bugfix to avoid null pointer exceptions being raised for groups with no colourscheme...
authorjprocter <Jim Procter>
Fri, 2 May 2008 13:04:01 +0000 (13:04 +0000)
committerjprocter <Jim Procter>
Fri, 2 May 2008 13:04:01 +0000 (13:04 +0000)
src/jalview/appletgui/AnnotationColourChooser.java

index 2db2bd0..c932962 100755 (executable)
-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
- */\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import java.awt.Rectangle;\r
-\r
-public class AnnotationColourChooser\r
-    extends Panel implements ActionListener,\r
-    AdjustmentListener, ItemListener, MouseListener\r
-{\r
-  Frame frame;\r
-  AlignViewport av;\r
-  AlignmentPanel ap;\r
-  ColourSchemeI oldcs;\r
-  Hashtable oldgroupColours;\r
-  jalview.datamodel.AlignmentAnnotation currentAnnotation;\r
-  boolean adjusting = false;\r
-\r
-  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)\r
-  {\r
-    try\r
-    {\r
-      jbInit();\r
-    }\r
-    catch (Exception ex)\r
-    {}\r
-\r
-    oldcs = av.getGlobalColourScheme();\r
-    if (av.alignment.getGroups() != null)\r
-    {\r
-      oldgroupColours = new Hashtable();\r
-      Vector allGroups = ap.av.alignment.getGroups();\r
-      SequenceGroup sg;\r
-      for (int g = 0; g < allGroups.size(); g++)\r
-      {\r
-        sg = (SequenceGroup) allGroups.elementAt(g);\r
-        oldgroupColours.put(sg, sg.cs);\r
-      }\r
-    }\r
-    this.av = av;\r
-    this.ap = ap;\r
-\r
-    slider.addAdjustmentListener(this);\r
-    slider.addMouseListener(this);\r
-\r
-    if (av.alignment.getAlignmentAnnotation() == null)\r
-    {\r
-      return;\r
-    }\r
-\r
-    if (oldcs instanceof AnnotationColourGradient)\r
-    {\r
-      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;\r
-      minColour.setBackground(acg.getMinColour());\r
-      maxColour.setBackground(acg.getMaxColour());\r
-    }\r
-    else\r
-    {\r
-      minColour.setBackground(Color.orange);\r
-      maxColour.setBackground(Color.red);\r
-    }\r
-\r
-    adjusting = true;\r
-\r
-    Vector list = new Vector();\r
-    int index = 1;\r
-    for (int i = 0; i < av.alignment.getAlignmentAnnotation().length; i++)\r
-    {\r
-      String label = av.alignment.getAlignmentAnnotation()[i].label;\r
-      if (!list.contains(label))\r
-        list.addElement(label);\r
-      else\r
-        list.addElement(label+"_"+(index++));\r
-    }\r
-\r
-    for (int i = 0; i < list.size(); i++)\r
-    {\r
-        annotations.addItem(list.elementAt(i).toString());\r
-    }\r
-\r
-    threshold.addItem("No Threshold");\r
-    threshold.addItem("Above Threshold");\r
-    threshold.addItem("Below Threshold");\r
-\r
-    adjusting = false;\r
-\r
-    changeColour();\r
-\r
-    frame = new Frame();\r
-    frame.add(this);\r
-    jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145);\r
-    validate();\r
-  }\r
-\r
-  public AnnotationColourChooser()\r
-  {\r
-    try\r
-    {\r
-      jbInit();\r
-    }\r
-    catch (Exception ex)\r
-    {\r
-      ex.printStackTrace();\r
-    }\r
-  }\r
-\r
-  private void jbInit()\r
-      throws Exception\r
-  {\r
-    minColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
-    minColour.setLabel("Min Colour");\r
-    minColour.addActionListener(this);\r
-\r
-    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
-    maxColour.setLabel("Max Colour");\r
-    maxColour.addActionListener(this);\r
-\r
-    thresholdIsMin.addItemListener(this);\r
-    ok.setLabel("OK");\r
-    ok.addActionListener(this);\r
-\r
-    cancel.setLabel("Cancel");\r
-    cancel.addActionListener(this);\r
-\r
-    this.setLayout(borderLayout1);\r
