanel ap;
+@SuppressWarnings("serial")
+public class AnnotationColourChooser extends AnnotationRowFilter
+{
 
   ColourSchemeI oldcs;
 
-  Hashtable oldgroupColours;
-
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
 
-  boolean adjusting = false;
   /**
-   * enabled if the user is dragging the slider - try to keep updates to a minimun
+   * enabled if the user is dragging the slider - try to keep updates to a
+   * minimun
    */
-  boolean sliderDragging = false;
+
+  JComboBox<String> annotations;
+
+  JButton defColours = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JPanel jPanel2 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  private JComboBox<String> threshold = new JComboBox<String>();
 
   public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
   {
+    super(av, ap);
     oldcs = av.getGlobalColourScheme();
     if (av.getAlignment().getGroups() != null)
     {
-      oldgroupColours = new Hashtable();
+      oldgroupColours = new Hashtable<SequenceGroup, ColourSchemeI>();
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
         if (sg.cs != null)
@@ -69,49 +86,15 @@ public class AnnotationColourChooser extends JPanel
         }
       }
     }
-    this.av = av;
-    this.ap = ap;
     frame = new JInternalFrame();
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
+    Desktop.addInternalFrame(frame,
+            MessageManager.getString("label.colour_by_annotation"), 520,
+            215);
 
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        if (!adjusting)
-        {
-          thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
-          valueChanged(!sliderDragging);
-        }
-      }
-    });
-    slider.addMouseListener(new MouseAdapter()
-    {
-      @Override
-      public void mousePressed(MouseEvent e)
-      {
-        sliderDragging=true;
-        super.mousePressed(e);
-      }
-
-      @Override
-      public void mouseDragged(MouseEvent e)
-      {
-        sliderDragging=true;
-        super.mouseDragged(e);
-      }
-      public void mouseReleased(MouseEvent evt)
-      {
-        if (sliderDragging)
-        {
-          sliderDragging=false;
-          valueChanged(true);
-        }
-        ap.paintAlignment(true);
-      }
-    });
+    addSliderChangeListener();
+    addSliderMouseListeners();
 
     if (av.getAlignment().getAlignmentAnnotation() == null)
     {
@@ -125,21 +108,20 @@ public class AnnotationColourChooser extends JPanel
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      currentColours.setSelected(acg.isPredefinedColours() || acg.getBaseColour()!=null);
-      if (!acg.isPredefinedColours() && acg.getBaseColour()==null)
+      currentColours.setSelected(acg.isPredefinedColours()
+              || acg.getBaseColour() != null);
+      if (!acg.isPredefinedColours() && acg.getBaseColour() == null)
       {
         minColour.setBackground(acg.getMinColour());
         maxColour.setBackground(acg.getMaxColour());
       }
       seqAssociated.setSelected(acg.isSeqAssociated());
-      
+
     }
-    annotations = new JComboBox(
+    annotations = new JComboBox<String>(
             getAnnotationItems(seqAssociated.isSelected()));
 
-    threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
-    threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
-    threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
+    populateThresholdComboBox(threshold);
 
     if (oldcs instanceof AnnotationColourGradient)
     {
@@ -148,17 +130,18 @@ public class AnnotationColourChooser extends JPanel
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
-        threshold.setSelectedIndex(0);
+        getThreshold().setSelectedIndex(0);
         break;
       case AnnotationColourGradient.ABOVE_THRESHOLD:
-        threshold.setSelectedIndex(1);
+        getThreshold().setSelectedIndex(1);
         break;
       case AnnotationColourGradient.BELOW_THRESHOLD:
-        threshold.setSelectedIndex(2);
+        getThreshold().setSelectedIndex(2);
         break;
       default:
         throw new Error(
-                "Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+                MessageManager
+                        .getString("error.implementation_error_dont_know_about_thereshold_setting"));
       }
       thresholdIsMin.setSelected(acg.thresholdIsMinMax);
       thresholdValue.setText("" + acg.getAnnotationThreshold());
@@ -170,61 +153,11 @@ public class AnnotationColourChooser extends JPanel
     } catch (Exception ex)
     {
     }
-
     adjusting = false;
 
