X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=2b9787ff8ecdfff12bd920b7b50a13f765653d95;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=d49a4b6e70277e24eb7d9cd6863ab6b749c3c043;hpb=59c22b05925dd3b4d148c1ce0e43eea12bc64ba7;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index d49a4b6..2b9787f 100755
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,462 +1,579 @@
-/*
-* 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;
-  boolean adjusting = false;
-
-  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);
-
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {}
-
-    slider.addChangeListener(new ChangeListener()
-    {
-      public void stateChanged(ChangeEvent evt)
-      {
-        if(!adjusting)
-        {
-          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);
-    }
-
-    adjusting = true;
-    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");
-
-    adjusting = false;
-
-    changeColour();
-
-  }
-
-  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.setPaintLabels(false);
-    slider.setPaintTicks(true);
-    slider.setBackground(Color.white);
-    slider.setEnabled(false);
-    slider.setOpaque(false);
-    slider.setPreferredSize(new Dimension(150, 32));
-    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 (adjusting)
-      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;
-
-    slider.setEnabled(true);
-    thresholdValue.setEnabled(true);
-
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
-    {
-      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));
-    }
-
-    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.setMinorTickSpacing( (int) (range / 100f));
-      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);
-
-    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)
-  {
-    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()
-  {
-    if (currentColours.isSelected()
-        && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
-    {
-      changeColour();
-    }
-
-    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 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+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 java.awt.Dimension;
+
+public class AnnotationColourChooser extends JPanel
+{
+  JInternalFrame frame;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  ColourSchemeI oldcs;
+
+  Hashtable oldgroupColours;
+
+  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+
+  boolean adjusting = false;
+
+  public AnnotationColourChooser(AlignViewport av, final 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);
+        if (sg.cs != null)
+        {
+          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", 520, 215);
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        if (!adjusting)
+        {
+          thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+          valueChanged();
+        }
+      }
+    });
+    slider.addMouseListener(new MouseAdapter()
+    {
+      public void mouseReleased(MouseEvent evt)
+      {
+        ap.paintAlignment(true);
+      }
+    });
+
+    if (av.alignment.getAlignmentAnnotation() == null)
+    {
+      return;
+    }
+
+    // Always get default shading from preferences.
+    setDefaultMinMax();
+    
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      currentColours.setSelected(acg.predefinedColours);
+      if (!acg.predefinedColours)
+      {
+    	minColour.setBackground(acg.getMinColour());
+        maxColour.setBackground(acg.getMaxColour());
+      }
+    }
+
+    adjusting = true;
+    Vector list = new Vector();
+    int index = 1;
+    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)
+    {
+      String label = av.alignment.getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+        list.addElement(label);
+      else
+        list.addElement(label + "_" + (index++));
+    }
+
+    annotations = new JComboBox(list);
+
+    threshold.addItem("No Threshold");
+    threshold.addItem("Above Threshold");
+    threshold.addItem("Below Threshold");
+
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      annotations.setSelectedItem(acg.getAnnotation());
+      switch (acg.getAboveThreshold()) {
+      case AnnotationColourGradient.NO_THRESHOLD:
+          threshold.setSelectedItem("No Threshold");
+        break;
+      case AnnotationColourGradient.ABOVE_THRESHOLD:
+          threshold.setSelectedItem("Above Threshold");
+        break;
+      case AnnotationColourGradient.BELOW_THRESHOLD:
+        threshold.setSelectedItem("Below Threshold");
+        break;
+        default:
+          throw new Error("Implementation error: don't know about threshold setting for current AnnotationColourGradient.");
+      }
+      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdValue.setText(""+acg.getAnnotationThreshold());
+    }
+
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+    }
+
+    adjusting = false;
+
+    changeColour();
+    validate();
+
+  }
+
+  private void setDefaultMinMax()
+  {
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+  }
+
+  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("Minimum Colour");
+    minColour.addMouseListener(new MouseAdapter()
+    {
+      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("Maximum Colour");
+    maxColour.addMouseListener(new MouseAdapter()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (maxColour.isEnabled())
+        {
+          maxColour_actionPerformed();
+        }
+      }
+    });
+    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);
+      }
+    });
+    defColours.setOpaque(false);
+    defColours.setText("Defaults");
+    defColours.setToolTipText("Reset min and max colours to defaults from user preferences.");
+    defColours.addActionListener(new ActionListener()
+    {
+      
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        resetColours_actionPerformed(arg0);
+      }
+    });
+    
+    annotations.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        annotations_actionPerformed(e);
+      }
+    });
+    threshold.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        threshold_actionPerformed(e);
+      }
+    });
+    thresholdValue.addActionListener(new ActionListener()
+    {
+      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("Use Original Colours");
+    currentColours.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        currentColours_actionPerformed(e);
+      }
+    });
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setFont(JvSwingUtils.getLabelFont());
+    thresholdIsMin.setText("Threshold is Min/Max");
+    thresholdIsMin.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        thresholdIsMin_actionPerformed(actionEvent);
+      }
+    });
+    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);
+    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(threshold);
+    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);
+  }
+
+  protected void resetColours_actionPerformed(ActionEvent arg0)
+  {
+    setDefaultMinMax();
+    changeColour();
+  }
+
+  JComboBox annotations;
+
+  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();
+
+  public void minColour_actionPerformed()
+  {
+    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()
+  {
+    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 (adjusting)
+    {
+      return;
+    }
+
+    currentAnnotation = av.alignment.getAlignmentAnnotation()[annotations
+            .getSelectedIndex()];
+
+    int aboveThreshold = -1;
+    if (threshold.getSelectedItem().equals("Above Threshold"))
+    {
+      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+    }
+    else if (threshold.getSelectedItem().equals("Below Threshold"))
+    {
+      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);
+    }
+
+    if (currentAnnotation.graphMin == 0f
+            && currentAnnotation.graphMax == 0f)
+    {
+      acg.predefinedColours = true;
+    }
+
+    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
+    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);
+        }
+
+      }
+    }
+    // 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()
+  {
+    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)
+  {
+    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()
+  {
+    if (currentColours.isSelected()
+            && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+    {
+      changeColour();
+    }
+
+    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+    ap.paintAlignment(false);
+  }
+
+  public void currentColours_actionPerformed(ActionEvent e)
+  {
+    if (currentColours.isSelected())
+    {
+      reset();
+    }
+
+    maxColour.setEnabled(!currentColours.isSelected());
+    minColour.setEnabled(!currentColours.isSelected());
+
+    changeColour();
+  }
+
+  public void thresholdIsMin_actionPerformed(ActionEvent actionEvent)
+  {
+    changeColour();
+  }
+
+}