-    jPanel2.setLayout(flowLayout1);\r
-    annotations.addItemListener(this);\r
-\r
-    jPanel1.setBackground(Color.white);\r
-    jPanel2.setBackground(Color.white);\r
-    threshold.addItemListener(this);\r
-    jPanel3.setLayout(null);\r
-    thresholdValue.addActionListener(this);\r
-\r
-    slider.setBackground(Color.white);\r
-    slider.setEnabled(false);\r
-    slider.setBounds(new Rectangle(153, 3, 93, 21));\r
-    thresholdValue.setEnabled(false);\r
-    thresholdValue.setBounds(new Rectangle(248, 2, 79, 22));\r
-    thresholdValue.setColumns(5);\r
-    jPanel3.setBackground(Color.white);\r
-    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
-    currentColours.setLabel("Use Original Colours");\r
-    currentColours.addItemListener(this);\r
-\r
-    threshold.setBounds(new Rectangle(11, 3, 139, 22));\r
-    thresholdIsMin.setBackground(Color.white);\r
-    thresholdIsMin.setLabel("Threshold is min/max");\r
-    thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));\r
-    jPanel1.add(ok);\r
-    jPanel1.add(cancel);\r
-    jPanel2.add(annotations);\r
-    jPanel2.add(currentColours);\r
-    jPanel2.add(minColour);\r
-    jPanel2.add(maxColour);\r
-    jPanel3.add(threshold);\r
-    jPanel3.add(slider);\r
-    jPanel3.add(thresholdValue);\r
-    jPanel3.add(thresholdIsMin);\r
-    this.add(jPanel2, java.awt.BorderLayout.NORTH);\r
-    this.add(jPanel3, java.awt.BorderLayout.CENTER);\r
-    this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
-  }\r
-\r
-  Choice annotations = new Choice();\r
-  Button minColour = new Button();\r
-  Button maxColour = new Button();\r
-  Button ok = new Button();\r
-  Button cancel = new Button();\r
-  Panel jPanel1 = new Panel();\r
-  Panel jPanel2 = new Panel();\r
-  Choice threshold = new Choice();\r
-  FlowLayout flowLayout1 = new FlowLayout();\r
-  Panel jPanel3 = new Panel();\r
-  Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);\r
-  TextField thresholdValue = new TextField(20);\r
-  Checkbox currentColours = new Checkbox();\r
-  BorderLayout borderLayout1 = new BorderLayout();\r
-  Checkbox thresholdIsMin = new Checkbox();\r
-\r
-  public void actionPerformed(ActionEvent evt)\r
-  {\r
-    if (evt.getSource() == thresholdValue)\r
-    {\r
-      try\r
-      {\r
-        float f = new Float(thresholdValue.getText()).floatValue();\r
-        slider.setValue( (int) (f * 1000));\r
-        adjustmentValueChanged(null);\r
-      }\r
-      catch (NumberFormatException ex)\r
-      {}\r
-    }\r
-    else if (evt.getSource() == minColour)\r
-    {\r
-      minColour_actionPerformed(null);\r
-    }\r
-    else if (evt.getSource() == maxColour)\r
-    {\r
-      maxColour_actionPerformed(null);\r
-    }\r
-\r
-    else if (evt.getSource() == ok)\r
-    {\r
-      changeColour();\r
-      frame.setVisible(false);\r
-    }\r
-    else if (evt.getSource() == cancel)\r
-    {\r
-      reset();\r
-      ap.paintAlignment(true);\r
-      frame.setVisible(false);\r
-    }\r
-\r
-    else\r
-    {\r
-      changeColour();\r
-    }\r
-  }\r
-\r
-  public void itemStateChanged(ItemEvent evt)\r
-  {\r
-    if (evt.getSource() == currentColours)\r
-    {\r
-      if (currentColours.getState())\r
-      {\r
-        reset();\r
-      }\r
-\r
-      maxColour.setEnabled(!currentColours.getState());\r
-      minColour.setEnabled(!currentColours.getState());\r
-\r
-    }\r
-\r
-    changeColour();\r
-  }\r
-\r
-  public void adjustmentValueChanged(AdjustmentEvent evt)\r
-  {\r
-    if (!adjusting)\r
-    {\r
-      thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");\r
