X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=unused%2Fappletgui%2FAnnotationColourChooser.java;fp=unused%2Fappletgui%2FAnnotationColourChooser.java;h=ef6622649b4fa3e517eee2ef787c856efeb6d471;hb=6319110ce33faa76ee6cf9832e78faa224510fed;hp=d98154a9b30f60aeb3e9aa2a004d7ec7cbbd58cb;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44;p=jalviewjs.git

diff --git a/unused/appletgui/AnnotationColourChooser.java b/unused/appletgui/AnnotationColourChooser.java
index d98154a..ef66226 100644
--- a/unused/appletgui/AnnotationColourChooser.java
+++ b/unused/appletgui/AnnotationColourChooser.java
@@ -1,581 +1,581 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.appletgui;
-
-import jalview.bin.JalviewLite;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-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.Font;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.AdjustmentEvent;
-import java.awt.event.AdjustmentListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JFrame;
-import javax.swing.JPanel;
-import javax.swing.JScrollBar;
-import javax.swing.JTextField;
-
-public class AnnotationColourChooser extends JPanel implements
-        ActionListener, AdjustmentListener, ItemListener, MouseListener
-{
-  JFrame frame;
-
-  AlignViewport av;
-
-  AlignmentPanel ap;
-
-  ColourSchemeI oldcs;
-
-  Hashtable oldgroupColours;
-
-  AlignmentAnnotation currentAnnotation;
-
-  boolean adjusting = false;
-
-  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
-  {
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-    }
-
-    oldcs = av.getGlobalColourScheme();
-    if (av.getAlignment().getGroups() != null)
-    {
-      oldgroupColours = new Hashtable();
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
-      {
-        if (sg.cs != null)
-        {
-          oldgroupColours.put(sg, sg.cs);
-        }
-        else
-        {
-          oldgroupColours.put(sg, "null");
-        }
-      }
-    }
-    this.av = av;
-    this.ap = ap;
-
-    slider.addAdjustmentListener(this);
-    slider.addMouseListener(this);
-
-    if (av.getAlignment().getAlignmentAnnotation() == null)
-    {
-      return;
-    }
-
-    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.setState(acg.isSeqAssociated());
-    }
-
-    Vector list = new Vector();
-    int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
-    {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
-      if (!list.contains(label))
-      {
-        list.addElement(label);
-      }
-      else
-      {
-        list.addElement(label + "_" + (index++));
-      }
-    }
-
-    for (int i = 0; i < list.size(); i++)
-    {
-      annotations.addItem(list.elementAt(i).toString());
-    }
-
-    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"));
-
-    if (oldcs instanceof AnnotationColourGradient)
-    {
-      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      annotations.select(acg.getAnnotation());
-      switch (acg.getAboveThreshold())
-      {
-      case AnnotationColourGradient.NO_THRESHOLD:
-        threshold.select(0);
-        break;
-      case AnnotationColourGradient.ABOVE_THRESHOLD:
-        threshold.select(1);
-        break;
-      case AnnotationColourGradient.BELOW_THRESHOLD:
-        threshold.select(1);
-        break;
-      default:
-        throw new Error(
-                MessageManager
-                        .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
-      }
-      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
-      thresholdValue.setText("" + acg.getAnnotationThreshold());
-    }
-
-    adjusting = false;
-
-    changeColour();
-
-    frame = new JFrame();
-    frame.add(this);
-    JalviewLite.addFrame(frame,
-            MessageManager.getString("label.colour_by_annotation"), 560,
-            175);
-    validate();
-  }
-
-  private void setDefaultMinMax()
-  {
-    minColour.setBackground(av.applet.getDefaultColourParameter(
-            "ANNOTATIONCOLOUR_MIN", Color.orange));
-    maxColour.setBackground(av.applet.getDefaultColourParameter(
-            "ANNOTATIONCOLOUR_MAX", Color.red));
-
-  }
-
-  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.setLabel(MessageManager.getString("label.min_colour"));
-    minColour.addActionListener(this);
-
-    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    maxColour.setLabel(MessageManager.getString("label.max_colour"));
-    maxColour.addActionListener(this);
-
-    thresholdIsMin.addItemListener(this);
-    ok.setLabel(MessageManager.getString("action.ok"));
-    ok.addActionListener(this);
-
-    cancel.setLabel(MessageManager.getString("action.cancel"));
