X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=adfb520c2236b045384a6b70417e7de2a207ebe9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=49e835de3420d933ef681eb44592c9465041c521;hpb=09003bd97d75ad14cd000fc581d6ec93b7a08bcb;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index 49e835d..adfb520
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,439 +1,484 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* 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., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.gui;
-
-import javax.swing.*;
-import java.awt.event.*;
-import java.awt.*;
-
-import jalview.schemes.*;
-import javax.swing.event.*;
-import java.util.*;
-import jalview.datamodel.SequenceGroup;
-
-public class AnnotationColourChooser
-    extends JPanel
-{
-  JInternalFrame frame;
-  AlignViewport av;
-  AlignmentPanel ap;
-  ColourSchemeI oldcs;
-  Hashtable oldgroupColours;
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;
-
-  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
-  {
-    oldcs = av.getGlobalColourScheme();
-    if (av.alignment.getGroups() != null)
-    {
-      oldgroupColours = new Hashtable();
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        oldgroupColours.put(sg, sg.cs);
-      }
-    }
-    this.av = av;
-    this.ap = ap;
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    frame.setLayer(JLayeredPane.PALETTE_LAYER);
-    Desktop.addInternalFrame(frame, "Colour by Annotation", 480, 145, false);
-
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {}
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
-        valueChanged();
-      }
-    });
-
-    if (av.alignment.getAlignmentAnnotation() == null)
-      return;
-
-    if (oldcs instanceof AnnotationColourGradient)
-    {
-      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      minColour.setBackground(acg.getMinColour());
-      maxColour.setBackground(acg.getMaxColour());
-    }
-    else
-    {
-      minColour.setBackground(Color.orange);
-      maxColour.setBackground(Color.red);
-    }
-
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
-    {
-      if (av.alignment.getAlignmentAnnotation()[i].graph > 0)
-        annotations.addItem(av.alignment.getAlignmentAnnotation()[i].label);
-    }
-
-    threshold.addItem("No Threshold");
-    threshold.addItem("Above Threshold");
-    threshold.addItem("Below Threshold");
-
-  }
-
-  public AnnotationColourChooser()
-  {
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    minColour.setToolTipText("");
-    minColour.setMargin(new Insets(2, 2, 2, 2));
-    minColour.setText("Min Colour");
-    minColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        minColour_actionPerformed(e);
-      }
-    });
-    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    maxColour.setMargin(new Insets(2, 2, 2, 2));
-    maxColour.setText("Max Colour");
-    maxColour.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        maxColour_actionPerformed(e);
-      }
-    });
-    ok.setOpaque(false);
-    ok.setText("OK");
-    ok.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        ok_actionPerformed(e);
-      }
-    });
-    cancel.setOpaque(false);
-    cancel.setText("Cancel");
-    cancel.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        cancel_actionPerformed(e);
-      }
-    });
-    this.setLayout(borderLayout1);
-    jPanel2.setLayout(flowLayout1);
-    annotations.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        annotations_actionPerformed(e);
-      }
-    });
-    jPanel1.setBackground(Color.white);
-    jPanel2.setBackground(Color.white);
-    threshold.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        threshold_actionPerformed(e);
-      }
-    });
-    jPanel3.setLayout(flowLayout2);
-    thresholdValue.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        thresholdValue_actionPerformed(e);
-      }
-    });
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(10);
-    jPanel3.setBackground(Color.white);
-    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    currentColours.setOpaque(false);
-    currentColours.setText("Use Original Colours");
-    currentColours.addActionListener(new ActionListener()
-    {
-      public void actionPerformed(ActionEvent e)
-      {
-        currentColours_actionPerformed(e);
-      }
-    });
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-    jPanel2.add(annotations);
-    jPanel2.add(currentColours);
-    jPanel2.add(minColour);
-    jPanel2.add(maxColour);
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);
-    jPanel3.add(threshold);
-    jPanel3.add(slider);
-    jPanel3.add(thresholdValue);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-    this.add(jPanel2, java.awt.BorderLayout.NORTH);