-    changeColour();
+    updateView();
     frame.invalidate();
     frame.pack();
-
-  }
-
-  private Vector<String> getAnnotationItems(boolean isSeqAssociated)
-  {
-    Vector<String> list = new Vector<String>();
-    int index = 1;
-    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
-    boolean enableSeqAss = false;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
-      {
-        if (isSeqAssociated)
-        {
-          continue;
-        }
-      }
-      else
-      {
-        enableSeqAss = true;
-      }
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-      {
-        anmap[list.size()] = i;
-        list.addElement(label);
-
-      }
-      else
-      {
-        if (!isSeqAssociated)
-        {
-          anmap[list.size()] = i;
-          list.addElement(label + "_" + (index++));
-        }
-      }
-    }
-    seqAssociated.setEnabled(enableSeqAss);
-    annmap = new int[list.size()];
-    System.arraycopy(anmap, 0, annmap, 0, annmap.length);
-    return list;
-  }
-  private void setDefaultMinMax()
-  {
-    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
-            Color.orange));
-    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
-            Color.red));
   }
 
   public AnnotationColourChooser()
@@ -246,6 +179,7 @@ public class AnnotationColourChooser extends JPanel
     minColour.setToolTipText(MessageManager.getString("label.min_colour"));
     minColour.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         if (minColour.isEnabled())
@@ -260,6 +194,7 @@ public class AnnotationColourChooser extends JPanel
     maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
     maxColour.addMouseListener(new MouseAdapter()
     {
+      @Override
       public void mousePressed(MouseEvent e)
       {
         if (maxColour.isEnabled())
@@ -272,6 +207,7 @@ public class AnnotationColourChooser extends JPanel
     ok.setText(MessageManager.getString("action.ok"));
     ok.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         ok_actionPerformed(e);
@@ -281,6 +217,7 @@ public class AnnotationColourChooser extends JPanel
     cancel.setText(MessageManager.getString("action.cancel"));
     cancel.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         cancel_actionPerformed(e);
@@ -288,8 +225,8 @@ public class AnnotationColourChooser extends JPanel
     });
     defColours.setOpaque(false);
     defColours.setText(MessageManager.getString("action.set_defaults"));
-    defColours
-            .setToolTipText(MessageManager.getString("label.reset_min_max_colours_to_defaults"));
+    defColours.setToolTipText(MessageManager
+            .getString("label.reset_min_max_colours_to_defaults"));
     defColours.addActionListener(new ActionListener()
     {
 
@@ -302,13 +239,15 @@ public class AnnotationColourChooser extends JPanel
 
     annotations.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         annotations_actionPerformed(e);
       }
     });
-    threshold.addActionListener(new ActionListener()
+    getThreshold().addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         threshold_actionPerformed(e);
@@ -316,6 +255,7 @@ public class AnnotationColourChooser extends JPanel
     });
     thresholdValue.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         thresholdValue_actionPerformed(e);
@@ -331,9 +271,11 @@ public class AnnotationColourChooser extends JPanel
     thresholdValue.setColumns(7);
     currentColours.setFont(JvSwingUtils.getLabelFont());
     currentColours.setOpaque(false);
-    currentColours.setText(MessageManager.getString("label.use_original_colours"));
+    currentColours.setText(MessageManager
+            .getString("label.use_original_colours"));
     currentColours.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent e)
       {
         currentColours_actionPerformed(e);
@@ -341,9 +283,11 @@ public class AnnotationColourChooser extends JPanel
     });
     thresholdIsMin.setBackground(Color.white);
     thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
-    thresholdIsMin.setText(MessageManager.getString("label.threshold_minmax"));
+    thresholdIsMin.setText(MessageManager
+            .getString("label.threshold_minmax"));
     thresholdIsMin.addActionListener(new ActionListener()
     {
+      @Override
       public void actionPerformed(ActionEvent actionEvent)
       {
         thresholdIsMin_actionPerformed(actionEvent);
@@ -351,14 +295,15 @@ public class AnnotationColourChooser extends JPanel
     });
     seqAssociated.setBackground(Color.white);
     seqAssociated.setFont(JvSwingUtils.getLabelFont());
-    seqAssociated.setText(MessageManager.getString("label.per_sequence_only"));
+    seqAssociated.setText(MessageManager
+            .getString("label.per_sequence_only"));
     seqAssociated.addActionListener(new ActionListener()
     {
 
       @Override
       public void actionPerformed(ActionEvent arg0)
       {
-        seqAssociated_actionPerformed(arg0);
+        seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
       }
     });
 
@@ -377,7 +322,7 @@ public class AnnotationColourChooser extends JPanel
     colpanel.add(minColour);
     colpanel.add(maxColour);
     jPanel2.add(colpanel, "wrap");
-    jPanel2.add(threshold);
+    jPanel2.add(getThreshold());
     jPanel2.add(defColours, "skip 1, wrap");
     jPanel2.add(thresholdIsMin);
     jPanel2.add(slider, "grow");
@@ -387,324 +332,153 @@ public class AnnotationColourChooser extends JPanel
     this.validate();
   }
 