-      if (currentColours.getState()\r
-          && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))\r
-      {\r
-        changeColour();\r
-      }\r
-\r
-      currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;\r
-      ap.paintAlignment(false);\r
-    }\r
-  }\r
-\r
-  public void minColour_actionPerformed(Color newCol)\r
-  {\r
-    if (newCol != null)\r
-    {\r
-      minColour.setBackground(newCol);\r
-      minColour.repaint();\r
-      changeColour();\r
-    }\r
-    else\r
-    {\r
-      new UserDefinedColours(this, "Min Colour",\r
-                             minColour.getBackground());\r
-    }\r
-\r
-  }\r
-\r
-  public void maxColour_actionPerformed(Color newCol)\r
-  {\r
-    if (newCol != null)\r
-    {\r
-      maxColour.setBackground(newCol);\r
-      maxColour.repaint();\r
-      changeColour();\r
-    }\r
-    else\r
-    {\r
-      new UserDefinedColours(this, "Max Colour",\r
-                             maxColour.getBackground());\r
-    }\r
-  }\r
-\r
-  void changeColour()\r
-  {\r
-    // Check if combobox is still adjusting\r
-    if (adjusting)\r
-    {\r
-      return;\r
-    }\r
-\r
-\r
-    currentAnnotation = av.alignment.getAlignmentAnnotation()\r
-        [annotations.getSelectedIndex()];\r
-\r
-    int aboveThreshold = -1;\r
-    if (threshold.getSelectedItem().equals("Above Threshold"))\r
-    {\r
-      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;\r
-    }\r
-    else if (threshold.getSelectedItem().equals("Below Threshold"))\r
-    {\r
-      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;\r
-    }\r
-\r
-    slider.setEnabled(true);\r
-    thresholdValue.setEnabled(true);\r
-\r
-    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)\r
-    {\r
-      slider.setEnabled(false);\r
-      thresholdValue.setEnabled(false);\r
-      thresholdValue.setText("");\r
-    }\r
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD &&\r
-             currentAnnotation.threshold == null)\r
-    {\r
-      currentAnnotation.setThreshold(new jalview.datamodel.GraphLine\r
-                                     ( (currentAnnotation.graphMax -\r
-                                        currentAnnotation.graphMin) / 2f,\r
-                                      "Threshold",\r
-                                      Color.black));\r
-    }\r
-\r
-    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)\r
-    {\r
-      adjusting = true;\r
-\r
-      slider.setMinimum( (int) (currentAnnotation.graphMin * 1000));\r
-      slider.setMaximum( (int) (currentAnnotation.graphMax * 1000));\r
-      slider.setValue( (int) (currentAnnotation.threshold.value * 1000));\r
-      thresholdValue.setText(currentAnnotation.threshold.value + "");\r
-      slider.setEnabled(true);\r
-      thresholdValue.setEnabled(true);\r
-      adjusting = false;\r
-    }\r
-\r
-    AnnotationColourGradient acg = null;\r
-    if (currentColours.getState())\r
-    {\r
-      acg = new AnnotationColourGradient(\r
-          currentAnnotation,\r
-          av.getGlobalColourScheme(), aboveThreshold);\r
-    }\r
-    else\r
-    {\r
-      acg =\r
-          new AnnotationColourGradient(\r
-              currentAnnotation,\r
-              minColour.getBackground(),\r
-              maxColour.getBackground(),\r
-              aboveThreshold);\r
-    }\r
-\r
-    if (currentAnnotation.graphMin == 0f && currentAnnotation.graphMax == 0f)\r
-    {\r
-      acg.predefinedColours = true;\r
-    }\r
-\r
-    acg.thresholdIsMinMax = thresholdIsMin.getState();\r
-\r
-    av.setGlobalColourScheme(acg);\r
-\r
-    if (av.alignment.getGroups() != null)\r
-    {\r
