X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=9afe54fdc0531ce963bb2757a5ec12069f440bdc;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=b748c85c01c57390eb0631a225890b0227aaaef8;hpb=4c843061ffa7a830585172ffe7ff8c9014213a7a;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
old mode 100755
new mode 100644
index b748c85..9afe54f
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,467 +1,710 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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;
-import java.awt.Dimension;
-import javax.swing.BorderFactory;
-
-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);
-        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", 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.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(new java.awt.Font("Verdana", Font.PLAIN, 11));
-    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);
-      }
-    });
-    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();
-  JPanel minColour = new JPanel();
-  JPanel maxColour = new JPanel();
-  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()
-  {
-    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;
-
-    // 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.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 2.8.2)
+ * Copyright (C) 2014 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 java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+import javax.swing.event.*;
+
+import net.miginfocom.swing.MigLayout;
+
+import jalview.bin.Cache;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.util.MessageManager;
+
+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;
+  /**
+   * enabled if the user is dragging the slider - try to keep updates to a minimun
+   */
+  boolean sliderDragging = false;
+
+  public AnnotationColourChooser(AlignViewport av, final AlignmentPanel ap)
+  {
+    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);
+        }
+      }
+    }
+    this.av = av;
+    this.ap = ap;
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    frame.setLayer(JLayeredPane.PALETTE_LAYER);
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.colour_by_annotation"), 520, 215);
+
+    slider.addChangeListener(new ChangeListener()
+    {
+      public void stateChanged(ChangeEvent evt)
+      {
+        if (!adjusting)
+        {
+          thresholdValue.setText(((float) slider.getValue() / 1000f) + "");
+          valueChanged(!sliderDragging);
+        }
+      }
+    });
+    slider.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mousePressed(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mousePressed(e);
+      }
+
+      @Override
+      public void mouseDragged(MouseEvent e)
+      {
+        sliderDragging=true;
+        super.mouseDragged(e);
+      }
+      public void mouseReleased(MouseEvent evt)
+      {
+        if (sliderDragging)
+        {
+          sliderDragging=false;
+          valueChanged(true);
+        }
+        ap.paintAlignment(true);
+      }
+    });
+
+    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(
+            getAnnotationItems(seqAssociated.isSelected()));
+
+    threshold.addItem(MessageManager.getString("label.threshold_feature_no_thereshold"));
+    threshold.addItem(MessageManager.getString("label.threshold_feature_above_thereshold"));
+    threshold.addItem(MessageManager.getString("label.threshold_feature_below_thereshold"));
+
+    if (oldcs instanceof AnnotationColourGradient)
+    {
+      AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
+      annotations.setSelectedItem(acg.getAnnotation());
+      switch (acg.getAboveThreshold())
+      {
+      case AnnotationColourGradient.NO_THRESHOLD:
+        threshold.setSelectedIndex(0);
+        break;
+      case AnnotationColourGradient.ABOVE_THRESHOLD:
+        threshold.setSelectedIndex(1);
+        break;
+      case AnnotationColourGradient.BELOW_THRESHOLD:
+        threshold.setSelectedIndex(2);
+        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();
+    frame.invalidate();
+    frame.pack();
+
+  }
+
+  private Vector<String> getAnnotationItems(boolean isSeqAssociated)
+  {
+    Vector<String> list = new Vector<String>();
+    int index = 1;
+    int[] anmap = new int[av.getAlignment().getAlignmentAnnotation().length];
