diff --git a/uk/ac/sanger/artemis/components/AlignmentViewer.java b/uk/ac/sanger/artemis/components/AlignmentViewer.java
index 3c306976e0ebe094de3fc394479f503bbd5c0551..f3f8f7c801ea727055ef72dee00063e157d13ae4 100644
--- a/uk/ac/sanger/artemis/components/AlignmentViewer.java
+++ b/uk/ac/sanger/artemis/components/AlignmentViewer.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AlignmentViewer.java,v 1.5 2004-09-20 08:43:11 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/AlignmentViewer.java,v 1.6 2004-09-20 12:51:11 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -43,7 +43,7 @@ import javax.swing.*;
* ComparisonData object.
*
* @author Kim Rutherford
- * @version $Id: AlignmentViewer.java,v 1.5 2004-09-20 08:43:11 tjc Exp $
+ * @version $Id: AlignmentViewer.java,v 1.6 2004-09-20 12:51:11 tjc Exp $
**/
public class AlignmentViewer extends CanvasPanel
@@ -179,7 +179,7 @@ public class AlignmentViewer extends CanvasPanel
private boolean disable_selection_from_ranges = false;
/** user defined colours */
- private boolean userColour = false;
+ private boolean reverseMatchColour = false;
/** colour for reverse matches */
private Color revMatchColour = Color.blue;
/** colour for matches */
@@ -531,10 +531,10 @@ public class AlignmentViewer extends CanvasPanel
{
public void actionPerformed(ActionEvent _)
{
- if(getSubjectDisplay ().isRevCompDisplay ())
- getSubjectDisplay ().setRevCompDisplay (false);
+ if(getSubjectDisplay().isRevCompDisplay ())
+ getSubjectDisplay().setRevCompDisplay (false);
else
- getSubjectDisplay ().setRevCompDisplay (true);
+ getSubjectDisplay().setRevCompDisplay (true);
}
});
@@ -656,42 +656,53 @@ public class AlignmentViewer extends CanvasPanel
popup.addSeparator();
- final JCheckBoxMenuItem userDefinedColour =
- new JCheckBoxMenuItem("Use Defined Colour",userColour);
- userDefinedColour.addItemListener(new ItemListener()
+ final JCheckBoxMenuItem sameColour =
+ new JCheckBoxMenuItem("Colour reverse & forward matches the same",reverseMatchColour);
+ sameColour.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
- userColour = userDefinedColour.getState();
+ reverseMatchColour = sameColour.getState();
repaintCanvas();
}
});
- popup.add(userDefinedColour);
+ popup.add(sameColour);
JMenuItem colourMatches = new JMenuItem("Colour matches...");
colourMatches.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent event)
{
- matchColour = JColorChooser.showDialog(AlignmentViewer.this,
- "Colour Matches", matchColour);
- repaintCanvas();
+ ColorChooserShades shades = createColours("Colour Matches",
+ red_percent_id_colours[NUMBER_OF_SHADES-1]);
+ if(shades != null)
+ {
+ red_percent_id_colours = shades.getDefinedColour();
+ repaintCanvas();
+ }
}
});
popup.add(colourMatches);
- JMenuItem colourRevMatches = new JMenuItem("Colour reverse matches...");
- colourRevMatches.addActionListener(new ActionListener()
+ if(!reverseMatchColour)
{
- public void actionPerformed(ActionEvent event)
+ JMenuItem colourRevMatches = new JMenuItem("Colour reverse matches...");
+ colourRevMatches.addActionListener(new ActionListener()
{
- revMatchColour = JColorChooser.showDialog(AlignmentViewer.this,
- "Colour Reverse Matches", revMatchColour);
- repaintCanvas();
- }
- });
- popup.add(colourRevMatches);
-
+ public void actionPerformed(ActionEvent event)
+ {
+ ColorChooserShades shades = createColours("Colour Reverse Matches",
+ blue_percent_id_colours[NUMBER_OF_SHADES-1]);
+ if(shades != null)
+ {
+ blue_percent_id_colours = shades.getDefinedColour();
+ repaintCanvas();
+ }
+ }
+ });
+ popup.add(colourRevMatches);
+ }
+
popup.addSeparator();
final JCheckBoxMenuItem offer_to_flip_item =
@@ -728,6 +739,34 @@ public class AlignmentViewer extends CanvasPanel
}
+ private ColorChooserShades createColours(String title, Color initialColour)
+ {
+ //Make sure we have nice window decorations.
+ JFrame.setDefaultLookAndFeelDecorated(true);
+
+ //Create and set up the window.
+ JFrame frame = new JFrame("ColorChooserDemo");
+ frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+ //Create and set up the content pane.
+ ColorChooserShades newContentPane = new ColorChooserShades(title,initialColour);
+
+ Object[] possibleValues = { "OK", "CANCEL" };
+ int select = JOptionPane.showOptionDialog(null,
+ newContentPane,
+ "Colour Selection",
+ JOptionPane.DEFAULT_OPTION,
+ JOptionPane.QUESTION_MESSAGE,null,
+ possibleValues, possibleValues[0]);
+
+ if(select == 0)
+ return newContentPane;
+
+ return null;
+ }
+
+
+
/**
* Handle a mouse press event on the drawing canvas - select on click,
* select and broadcast it on double click.