-  }
-
-  JComboBox annotations = new JComboBox();
-  JButton minColour = new JButton();
-  JButton maxColour = 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();
-  FlowLayout flowLayout1 = new FlowLayout();
-  JPanel jPanel3 = new JPanel();
-  FlowLayout flowLayout2 = new FlowLayout();
-  JSlider slider = new JSlider();
-  JTextField thresholdValue = new JTextField(20);
-  JCheckBox currentColours = new JCheckBox();
-
-  public void minColour_actionPerformed(ActionEvent e)
-  {
-    Color col = JColorChooser.showDialog(this,
-                                         "Select Colour for Minimum Value",
-                                         minColour.getBackground());
-    if (col != null)
-      minColour.setBackground(col);
-    minColour.repaint();
-    changeColour();
-  }
-
-  public void maxColour_actionPerformed(ActionEvent e)
-  {
-    Color col = JColorChooser.showDialog(this,
-                                         "Select Colour for Maximum Value",
-                                         maxColour.getBackground());
-    if (col != null)
-      maxColour.setBackground(col);
-    maxColour.repaint();
-    changeColour();
-  }
-
-  void changeColour()
-  {
-    // Check if combobox is still adjusting
-    if (threshold.getSelectedIndex() == -1)
-      return;
-
-    // We removed the non-graph annotations when filling the combobox
-    // so allow for them again here
-    int nograph = 0, graph = -1;
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
-    {
-      if (av.alignment.getAlignmentAnnotation()[i].graph == 0)
-        nograph++;
-      else
-        graph++;
-
-      if (graph == annotations.getSelectedIndex())
-        break;
-    }
-
-    currentAnnotation = av.alignment.getAlignmentAnnotation()[graph + nograph];
-
-    int aboveThreshold = -1;
-    if (threshold.getSelectedItem().equals("Above Threshold"))
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
-    else if (threshold.getSelectedItem().equals("Below Threshold"))
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
-
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
-    {
-      currentAnnotation.threshold = null;
-      slider.setEnabled(false);
-      thresholdValue.setEnabled(false);
-      thresholdValue.setText("");
-    }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&
-             currentAnnotation.threshold == null)
-    {
-      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine
-                                     ( (currentAnnotation.graphMax -
-                                        currentAnnotation.graphMin) / 2f,
-                                      "Threshold",
-                                      Color.black));
-      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.setMinorTickSpacing( (int) (range / 100f));
-      slider.setEnabled(true);
-      thresholdValue.setEnabled(true);
-    }
-
-    AnnotationColourGradient acg = null;
-    if (currentColours.isSelected())
-      acg = new AnnotationColourGradient(
-          currentAnnotation,
-          av.getGlobalColourScheme(), aboveThreshold);
-    else
-      acg =
-          new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
-
-    av.setGlobalColourScheme(acg);
-
-    if (av.alignment.getGroups() != null)
-    {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-
-        if (sg.cs == null)
-        {
-          continue;
-        }
-
-        if (currentColours.isSelected())
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              sg.cs, aboveThreshold);
-        else
-          sg.cs = new AnnotationColourGradient(
-              currentAnnotation,
-              minColour.getBackground(),
-              maxColour.getBackground(),
-              aboveThreshold);
-
-      }
-    }
-
-    ap.repaint();
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    reset();
-    try
-    {
-      frame.setClosed(true);
-    }
-    catch (Exception ex)
-    {}
-  }
-
-
-  void reset()
-  {
-    av.setGlobalColourScheme(oldcs);
-    if (av.alignment.getGroups() != null)
-    {
-      Vector allGroups = ap.av.alignment.getGroups();
-      SequenceGroup sg;
-      for (int g = 0; g < allGroups.size(); g++)
-      {
-        sg = (SequenceGroup) allGroups.get(g);
-        sg.cs = (ColourSchemeI)oldgroupColours.get(sg);
-      }
-    }
-  }
-
-  public void thresholdCheck_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    if(currentAnnotation!=null)
-      currentAnnotation.threshold = null;
-    changeColour();
-  }
-
-  public void threshold_actionPerformed(ActionEvent e)
-  {
-    changeColour();
-  }
-
-  public void thresholdValue_actionPerformed(ActionEvent e)
-  {
-    try
-    {
-      float f = Float.parseFloat(thresholdValue.getText());
-      slider.setValue( (int) (f * 1000));
-    }