-    cancel.addActionListener(this);
-
-    defColours.setLabel(MessageManager.getString("action.set_defaults"));
-    defColours.addActionListener(this);
-
-    annotations.addItemListener(this);
-
-    thresholdValue.addActionListener(this);
-    slider.setBackground(Color.white);
-    slider.setPreferredSize(new Dimension(193, 21));
-    slider.setEnabled(false);
-    thresholdValue.setPreferredSize(new Dimension(79, 22));
-    thresholdValue.setEnabled(false);
-    thresholdValue.setColumns(5);
-    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    currentColours.setLabel(MessageManager
-            .getString("label.use_original_colours"));
-    currentColours.addItemListener(this);
-
-    thresholdIsMin.setBackground(Color.white);
-    thresholdIsMin.setLabel(MessageManager
-            .getString("label.threshold_minmax"));
-
-    this.setLayout(borderLayout1);
-
-    jPanel1.setBackground(Color.white);
-
-    jPanel2.setLayout(new FlowLayout());
-    jPanel2.setBackground(Color.white);
-    threshold.addItemListener(this);
-    jPanel3.setLayout(new FlowLayout());
-    jPanel3.setBackground(Color.white);
-    JPanel jPanel4 = new JPanel();
-    jPanel4.setLayout(new BorderLayout());
-    jPanel4.setBackground(Color.white);
-
-    jPanel1.add(ok);
-    jPanel1.add(cancel);
-
-    jPanel2.add(annotations);
-    jPanel2.add(currentColours);
-    jPanel2.add(minColour);
-    jPanel2.add(maxColour);
-
-    jPanel4.add(thresholdIsMin, BorderLayout.WEST);
-    jPanel4.add(slider, BorderLayout.CENTER);
-    jPanel4.add(thresholdValue, BorderLayout.EAST);
-
-    JPanel jPanel34 = new JPanel();
-    jPanel34.setLayout(new BorderLayout());
-    jPanel34.setBackground(Color.white);
-    jPanel34.add(jPanel2, BorderLayout.NORTH);
-    jPanel34.add(threshold, BorderLayout.WEST);
-    jPanel3.add(defColours);
-    jPanel34.add(jPanel3, BorderLayout.EAST);
-    jPanel34.add(jPanel4, BorderLayout.SOUTH);
-
-    this.add(jPanel34, java.awt.BorderLayout.CENTER);
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
-
-  }
-
-  Choice annotations = new Choice();
-
-  JButton minColour = new JButton();
-
-  JButton maxColour = new JButton();
-
-  JButton ok = new JButton();
-
-  JButton cancel = new JButton();
-
-  JButton defColours = new JButton();
-
-  JPanel jPanel1 = new JPanel();
-
-  JPanel jPanel2 = new JPanel();
-
-  Choice threshold = new Choice();
-
-  FlowLayout flowLayout1 = new FlowLayout();
-
-  JPanel jPanel3 = new JPanel();
-
-  JScrollBar slider = new JScrollBar(JScrollBar.HORIZONTAL);
-
-  JTextField thresholdValue = new JTextField(20);
-
-  JCheckBox currentColours = new JCheckBox();
-
-  BorderLayout borderLayout1 = new BorderLayout();
-
-  JCheckBox thresholdIsMin = new JCheckBox();
-
-  public void actionPerformed(ActionEvent evt)
-  {
-    if (evt.getSource() == thresholdValue)
-    {
-      try
-      {
-        float f = new Float(thresholdValue.getText()).floatValue();
-        slider.setValue((int) (f * 1000));
-        adjustmentValueChanged(null);
-      } catch (NumberFormatException ex)
-      {
-      }
-    }
-    else if (evt.getSource() == minColour)
-    {
-      minColour_actionPerformed(null);
-    }
-    else if (evt.getSource() == maxColour)
-    {
-      maxColour_actionPerformed(null);
-    }
-    else if (evt.getSource() == defColours)
-    {
-      defColour_actionPerformed();
-    }
-    else if (evt.getSource() == ok)
-    {
-      changeColour();
-      frame.setVisible(false);
-    }
-    else if (evt.getSource() == cancel)
-    {
-      reset();
-      ap.paintAlignment(true);
-      frame.setVisible(false);
-    }
-
-    else
-    {
-      changeColour();
-    }
-  }
-
-  public void itemStateChanged(ItemEvent evt)
-  {
-    if (evt.getSource() == currentColours)
-    {
-      if (currentColours.isSelected())
-      {
-        reset();
-      }
-
-      maxColour.setEnabled(!currentColours.isSelected());
-      minColour.setEnabled(!currentColours.isSelected());
-
-    }
-
-    changeColour();
-  }
-
-  public void adjustmentValueChanged(AdjustmentEvent evt)
-  {
-    if (!adjusting)
-    {
-      thresholdValue.setText((slider.getValue() / 1000f) + "");
-      if (currentColours.isSelected()
-              && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
-      {
-        changeColour();
-      }
-
-      currentAnnotation.threshold.value = slider.getValue() / 1000f;
-      ap.paintAlignment(false);
-    }
-  }
-
-  public void minColour_actionPerformed(Color newCol)
-  {
-    if (newCol != null)
-    {
-      minColour.setBackground(newCol);
-      minColour.repaint();
-      changeColour();
-    }
-    else
-    {