-  protected void seqAssociated_actionPerformed(ActionEvent arg0)
-  {
-    adjusting = true;
-    String cursel = (String) annotations.getSelectedItem();
-    boolean isvalid = false, isseqs = seqAssociated.isSelected();
-    this.annotations.removeAllItems();
-    for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
-    {
-      if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
-      {
-        isvalid = true;
-        cursel = anitem;
-      }
-      this.annotations.addItem(anitem);
-    }
-    adjusting = false;
-    if (isvalid)
-    {
-      this.annotations.setSelectedItem(cursel);
-    }
-    else
-    {
-      if (annotations.getItemCount() > 0)
-      {
-        annotations.setSelectedIndex(0);
-      }
-    }
-  }
-
   protected void resetColours_actionPerformed(ActionEvent arg0)
   {
     setDefaultMinMax();
-    changeColour();
+    updateView();
   }
 
-  JComboBox annotations;
-
-  int[] annmap;
-
-  JPanel minColour = new JPanel();
-
-  JPanel maxColour = new JPanel();
-
-  JButton defColours = new JButton();
-
-  JButton ok = new JButton();
-
-  JButton cancel = new JButton();
-
-  JPanel jPanel1 = new JPanel();
-
-  JPanel jPanel2 = new JPanel();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  JComboBox threshold = new JComboBox();
-
-  JSlider slider = new JSlider();
-
-  JTextField thresholdValue = new JTextField(20);
-
-  JCheckBox currentColours = new JCheckBox();
-
-  JCheckBox thresholdIsMin = new JCheckBox();
-
-  JCheckBox seqAssociated = new JCheckBox();
+  private void setDefaultMinMax()
+  {
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+            Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+            Color.red));
+  }
 
   public void minColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            "Select Colour for Minimum Value", minColour.getBackground());
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
     if (col != null)
     {
       minColour.setBackground(col);
     }
     minColour.repaint();
-    changeColour();
+    updateView();
   }
 
   public void maxColour_actionPerformed()
   {
     Color col = JColorChooser.showDialog(this,
-            "Select Colour for Maximum Value", maxColour.getBackground());
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
     if (col != null)
     {
       maxColour.setBackground(col);
     }
     maxColour.repaint();
-    changeColour();
+    updateView();
   }
 
-  void changeColour()
+  public void reset()
   {
-    // Check if combobox is still adjusting
-    if (adjusting)
-    {
-      return;
-    }
-
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[annmap[annotations
-            .getSelectedIndex()]];
-
-    int aboveThreshold = -1;
-    if (threshold.getSelectedIndex()==1)
-    {
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
-    }
-    else if (threshold.getSelectedIndex()==2)
-    {
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
-    }
-
-    slider.setEnabled(true);
-    thresholdValue.setEnabled(true);
-    thresholdIsMin.setEnabled(true);
-
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
-    {
-      slider.setEnabled(false);
-      thresholdValue.setEnabled(false);
-      thresholdValue.setText("");
-      thresholdIsMin.setEnabled(false);
-    }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
-            && currentAnnotation.threshold == null)
-    {
-      currentAnnotation
-              .setThreshold(new jalview.datamodel.GraphLine(
-                      (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
-                      "Threshold", Color.black));
-    }
-
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
-    {
-      adjusting = true;
-      float range = currentAnnotation.graphMax * 1000
-              - currentAnnotation.graphMin * 1000;
-
-      slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
-      slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
-      slider.setValue((int) (currentAnnotation.threshold.value * 1000));
-      thresholdValue.setText(currentAnnotation.threshold.value + "");
-      slider.setMajorTickSpacing((int) (range / 10f));
-      slider.setEnabled(true);
-      thresholdValue.setEnabled(true);
-      adjusting = false;
-    }
-
-    AnnotationColourGradient acg = null;
-    if (currentColours.isSelected())
-    {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              av.getGlobalColourScheme(), aboveThreshold);
-    }
-    else
-    {
-      acg = new AnnotationColourGradient(currentAnnotation,
-              minColour.getBackground(), maxColour.getBackground(),
-              aboveThreshold);
-    }
-    acg.setSeqAssociated(seqAssociated.isSelected());
-
-    if (currentAnnotation.graphMin == 0f
-            && currentAnnotation.graphMax == 0f)
-    {
-      acg.setPredefinedColours(true);
-    }
-
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
-
-    av.setGlobalColourScheme(acg);
-
+    av.setGlobalColourScheme(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
 
       for (SequenceGroup sg : ap.av.getAlignment().getGroups())
       {
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        if (currentColours.isSelected())
-        {
-          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
-                  aboveThreshold);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
-
-        }
-        else
-        {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  aboveThreshold);
-          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
-                  .isSelected());
-        }
-
+        sg.cs = oldgroupColours.get(sg);
       }
     }
-    ap.alignmentChanged();
-    // ensure all associated views (overviews, structures, etc) are notified of
-    // updated colours.
-    ap.paintAlignment(true);
   }
 