-    catch (NumberFormatException ex)
-    {}
-  }
-
-  public void valueChanged()
-  {
-    currentAnnotation.threshold.value = (float)slider.getValue()/1000f;
-    ap.repaint();
-  }
-
-  public void currentColours_actionPerformed(ActionEvent e)
-  {
-    if(currentColours.isSelected())
-    {
-      reset();
-    }
-
-    maxColour.setEnabled(!currentColours.isSelected());
-    minColour.setEnabled(!currentColours.isSelected());
-
-    changeColour();
-  }
-
-}
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.bin.Cache;
+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;
+
+import net.miginfocom.swing.MigLayout;
+
+@SuppressWarnings("serial")
+public class AnnotationColourChooser extends AnnotationRowFilter
+{
+
+  ColourSchemeI oldcs;
+
+  Hashtable<SequenceGroup, ColourSchemeI> oldgroupColours;
+
+  /**
+   * enabled if the user is dragging the slider - try to keep updates to a
+   * minimun
+   */
+
+  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<SequenceGroup, ColourSchemeI>();
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        if (sg.cs != null)
+        {
+          oldgroupColours.put(sg, sg.cs);
+        }
+      }
+    }
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame,
+            MessageManager.getString("label.colour_by_annotation"), 520,
+            215);
+
+    addSliderChangeListener();
+    addSliderMouseListeners();
+
+    if (av.getAlignment().getAlignmentAnnotation() == null)
+    {
+      return;
+    }
+
+    // Always get default shading from preferences.
+    setDefaultMinMax();
+
+    adjusting = true;
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      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<String>(
+            getAnnotationItems(seqAssociated.isSelected()));
+
+    populateThresholdComboBox(threshold);
+
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      annotations.setSelectedItem(acg.getAnnotation());
+      switch (acg.getAboveThreshold())
+      {
+      case AnnotationColourGradient.NO_THRESHOLD:
+        getThreshold().setSelectedIndex(0);
+        break;
+      case AnnotationColourGradient.ABOVE_THRESHOLD:
+        getThreshold().setSelectedIndex(1);
+        break;
+      case AnnotationColourGradient.BELOW_THRESHOLD:
+        getThreshold().setSelectedIndex(2);
+        break;
+      default:
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_dont_know_about_thereshold_setting"));
+      }
+      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdValue.setText("" + acg.getAnnotationThreshold());
+    }
+
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+    }
+    adjusting = false;
+
+    updateView();
+    frame.invalidate();
+    frame.pack();
+  }
+
+  public AnnotationColourChooser()
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  private void jbInit() throws Exception
+  {
+    minColour.setFont(JvSwingUtils.getLabelFont());
+    minColour.setBorder(BorderFactory.createEtchedBorder());
+    minColour.setPreferredSize(new Dimension(40, 20));
+    minColour.setToolTipText(MessageManager.getString("label.min_colour"));
+    minColour.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        if (minColour.isEnabled())
+        {
+          minColour_actionPerformed();
+        }
+      }
+    });
+    maxColour.setFont(JvSwingUtils.getLabelFont());
+    maxColour.setBorder(BorderFactory.createEtchedBorder());
+    maxColour.setPreferredSize(new Dimension(40, 20));
+    maxColour.setToolTipText(MessageManager.getString("label.max_colour"));
+    maxColour.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        if (maxColour.isEnabled())
+        {
+          maxColour_actionPerformed();
+        }
+      }
+    });
+    ok.setOpaque(false);
+    ok.setText(MessageManager.getString("action.ok"));
+    ok.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setOpaque(false);
+    cancel.setText(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        cancel_actionPerformed(e);
+      }
+    });
+    defColours.setOpaque(false);
+    defColours.setText(MessageManager.getString("action.set_defaults"));
+    defColours.setToolTipText(MessageManager
+            .getString("label.reset_min_max_colours_to_defaults"));
+    defColours.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        resetColours_actionPerformed(arg0);
+      }
+    });
+
+    annotations.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        annotations_actionPerformed(e);
+      }
+    });
+    getThreshold().addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed(e);
+      }
+    });
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        thresholdValue_actionPerformed(e);
+      }
+    });
+    slider.setPaintLabels(false);
+    slider.setPaintTicks(true);
