From 019e52224d86e5c6ecb48fe7761d2ce6a14e0f20 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 12 Jun 2012 11:16:45 +0100
Subject: [PATCH] add colour to BAM menu to identify read colours
---
.../artemis/components/alignment/BamView.java | 58 +++++++++++++++++--
.../components/alignment/CoveragePanel.java | 1 +
2 files changed, 55 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index b5be95af4..70937b386 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -50,6 +50,7 @@ import java.awt.event.KeyEvent;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.awt.event.MouseMotionListener;
+import java.awt.image.BufferedImage;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileOutputStream;
@@ -72,6 +73,7 @@ import javax.swing.BorderFactory;
import javax.swing.Box;
import javax.swing.BoxLayout;
import javax.swing.ButtonGroup;
+import javax.swing.ImageIcon;
import javax.swing.JButton;
import javax.swing.JCheckBox;
import javax.swing.JCheckBoxMenuItem;
@@ -2162,9 +2164,11 @@ public class BamView extends JPanel
private void addToViewMenu(final int thisBamIndex)
{
- File f = new File(bamList.get(thisBamIndex));
+ final File f = new File(bamList.get(thisBamIndex));
final JCheckBoxMenuItem cbBam = new JCheckBoxMenuItem(
- f.getName(), true);
+ f.getName(),
+ getImageIcon(getColourByCoverageColour(thisBamIndex)),
+ true);
bamFilesMenu.add(cbBam);
cbBam.addActionListener(new ActionListener()
{
@@ -2179,8 +2183,48 @@ public class BamView extends JPanel
}
});
}
-
+ /**
+ * Refresh the colour of the icons used to identify the
+ * BAM files.
+ */
+ protected void refreshColourOfBamMenu()
+ {
+ final Component cs[] = bamFilesMenu.getMenuComponents();
+ for(Component c : cs)
+ {
+ if(c instanceof JCheckBoxMenuItem)
+ {
+ final JCheckBoxMenuItem cbBam = (JCheckBoxMenuItem) c;
+ final String bam = cbBam.getText();
+
+ for(int i=0; i<bamList.size(); i++)
+ {
+ final File f = new File(bamList.get(i));
+ if(f.getName().equals(bam))
+ {
+ cbBam.setIcon(getImageIcon(getColourByCoverageColour(i)));
+ break;
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Create an icon of a box using the given colour.
+ * @param c
+ * @return
+ */
+ private ImageIcon getImageIcon(Color c)
+ {
+ BufferedImage image = (BufferedImage)this.createImage(10, 10);
+ Graphics2D g2 = image.createGraphics();
+ g2.setColor(c);
+ g2.fillRect(0, 0, 10, 10);
+ return new ImageIcon(image);
+ }
+
private void createMenus(JComponent menu)
{
final JMenuItem addBam = new JMenuItem("Add BAM ...");
@@ -3042,12 +3086,18 @@ public class BamView extends JPanel
*/
private Color getColourByCoverageColour(SAMRecord samRecord)
{
- LineAttributes lines[] = CoveragePanel.getLineAttributes(bamList.size());
int fileIndex = 0;
if(bamList.size()>1)
fileIndex = (Integer) samRecord.getAttribute("FL");
+ return getColourByCoverageColour(fileIndex);
+ }
+
+ private Color getColourByCoverageColour(final int fileIndex)
+ {
+ LineAttributes lines[] = CoveragePanel.getLineAttributes(bamList.size());
return lines[fileIndex].getLineColour();
}
+
protected int getMaxBases()
{
diff --git a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
index 3a287fcf1..31b2de553 100644
--- a/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
+++ b/uk/ac/sanger/artemis/components/alignment/CoveragePanel.java
@@ -87,6 +87,7 @@ import net.sf.samtools.SAMRecord;
lines =
LineAttributes.configurePlots(bamView.bamList,
getLineAttributes(size), CoveragePanel.this);
+ bamView.refreshColourOfBamMenu();
}
});
menu.add(configure);
--
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