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-    try
-    {
-      frame.setClosed(true);
-    } catch (Exception ex)
-    {
-    }
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    reset();
-    // ensure all original colouring is propagated to listeners.
-    ap.paintAlignment(true);
-    try
-    {
-      frame.setClosed(true);
-    } catch (Exception ex)
-    {
-    }
-  }
-
-  void reset()
+  public void valueChanged(boolean updateAllAnnotation)
   {
-    av.setGlobalColourScheme(oldcs);
-    if (av.getAlignment().getGroups() != null)
+    if (slider.isEnabled())
     {
-
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      if (currentColours.isSelected()
+              && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
       {
-        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);
+        updateView();
       }
+      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      propagateSeqAssociatedThreshold(updateAllAnnotation,
+              getCurrentAnnotation());
+      ap.paintAlignment(false);
     }
   }
 
-  public void thresholdCheck_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
+  public JComboBox<String> getThreshold()
   {
-    changeColour();
+    return threshold;
   }
 
-  public void threshold_actionPerformed(ActionEvent e)
+  public void setThreshold(JComboBox<String> threshold)
   {
-    changeColour();
+    this.threshold = threshold;
   }
 
-  public void thresholdValue_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue((int) (f * 1000));
-    } catch (NumberFormatException ex)
-    {
-    }
-  }
-
-  public void valueChanged(boolean updateAllAnnotation)
+  public void currentColours_actionPerformed(ActionEvent e)
   {
-    if (currentColours.isSelected()
-            && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+    if (currentColours.isSelected())
     {
-      changeColour();
+      reset();
     }
-    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
-    propagateSeqAssociatedThreshold(updateAllAnnotation);
-    ap.paintAlignment(false);
+    maxColour.setEnabled(!currentColours.isSelected());
+    minColour.setEnabled(!currentColours.isSelected());
+    updateView();
   }
 
-  private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+  @Override
+  public void updateView()
   {
-    if (currentAnnotation.sequenceRef == null
-            || currentAnnotation.threshold == null)
+    // Check if combobox is still adjusting
+    if (adjusting)
     {
       return;
     }
-    // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
 
-    float thr = currentAnnotation.threshold.value;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
-      if (aa.label.equals(currentAnnotation.label))
-      {
-        aa.threshold.value = thr;
-      }
-    }
-  }
+    setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+            .getSelectedIndex()]]);
 
-  public void currentColours_actionPerformed(ActionEvent e)
-  {
-    if (currentColours.isSelected())
+    int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+            .getSelectedIndex());
+
+    slider.setEnabled(true);
+    thresholdValue.setEnabled(true);
+    thresholdIsMin.setEnabled(true);
+
+    if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
-      reset();
+      slider.setEnabled(false);
+      thresholdValue.setEnabled(false);
+      thresholdValue.setText("");
+      thresholdIsMin.setEnabled(false);
+    }
+    else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
+            && getCurrentAnnotation().threshold == null)
+    {
+      getCurrentAnnotation()
+              .setThreshold(
+                      new jalview.datamodel.GraphLine(
+                              (getCurrentAnnotation().graphMax - getCurrentAnnotation().graphMin) / 2f,
+                              "Threshold", Color.black));
     }
 
-    maxColour.setEnabled(!currentColours.isSelected());
-    minColour.setEnabled(!currentColours.isSelected());
+    if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
+      float range = getCurrentAnnotation().graphMax * 1000
+              - getCurrentAnnotation().graphMin * 1000;
 
-    changeColour();
-  }
+      slider.setMinimum((int) (getCurrentAnnotation().graphMin * 1000));
+      slider.setMaximum((int) (getCurrentAnnotation().graphMax * 1000));
+      slider.setValue((int) (getCurrentAnnotation().threshold.value * 1000));
+      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
+      slider.setMajorTickSpacing((int) (range / 10f));
+      slider.setEnabled(true);
+      thresholdValue.setEnabled(true);
+      adjusting = false;
+    }
+    colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
 
-  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
-  {
-    changeColour();
+    ap.alignmentChanged();
+    // ensure all associated views (overviews, structures, etc) are notified of
+    // updated colours.
+    ap.paintAlignment(true);
   }
 
 }