-      Vector allGroups = ap.av.alignment.getGroups();\r
-      SequenceGroup sg;\r
-      for (int g = 0; g < allGroups.size(); g++)\r
-      {\r
-        sg = (SequenceGroup) allGroups.elementAt(g);\r
-\r
-        if (sg.cs == null)\r
-        {\r
-          continue;\r
-        }\r
-\r
-        if (currentColours.getState())\r
-        {\r
-          sg.cs = new AnnotationColourGradient(\r
-              currentAnnotation,\r
-              sg.cs, aboveThreshold);\r
-        }\r
-        else\r
-        {\r
-          sg.cs = new AnnotationColourGradient(\r
-              currentAnnotation,\r
-              minColour.getBackground(),\r
-              maxColour.getBackground(),\r
-              aboveThreshold);\r
-        }\r
-\r
-      }\r
-    }\r
-\r
-    ap.paintAlignment(false);\r
-  }\r
-\r
-  void reset()\r
-  {\r
-    av.setGlobalColourScheme(oldcs);\r
-    if (av.alignment.getGroups() != null)\r
-    {\r
-      Vector allGroups = ap.av.alignment.getGroups();\r
-      SequenceGroup sg;\r
-      for (int g = 0; g < allGroups.size(); g++)\r
-      {\r
-        sg = (SequenceGroup) allGroups.elementAt(g);\r
-        sg.cs = (ColourSchemeI) oldgroupColours.get(sg);\r
-      }\r
-    }\r
-    ap.paintAlignment(true);\r
-\r
-  }\r
-\r
-  public void mouseClicked(MouseEvent evt){}\r
-  public void mousePressed(MouseEvent evt){}\r
-  public void mouseReleased(MouseEvent evt){ ap.paintAlignment(true);}\r
-  public void mouseEntered(MouseEvent evt){}\r
-  public void mouseExited(MouseEvent evt){}\r
-\r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 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.appletgui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import java.awt.Rectangle;
+
+public class AnnotationColourChooser
+    extends Panel implements ActionListener,
+    AdjustmentListener, ItemListener, MouseListener
+{
+  Frame frame;
+  AlignViewport av;
+  AlignmentPanel ap;
+  ColourSchemeI oldcs;
+  Hashtable oldgroupColours;
+  jalview.datamodel.AlignmentAnnotation currentAnnotation;
+  boolean adjusting = false;
+
+  public AnnotationColourChooser(AlignViewport av, AlignmentPanel ap)
+  {
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {}
+
+    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.elementAt(g);
+        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.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;
+
+    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++));
+    }
+
+    for (int i = 0; i < list.size(); i++)
+    {
+        annotations.addItem(list.elementAt(i).toString());
+    }
+
+    threshold.addItem("No Threshold");
+    threshold.addItem("Above Threshold");
+    threshold.addItem("Below Threshold");
+
+    adjusting = false;
+
+    changeColour();
+
+    frame = new Frame();
+    frame.add(this);
+    jalview.bin.JalviewLite.addFrame(frame, "Colour by Annotation", 480, 145);
+    validate();
+  }
+
+  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("Min Colour");
+    minColour.addActionListener(this);
+
+    maxColour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    maxColour.setLabel("Max Colour");
+    maxColour.addActionListener(this);
+
+    thresholdIsMin.addItemListener(this);
+    ok.setLabel("OK");
+    ok.addActionListener(this);
+
+    cancel.setLabel("Cancel");
+    cancel.addActionListener(this);
+
+    this.setLayout(borderLayout1);
+    jPanel2.setLayout(flowLayout1);
+    annotations.addItemListener(this);
+
+    jPanel1.setBackground(Color.white);
+    jPanel2.setBackground(Color.white);
+    threshold.addItemListener(this);
+    jPanel3.setLayout(null);