@@ -1247,7 +1286,7 @@ public class AlignmentViewer extends CanvasPanel
g.setColor (Color.yellow);
else
{
- if(percent_id == -1 || userColour)
+ if(percent_id == -1)
{
if(this_match.isRevMatch())
g.setColor(revMatchColour);
@@ -1266,7 +1305,8 @@ public class AlignmentViewer extends CanvasPanel
(maximum_percent_id - minimum_percent_id));
}
- if(this_match.isRevMatch())
+ if(this_match.isRevMatch() &&
+ !reverseMatchColour)
g.setColor(blue_percent_id_colours[colour_index]);
else
g.setColor(red_percent_id_colours[colour_index]);
@@ -1702,12 +1742,12 @@ public class AlignmentViewer extends CanvasPanel
**/
private void makeColours()
{
- red_percent_id_colours = new Color [NUMBER_OF_SHADES];
- blue_percent_id_colours = new Color [NUMBER_OF_SHADES];
+ red_percent_id_colours = new Color[NUMBER_OF_SHADES];
+ blue_percent_id_colours = new Color[NUMBER_OF_SHADES];
- for(int i = 0 ; i < blue_percent_id_colours.length ; ++i)
+ for(int i = 0; i < blue_percent_id_colours.length; ++i)
{
- final int shade_value = 255 - (int) (256 * 1.0 * i / NUMBER_OF_SHADES);
+ final int shade_value = 255 - (int) (256 * i / NUMBER_OF_SHADES);
red_percent_id_colours[i] = new Color (255, shade_value, shade_value);
blue_percent_id_colours[i] = new Color (shade_value, shade_value, 255);
}
@@ -1721,4 +1761,104 @@ public class AlignmentViewer extends CanvasPanel
return comparison_data;
}
+ public class ColorChooserShades extends JPanel
+ implements javax.swing.event.ChangeListener
+ {
+ private JPanel bannerPanel = new JPanel(new BorderLayout());
+ private JColorChooser tcc;
+ private Color definedColour[] = new Color[NUMBER_OF_SHADES];
+ private JLabel banner[] = new JLabel[NUMBER_OF_SHADES];
+ private JSlider scaleColour;
+ private Box bacross = Box.createHorizontalBox();
+
+ public ColorChooserShades(String title, Color initialColour)
+ {
+ super(new BorderLayout());
+
+ Dimension d = new Dimension(35, 35);
+ double fract = (maximum_percent_id - minimum_percent_id)/
+ (NUMBER_OF_SHADES* 0.999);
+
+ for(int i = 0; i < NUMBER_OF_SHADES; ++i)
+ {
+ int percent_id = (int)(i*fract)+minimum_percent_id;
+ banner[i] = new JLabel(" "+percent_id+" ",JLabel.CENTER);
+ banner[i].setOpaque(true);
+ banner[i].setPreferredSize(d);
+// banner[i].setMaximumSize(d);
+ bacross.add(banner[i]);
+ }
+
+ //Set up color chooser for setting text color
+ tcc = new JColorChooser(initialColour);
+ tcc.getSelectionModel().addChangeListener(ColorChooserShades.this);
+ tcc.setBorder(BorderFactory.createTitledBorder(title));
+
+ //set scale
+ scaleColour = new JSlider(0,20,3);
+ scaleColour.addChangeListener(ColorChooserShades.this);
+
+ makeColours();
+
+ //Set up the banner at the top of the window
+ colourBox();
+ bannerPanel.add(bacross, BorderLayout.CENTER);
+ bannerPanel.add(scaleColour, BorderLayout.SOUTH);
+ bannerPanel.setBorder(BorderFactory.createTitledBorder("% ID Scale"));
+
+ add(bannerPanel, BorderLayout.CENTER);
+ add(tcc, BorderLayout.SOUTH);
+ }
+
+ public void stateChanged(javax.swing.event.ChangeEvent e)
+ {
+ makeColours();
+ colourBox();
+ bannerPanel.repaint();
+ repaint();
+ }
+
+ private void colourBox()
+ {
+ Dimension d = new Dimension(20, 35);
+ for(int i = 0; i < NUMBER_OF_SHADES; ++i)
+ {
+ banner[i].setBackground(definedColour[i]);
+ banner[i].repaint();
+ }
+ }
+
+
+ /**
+ * Return an array of colours that will be used for colouring the matches
+ * (depending on score).
+ **/
+ private void makeColours()
+ {
+ Color newColour = tcc.getColor();
+
+ for(int i = 0; i < NUMBER_OF_SHADES; ++i)
+ {
+ int R = newColour.getRed();
+ int G = newColour.getGreen();
+ int B = newColour.getBlue();
+
+ int scale = (NUMBER_OF_SHADES-i)*scaleColour.getValue()*5;
+ if((R+scale) < 255)
+ R += scale;
+ if((G+scale) < 255)
+ G += scale;
+ if((B+scale) < 255)
+ B += scale;
+
+ definedColour[i] = new Color(R,G,B);
+ }
+ }
+
+ public Color[] getDefinedColour()
+ {
+ return definedColour;
+ }
+ }
+
}