+    boolean enableSeqAss = false;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      if (av.getAlignment().getAlignmentAnnotation()[i].sequenceRef == null)
+      {
+        if (isSeqAssociated)
+        {
+          continue;
+        }
+      }
+      else
+      {
+        enableSeqAss = true;
+      }
+      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      if (!list.contains(label))
+      {
+        anmap[list.size()] = i;
+        list.addElement(label);
+
+      }
+      else
+      {
+        if (!isSeqAssociated)
+        {
+          anmap[list.size()] = i;
+          list.addElement(label + "_" + (index++));
+        }
+      }
+    }
+    seqAssociated.setEnabled(enableSeqAss);
+    annmap = new int[list.size()];
+    System.arraycopy(anmap, 0, annmap, 0, annmap.length);
+    return list;
+  }
+  private void setDefaultMinMax()
+  {
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+            Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+            Color.red));
+  }
+
+  public AnnotationColourChooser()
+  {
+    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()
+    {
+      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()
+    {
+      public void mousePressed(MouseEvent e)
+      {
+        if (maxColour.isEnabled())
+        {
+          maxColour_actionPerformed();
+        }
+      }
+    });
+    ok.setOpaque(false);
+    ok.setText(MessageManager.getString("action.ok"));
+    ok.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        ok_actionPerformed(e);
+      }
+    });
+    cancel.setOpaque(false);
+    cancel.setText(MessageManager.getString("action.cancel"));
+    cancel.addActionListener(new ActionListener()
+    {
+      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()
+    {
+      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(MessageManager.getString("label.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(MessageManager.getString("label.threshold_minmax"));
+    thresholdIsMin.addActionListener(new ActionListener()
+    {
+      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);
+      }
+    });
+
+    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(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);
+    this.validate();
+  }
+
+  protected void seqAssociated_actionPerformed(ActionEvent arg0)
+  {
+    adjusting = true;
+    String cursel = (String) annotations.getSelectedItem();
+    boolean isvalid = false, isseqs = seqAssociated.isSelected();
+    this.annotations.removeAllItems();
+    for (String anitem : getAnnotationItems(seqAssociated.isSelected()))
+    {
+      if (anitem.equals(cursel) || (isseqs && cursel.startsWith(anitem)))
+      {
+        isvalid = true;
+        cursel = anitem;
+      }
+      this.annotations.addItem(anitem);
+    }
+    adjusting = false;
+    if (isvalid)
+    {
+      this.annotations.setSelectedItem(cursel);
+    }
+    else
+    {
+      if (annotations.getItemCount() > 0)
+      {
+        annotations.setSelectedIndex(0);
+      }
+    }
+  }
+
+  protected void resetColours_actionPerformed(ActionEvent arg0)
+  {
+    setDefaultMinMax();
+    changeColour();
+  }
+
+  JComboBox annotations;
+
+  int[] annmap;
+
+  JPanel minColour = new JPanel();
+
+  JPanel maxColour = new JPanel();
+
+  JButton defColours = new JButton();
+
+  JButton ok = new JButton();
+
+  JButton cancel = new JButton();
+
+  JPanel jPanel1 = new JPanel();
+
+  JPanel jPanel2 = new JPanel();
+
+  BorderLayout borderLayout1 = new BorderLayout();
+
+  JComboBox threshold = new JComboBox();
+
+  JSlider slider = new JSlider();
+
+  JTextField thresholdValue = new JTextField(20);
+
+  JCheckBox currentColours = new JCheckBox();
+
+  JCheckBox thresholdIsMin = new JCheckBox();
+
+  JCheckBox seqAssociated = new JCheckBox();
+
+  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.getAlignment().getAlignmentAnnotation()[annmap[annotations
+            .getSelectedIndex()]];
+
+    int aboveThreshold = -1;
+    if (threshold.getSelectedIndex()==1)
+    {
+      aboveThreshold = AnnotationColourGradient.ABOVE_THRESHOLD;
+    }
+    else if (threshold.getSelectedIndex()==2)
+    {
+      aboveThreshold = AnnotationColourGradient.BELOW_THRESHOLD;
+    }
+
+    slider.setEnabled(true);
+    thresholdValue.setEnabled(true);
+    thresholdIsMin.setEnabled(true);
+
+    if (aboveThreshold == AnnotationColourGradient.NO_THRESHOLD)
+    {