+    thresholdValue.addActionListener(this);
+
+    slider.setBackground(Color.white);
+    slider.setEnabled(false);
+    slider.setBounds(new Rectangle(153, 3, 93, 21));
+    thresholdValue.setEnabled(false);
+    thresholdValue.setBounds(new Rectangle(248, 2, 79, 22));
+    thresholdValue.setColumns(5);
+    jPanel3.setBackground(Color.white);
+    currentColours.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+    currentColours.setLabel("Use Original Colours");
+    currentColours.addItemListener(this);
+
+    threshold.setBounds(new Rectangle(11, 3, 139, 22));
+    thresholdIsMin.setBackground(Color.white);
+    thresholdIsMin.setLabel("Threshold is min/max");
+    thresholdIsMin.setBounds(new Rectangle(328, 3, 135, 23));
+    jPanel1.add(ok);
+    jPanel1.add(cancel);
+    jPanel2.add(annotations);
+    jPanel2.add(currentColours);
+    jPanel2.add(minColour);
+    jPanel2.add(maxColour);
+    jPanel3.add(threshold);
+    jPanel3.add(slider);
+    jPanel3.add(thresholdValue);
+    jPanel3.add(thresholdIsMin);
+    this.add(jPanel2, java.awt.BorderLayout.NORTH);
+    this.add(jPanel3, java.awt.BorderLayout.CENTER);
+    this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+  }
+
+  Choice annotations = new Choice();
+  Button minColour = new Button();
+  Button maxColour = new Button();
+  Button ok = new Button();
+  Button cancel = new Button();
+  Panel jPanel1 = new Panel();
+  Panel jPanel2 = new Panel();
+  Choice threshold = new Choice();
+  FlowLayout flowLayout1 = new FlowLayout();
+  Panel jPanel3 = new Panel();
+  Scrollbar slider = new Scrollbar(Scrollbar.HORIZONTAL);
+  TextField thresholdValue = new TextField(20);
+  Checkbox currentColours = new Checkbox();
+  BorderLayout borderLayout1 = new BorderLayout();
+  Checkbox thresholdIsMin = new Checkbox();
+
+  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() == 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.getState())
+      {
+        reset();
+      }
+
+      maxColour.setEnabled(!currentColours.getState());
+      minColour.setEnabled(!currentColours.getState());
+
+    }
+
+    changeColour();
+  }
+
+  public void adjustmentValueChanged(AdjustmentEvent evt)
+  {
+    if (!adjusting)
+    {
+      thresholdValue.setText( ( (float) slider.getValue() / 1000f) + "");
+      if (currentColours.getState()
+          && ! (av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+      {
+        changeColour();
+      }
+
+      currentAnnotation.threshold.value = (float) 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());
+    }
+  }
+
+  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);
+
+    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;
+
+      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.getState())
+    {
+      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.getState();
+
+    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.elementAt(g);
+
+        if (sg.cs == null)
+        {
+          continue;
+        }
+
+        if (currentColours.getState())
+        {
+          sg.cs = new AnnotationColourGradient(
+              currentAnnotation,
+              sg.cs, aboveThreshold);
+        }
+        else
+        {
+          sg.cs = new AnnotationColourGradient(
+              currentAnnotation,
+              minColour.getBackground(),
+              maxColour.getBackground(),
+              aboveThreshold);
+        }
+
+      }
+    }
+
+    ap.paintAlignment(false);
+  }
+
+  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.elementAt(g);
+        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){}
+
+
+}