-      new UserDefinedColours(this, "Min Colour", minColour.getBackground());
-    }
-
-  }
-
-  public void maxColour_actionPerformed(Color newCol)
-  {
-    if (newCol != null)
-    {
-      maxColour.setBackground(newCol);
-      maxColour.repaint();
-      changeColour();
-    }
-    else
-    {
-      new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
-    }
-  }
-
-  public void defColour_actionPerformed()
-  {
-    setDefaultMinMax();
-    minColour.repaint();
-    maxColour.repaint();
-    changeColour();
-  }
-
-  void changeColour()
-  {
-    // Check if combobox is still adjusting
-    if (adjusting)
-    {
-      return;
-    }
-
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[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);
-      thresholdIsMin.setEnabled(false);
-      thresholdValue.setText("");
-    }
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
-            && currentAnnotation.threshold == null)
-    {
-      currentAnnotation
-              .setThreshold(new GraphLine(
-                      (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
-                      "Threshold", Color.black));
-    }
-
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
-    {
-      adjusting = true;
-
-      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.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.setPredefinedColours(true);
-    }
-
-    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
-
-    av.setGlobalColourScheme(acg);
-
-    // TODO: per group colour propagation not always desired
-    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);
-        }
-        else
-        {
-          sg.cs = new AnnotationColourGradient(currentAnnotation,
-                  minColour.getBackground(), maxColour.getBackground(),
-                  aboveThreshold);
-        }
-
-      }
-    }
-
-    // update colours in linked windows
-    ap.alignmentChanged();
-    ap.paintAlignment(true);
-  }
-
-  void reset()
-  {
-    av.setGlobalColourScheme(oldcs);
-    if (av.getAlignment().getGroups() != null)
-    {
-      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
-      {
-        Object cs = oldgroupColours.get(sg);
-        if (cs instanceof ColourSchemeI)
-        {
-          sg.cs = (ColourSchemeI) cs;
-        }
-        else
-        {
-          // probably the "null" string we set it to if it was null originally.
-          sg.cs = null;
-        }
-      }
-    }
-    ap.paintAlignment(true);
-
-  }
-
-  public void mouseClicked(MouseEvent evt)
-  {
-  }
-
-  public void mousePressed(MouseEvent evt)
-  {
-  }
-
-  public void mouseReleased(MouseEvent evt)
-  {
-    ap.paintAlignment(true);
-  }
-
-  public void mouseEntered(MouseEvent evt)
-  {
-  }
-
-  public void mouseExited(MouseEvent evt)
-  {
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.appletgui;
+
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+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.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.util.Hashtable;
+import java.util.Vector;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JFrame;
+import javax.swing.JPanel;
+import javax.swing.JScrollBar;
+import javax.swing.JTextField;
+
+public class AnnotationColourChooser extends JPanel implements
+        ActionListener, AdjustmentListener, ItemListener, MouseListener
+{
+  JFrame frame;
+
+  AlignViewport av;
+
+  AlignmentPanel ap;
+
+  ColourSchemeI oldcs;
+
+  Hashtable oldgroupColours;
+
+  AlignmentAnnotation currentAnnotation;
+
+  boolean adjusting = false;
+
+  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
+  {
+    try
+    {
+      jbInit();
+    } catch (Exception ex)
+    {
+    }
+
+    oldcs = av.getGlobalColourScheme();
+    if (av.getAlignment().getGroups() != null)
+    {
+      oldgroupColours = new Hashtable();
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        if (sg.cs != null)
+        {
+          oldgroupColours.put(sg, sg.cs);
+        }
+        else
+        {
+          oldgroupColours.put(sg, "null");
+        }
+      }
+    }
+    this.av = av;
+    this.ap = ap;
+
+    slider.addAdjustmentListener(this);
+    slider.addMouseListener(this);
+
+    if (av.getAlignment().getAlignmentAnnotation() == null)
+    {
+      return;
+    }
+
+    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.setState(acg.isSeqAssociated());
+    }
+
+    Vector list = new Vector();
+    int index = 1;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+      {
+        list.addElement(label);
+      }
+      else
+      {
+        list.addElement(label + "_" + (index++));
+      }
+    }
+
+    for (int i = 0; i < list.size(); i++)