+      slider.setEnabled(false);
+      thresholdValue.setEnabled(false);
+      thresholdValue.setText("");
+      thresholdIsMin.setEnabled(false);
+    }
+    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
+            && currentAnnotation.threshold == null)
+    {
+      currentAnnotation
+              .setThreshold(new jalview.datamodel.GraphLine(
+                      (currentAnnotation.graphMax - currentAnnotation.graphMin) / 2f,
+                      "Threshold", Color.black));
+    }
+
+    if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
+    {
+      adjusting = true;
+      float range = currentAnnotation.graphMax * 1000
+              - currentAnnotation.graphMin * 1000;
+
+      slider.setMinimum((int) (currentAnnotation.graphMin * 1000));
+      slider.setMaximum((int) (currentAnnotation.graphMax * 1000));
+      slider.setValue((int) (currentAnnotation.threshold.value * 1000));
+      thresholdValue.setText(currentAnnotation.threshold.value + "");
+      slider.setMajorTickSpacing((int) (range / 10f));
+      slider.setEnabled(true);
+      thresholdValue.setEnabled(true);
+      adjusting = false;
+    }
+
+    AnnotationColourGradient acg = null;
+    if (currentColours.isSelected())
+    {
+      acg = new AnnotationColourGradient(currentAnnotation,
+              av.getGlobalColourScheme(), aboveThreshold);
+    }
+    else
+    {
+      acg = new AnnotationColourGradient(currentAnnotation,
+              minColour.getBackground(), maxColour.getBackground(),
+              aboveThreshold);
+    }
+    acg.setSeqAssociated(seqAssociated.isSelected());
+
+    if (currentAnnotation.graphMin == 0f
+            && currentAnnotation.graphMax == 0f)
+    {
+      acg.setPredefinedColours(true);
+    }
+
+    acg.thresholdIsMinMax = thresholdIsMin.isSelected();
+
+    av.setGlobalColourScheme(acg);
+
+    if (av.getAlignment().getGroups() != null)
+    {
+
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        if (sg.cs == null)
+        {
+          continue;
+        }
+
+        if (currentColours.isSelected())
+        {
+          sg.cs = new AnnotationColourGradient(currentAnnotation, sg.cs,
+                  aboveThreshold);
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
+
+        }
+        else
+        {
+          sg.cs = new AnnotationColourGradient(currentAnnotation,
+                  minColour.getBackground(), maxColour.getBackground(),
+                  aboveThreshold);
+          ((AnnotationColourGradient) sg.cs).setSeqAssociated(seqAssociated
+                  .isSelected());
+        }
+
+      }
+    }
+    ap.alignmentChanged();
+    // ensure all associated views (overviews, structures, etc) are notified of
+    // updated colours.
+    ap.paintAlignment(true);
+  }
+
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    changeColour();
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    reset();
+    // ensure all original colouring is propagated to listeners.
+    ap.paintAlignment(true);
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  void reset()
+  {
+    av.setGlobalColourScheme(oldcs);
+    if (av.getAlignment().getGroups() != null)
+    {
+
+      for (SequenceGroup sg : ap.av.getAlignment().getGroups())
+      {
+        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(boolean updateAllAnnotation)
+  {
+    if (currentColours.isSelected()
+            && !(av.getGlobalColourScheme() instanceof AnnotationColourGradient))
+    {
+      changeColour();
+    }
+    currentAnnotation.threshold.value = (float) slider.getValue() / 1000f;
+    propagateSeqAssociatedThreshold(updateAllAnnotation);
+    ap.paintAlignment(false);
+  }
+
+  private void propagateSeqAssociatedThreshold(boolean allAnnotation)
+  {
+    if (currentAnnotation.sequenceRef == null
+            || currentAnnotation.threshold == null)
+    {
+      return;
+    }
+    // TODO: JAL-1327 only update visible annotation thresholds if allAnnotation is false, since we only need to provide a quick visual indicator
+
+    float thr = currentAnnotation.threshold.value;
+    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    {
+      AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
+      if (aa.label.equals(currentAnnotation.label))
+      {
+        aa.threshold.value = thr;
+      }
+    }
+  }
+
+  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();
+  }
+
+}