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setOpaque(false);
+    slider.setPreferredSize(new Dimension(100, 32));
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(7);
+    currentColours.setFont(JvSwingUtils.getLabelFont());
+    currentColours.setOpaque(false);
+    currentColours.setText(MessageManager
+            .getString("label.use_original_colours"));
+    currentColours.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        currentColours_actionPerformed(e);
+      }
+    });
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+    thresholdIsMin.setText(MessageManager
+            .getString("label.threshold_minmax"));
+    thresholdIsMin.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        thresholdIsMin_actionPerformed(actionEvent);
+      }
+    });
+    seqAssociated.setBackground(Color.white);
+    seqAssociated.setFont(JvSwingUtils.getLabelFont());
+    seqAssociated.setText(MessageManager
+            .getString("label.per_sequence_only"));
+    seqAssociated.addActionListener(new ActionListener()
+    {
+
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        seqAssociated_actionPerformed(arg0, annotations, seqAssociated);
+      }
+    });
+
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(new MigLayout("", "[left][center][right]", "[][][]"));
+    jPanel1.setBackground(Color.white);
+    jPanel2.setBackground(Color.white);
+
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel2.add(annotations, "grow, wrap");
+    jPanel2.add(seqAssociated);
+    jPanel2.add(currentColours);
+    JPanel colpanel = new JPanel(new FlowLayout());
+    colpanel.setBackground(Color.white);
+    colpanel.add(minColour);
+    colpanel.add(maxColour);
+    jPanel2.add(colpanel, "wrap");
+    jPanel2.add(getThreshold());
+    jPanel2.add(defColours, "skip 1, wrap");
+    jPanel2.add(thresholdIsMin);
+    jPanel2.add(slider, "grow");
+    jPanel2.add(thresholdValue, "grow");
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+    this.add(jPanel2, java.awt.BorderLayout.CENTER);
+    this.validate();
+  }
+
+  protected void resetColours_actionPerformed(ActionEvent arg0)
+  {
+    setDefaultMinMax();
+    updateView();
+  }
+
+  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,
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
+    if (col != null)
+    {
+      minColour.setBackground(col);
+    }
+    minColour.repaint();
+    updateView();
+  }
+
+  public void maxColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
+    if (col != null)
+    {
+      maxColour.setBackground(col);
+    }
+    maxColour.repaint();
+    updateView();
+  }
+
+  public void reset()
+  {
+    av.setGlobalColourScheme(oldcs);
+    if (av.getAlignment().getGroups() != null)
+    {
+
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        sg.cs = oldgroupColours.get(sg);
+      }
+    }
+  }
+
+  public void valueChanged(boolean updateAllAnnotation)
+  {
+    if (slider.isEnabled())
+    {
+      if (currentColours.isSelected()
+              && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+      {
+        updateView();
+      }
+      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      propagateSeqAssociatedThreshold(updateAllAnnotation,
+              getCurrentAnnotation());
+      ap.paintAlignment(false);
+    }
+  }
+
+  public JComboBox<String> getThreshold()
+  {
+    return threshold;
+  }
+
+  public void setThreshold(JComboBox<String> threshold)
+  {
+    this.threshold = threshold;
+  }
+
+  public void currentColours_actionPerformed(ActionEvent e)
+  {
+    if (currentColours.isSelected())
+    {
+      reset();
+    }
+    maxColour.setEnabled(!currentColours.isSelected());
+    minColour.setEnabled(!currentColours.isSelected());
+    updateView();
+  }
+
+  @Override
+  public void updateView()
+  {
+    // Check if combobox is still adjusting
+    if (adjusting)
+    {
+      return;
+    }
+
+    setCurrentAnnotation(av.getAlignment().getAlignmentAnnotation()[annmap[annotations
+            .getSelectedIndex()]]);
+
+    int selectedThresholdItem = getSelectedThresholdItem(getThreshold()
+            .getSelectedIndex());
+
+    slider.setEnabled(true);
+    thresholdValue.setEnabled(true);
+    thresholdIsMin.setEnabled(true);
+
+    if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
+    {
+      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));
+    }
+
+    if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
+      float range = getCurrentAnnotation().graphMax * 1000
+              - getCurrentAnnotation().graphMin * 1000;
+
+      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);
+
+    ap.alignmentChanged();
+    // ensure all associated views (overviews, structures, etc) are notified of
+    // updated colours.
+    ap.paintAlignment(true);
+  }
+
+}