+    {
+      annotations.addItem(list.elementAt(i).toString());
+    }
+
+    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"));
+
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      annotations.select(acg.getAnnotation());
+      switch (acg.getAboveThreshold())
+      {
+      case AnnotationColourGradient.NO_THRESHOLD:
+        threshold.select(0);
+        break;
+      case AnnotationColourGradient.ABOVE_THRESHOLD:
+        threshold.select(1);
+        break;
+      case AnnotationColourGradient.BELOW_THRESHOLD:
+        threshold.select(1);
+        break;
+      default:
+        throw new Error(
+                MessageManager
+                        .getString("error.implementation_error_dont_know_thereshold_annotationcolourgradient"));
+      }
+      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdValue.setText("" + acg.getAnnotationThreshold());
+    }
+
+    adjusting = false;
+
+    changeColour();
+
+    frame = new JFrame();
+    frame.add(this);
+    JalviewLite.addFrame(frame,
+            MessageManager.getString("label.colour_by_annotation"), 560,
+            175);
+    validate();
+  }
+
+  private void setDefaultMinMax()
+  {
+    minColour.setBackground(av.applet.getDefaultColourParameter(
+            "ANNOTATIONCOLOUR_MIN", Color.orange));
+    maxColour.setBackground(av.applet.getDefaultColourParameter(
+            "ANNOTATIONCOLOUR_MAX", Color.red));
+
+  }
+
+  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.setLabel(MessageManager.getString("label.min_colour"));
+    minColour.addActionListener(this);
+
+    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    maxColour.setLabel(MessageManager.getString("label.max_colour"));
+    maxColour.addActionListener(this);
+
+    thresholdIsMin.addItemListener(this);
+    ok.setLabel(MessageManager.getString("action.ok"));
+    ok.addActionListener(this);
+
+    cancel.setLabel(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(this);
+
+    defColours.setLabel(MessageManager.getString("action.set_defaults"));
+    defColours.addActionListener(this);
+
+    annotations.addItemListener(this);
+
+    thresholdValue.addActionListener(this);
+    slider.setBackground(Color.white);
+    slider.setPreferredSize(new Dimension(193, 21));
+    slider.setEnabled(false);
+    thresholdValue.setPreferredSize(new Dimension(79, 22));
+    thresholdValue.setEnabled(false);
+    thresholdValue.setColumns(5);
+    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    currentColours.setLabel(MessageManager
+            .getString("label.use_original_colours"));
+    currentColours.addItemListener(this);
+
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setLabel(MessageManager
+            .getString("label.threshold_minmax"));
+
+    this.setLayout(borderLayout1);
+
+    jPanel1.setBackground(Color.white);
+
+    jPanel2.setLayout(new FlowLayout());
+    jPanel2.setBackground(Color.white);
+    threshold.addItemListener(this);
+    jPanel3.setLayout(new FlowLayout());
+    jPanel3.setBackground(Color.white);
+    JPanel jPanel4 = new JPanel();
+    jPanel4.setLayout(new BorderLayout());
+    jPanel4.setBackground(Color.white);
+
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+
+    jPanel2.add(annotations);
+    jPanel2.add(currentColours);
+    jPanel2.add(minColour);
+    jPanel2.add(maxColour);
+
+    jPanel4.add(thresholdIsMin, BorderLayout.WEST);
+    jPanel4.add(slider, BorderLayout.CENTER);
+    jPanel4.add(thresholdValue, BorderLayout.EAST);
+
+    JPanel jPanel34 = new JPanel();
+    jPanel34.setLayout(new BorderLayout());
+    jPanel34.setBackground(Color.white);
+    jPanel34.add(jPanel2, BorderLayout.NORTH);
+    jPanel34.add(threshold, BorderLayout.WEST);
+    jPanel3.add(defColours);
+    jPanel34.add(jPanel3, BorderLayout.EAST);
+    jPanel34.add(jPanel4, BorderLayout.SOUTH);
+
+    this.add(jPanel34, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+
+  }
+
+  Choice annotations = new Choice();
+
+  JButton minColour = new JButton();
+
+  JButton maxColour = new JButton();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JButton defColours = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JPanel jPanel2 = new JPanel();
+
+  Choice threshold = new Choice();
+
+  FlowLayout flowLayout1 = new FlowLayout();
+
+  JPanel jPanel3 = new JPanel();
+
+  JScrollBar slider = new JScrollBar(JScrollBar.HORIZONTAL);
+
+  JTextField thresholdValue = new JTextField(20);
+
+  JCheckBox currentColours = new JCheckBox();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  JCheckBox thresholdIsMin = new JCheckBox();
+
+  public void actionPerformed(ActionEvent evt)
+  {
+    if (evt.getSource() == thresholdValue)
+    {
+      try
+      {
+        float f = new Float(thresholdValue.getText()).floatValue();
+        slider.setValue((int) (f * 1000));
+        adjustmentValueChanged(null);
+      } catch (NumberFormatException ex)
+      {
+      }
+    }
+    else if (evt.getSource() == minColour)
+    {
+      minColour_actionPerformed(null);
+    }
+    else if (evt.getSource() == maxColour)
+    {
+      maxColour_actionPerformed(null);
+    }
+    else if (evt.getSource() == defColours)
+    {
+      defColour_actionPerformed();
+    }
+    else if (evt.getSource() == ok)
+    {
+      changeColour();
+      frame.setVisible(false);
+    }
+    else if (evt.getSource() == cancel)
+    {
+      reset();
+      ap.paintAlignment(true);
+      frame.setVisible(false);
+    }
+
+    else
+    {
+      changeColour();
+    }
+  }
+
+  public void itemStateChanged(ItemEvent evt)
+  {
+    if (evt.getSource() == currentColours)
+    {
+      if (currentColours.isSelected())
+      {
+        reset();
+      }
+
+      maxColour.setEnabled(!currentColours.isSelected());
+      minColour.setEnabled(!currentColours.isSelected());
+
+    }
+
+    changeColour();
+  }
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    if (!adjusting)
+    {
+      thresholdValue.setText((slider.getValue() / 1000f) + "");
+      if (currentColours.isSelected()
+              && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+      {
+        changeColour();
+      }
+
+      currentAnnotation.threshold.value = slider.getValue() / 1000f;
+      ap.paintAlignment(false);
+    }
+  }
+
+  public void minColour_actionPerformed(Color newCol)
+  {
+    if (newCol != null)
+    {
+      minColour.setBackground(newCol);
+      minColour.repaint();
+      changeColour();
+    }
+    else
+    {
+      new UserDefinedColours(this, "Min Colour", minColour.getBackground());
+    }
+
+  }
+
+  public void maxColour_actionPerformed(Color newCol)
+  {
+    if (newCol != null)
+    {
+      maxColour.setBackground(newCol);
+      maxColour.repaint();
+      changeColour();
+    }
+    else
+    {
+      new UserDefinedColours(this, "Max Colour", maxColour.getBackground());
+    }
+  }
+
+  public void defColour_actionPerformed()
+  {
+    setDefaultMinMax();
+    minColour.repaint();
+    maxColour.repaint();
+    changeColour();
+  }
+
+  void changeColour()
+  {
+    // Check if combobox is still adjusting
+    if (adjusting)
+    {
+      return;
+    }
+
+    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[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);
+      thresholdIsMin.setEnabled(false);
+      thresholdValue.setText("");
+    }
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+            && currentAnnotation.threshold == null)
+    {
+      currentAnnotation
+              .setThreshold(new GraphLine(
+                      (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+                      "Threshold", Color.black));
+    }
+
+    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
+
+      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.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.setPredefinedColours(true);
+    }
+
+    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
+    av.setGlobalColourScheme(acg);
+
+    // TODO: per group colour propagation not always desired
+    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);
+        }
+        else
+        {
+          sg.cs = new AnnotationColourGradient(currentAnnotation,
+                  minColour.getBackground(), maxColour.getBackground(),
+                  aboveThreshold);
+        }
+
+      }
+    }
+
+    // update colours in linked windows
+    ap.alignmentChanged();
+    ap.paintAlignment(true);
+  }
+
+  void reset()
+  {
+    av.setGlobalColourScheme(oldcs);
+    if (av.getAlignment().getGroups() != null)
+    {
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        Object cs = oldgroupColours.get(sg);
+        if (cs instanceof ColourSchemeI)
+        {
+          sg.cs = (ColourSchemeI) cs;
+        }
+        else
+        {
+          // probably the "null" string we set it to if it was null originally.
+          sg.cs = null;
+        }
+      }
+    }
+    ap.paintAlignment(true);
+
+  }
+
+  public void mouseClicked(MouseEvent evt)
+  {
+  }
+
+  public void mousePressed(MouseEvent evt)
+  {
+  }
+
+  public void mouseReleased(MouseEvent evt)
+  {
+    ap.paintAlignment(true);
+  }
+
+  public void mouseEntered(MouseEvent evt)
+  {
+  }
+
+  public void mouseExited(MouseEvent evt)
+  {
+  }
+
+}