From 78a4818ee2d70a47726e90caa821a74a0a18b275 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 14 Oct 2009 09:02:41 +0000
Subject: [PATCH] provide an option to asynchronous display
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@12064 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/alignment/BamView.java | 137 +++++++++++++-----
1 file changed, 100 insertions(+), 37 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 19a308179..1235be0ce 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -154,6 +154,7 @@ public class BamView extends JPanel
private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
+ private boolean asynchronous = true;
private boolean showBaseAlignment = false;
private JCheckBoxMenuItem checkBoxStackView = new JCheckBoxMenuItem("Stack View");
@@ -179,6 +180,8 @@ public class BamView extends JPanel
private JPopupMenu popup;
private PopupMessageFrame popFrame = new PopupMessageFrame();
+ private PopupMessageFrame waitingFrame;
+
public static org.apache.log4j.Logger logger4j =
org.apache.log4j.Logger.getLogger(BamView.class);
@@ -1718,8 +1721,9 @@ public class BamView extends JPanel
}
- private void createViewMenu(JComponent view)
+ private void createMenus(JComponent view)
{
+ JMenu showMenu = new JMenu("Show");
JCheckBoxMenuItem checkBoxSingle = new JCheckBoxMenuItem("Single Reads");
checkBoxSingle.addActionListener(new ActionListener()
{
@@ -1729,7 +1733,7 @@ public class BamView extends JPanel
isSingle = !isSingle;
}
});
- view.add(checkBoxSingle);
+ showMenu.add(checkBoxSingle);
JCheckBoxMenuItem checkBoxSNPs = new JCheckBoxMenuItem("SNPs");
checkBoxSNPs.addActionListener(new ActionListener()
@@ -1746,9 +1750,23 @@ public class BamView extends JPanel
repaint();
}
});
- view.add(checkBoxSNPs);
- view.add(new JSeparator());
+ showMenu.add(checkBoxSNPs);
+
+ JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
+ checkBoxCoverage.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ isCoverage = !isCoverage;
+ coveragePanel.setVisible(isCoverage);
+ repaint();
+ }
+ });
+ showMenu.add(checkBoxCoverage);
+ view.add(showMenu);
+
+ JMenu viewMenu = new JMenu("Views");
ButtonGroup group = new ButtonGroup();
final JCheckBoxMenuItem checkBoxPairedStackView = new JCheckBoxMenuItem("Paired Stack View");
final JCheckBoxMenuItem checkBoxStrandStackView = new JCheckBoxMenuItem("Strand Stack View");
@@ -1775,7 +1793,7 @@ public class BamView extends JPanel
repaint();
}
});
- view.add(checkIsizeStackView);
+ viewMenu.add(checkIsizeStackView);
checkBoxStackView.addActionListener(new ActionListener()
@@ -1796,7 +1814,7 @@ public class BamView extends JPanel
repaint();
}
});
- view.add(checkBoxStackView);
+ viewMenu.add(checkBoxStackView);
checkBoxPairedStackView.addActionListener(new ActionListener()
@@ -1817,7 +1835,7 @@ public class BamView extends JPanel
repaint();
}
});
- view.add(checkBoxPairedStackView);
+ viewMenu.add(checkBoxPairedStackView);
checkBoxStrandStackView.addActionListener(new ActionListener()
{
@@ -1838,20 +1856,24 @@ public class BamView extends JPanel
repaint();
}
});
- view.add(checkBoxStrandStackView);
- view.add(new JSeparator());
+ viewMenu.add(checkBoxStrandStackView);
+ view.add(viewMenu);
+
- JCheckBoxMenuItem checkBoxCoverage = new JCheckBoxMenuItem("Coverage");
- checkBoxCoverage.addActionListener(new ActionListener()
+ if(feature_display != null)
{
- public void actionPerformed(ActionEvent e)
+ final JCheckBoxMenuItem checkBoxSync =
+ new JCheckBoxMenuItem("Asynchronous", asynchronous);
+ checkBoxSync.addActionListener(new ActionListener()
{
- isCoverage = !isCoverage;
- coveragePanel.setVisible(isCoverage);
- repaint();
- }
- });
- view.add(checkBoxCoverage);
+ public void actionPerformed(ActionEvent e)
+ {
+ asynchronous = checkBoxSync.isSelected();
+ }
+ });
+ view.add(checkBoxSync);
+ }
+
view.add(new JSeparator());
JMenu maxHeightMenu = new JMenu("Plot Height");
@@ -2142,7 +2164,14 @@ public class BamView extends JPanel
* Artemis event notification
*/
public void displayAdjustmentValueChanged(final DisplayAdjustmentEvent event)
- {
+ {
+ if(!asynchronous)
+ {
+ // if not asynchronous
+ displayAdjustmentWork(event);
+ return;
+ }
+
SwingWorker worker = new SwingWorker()
{
public Object construct()
@@ -2158,32 +2187,46 @@ public class BamView extends JPanel
if(event.getStart() != ((FeatureDisplay)event.getSource()).getForwardBaseAtLeftEdge())
{
+ if(waitingFrame == null)
+ waitingFrame = new PopupMessageFrame("waiting...");
+ waitingFrame.showWaiting();
return null;
}
- if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
- {
- laststart = -1;
- lastend = -1;
- BamView.this.startBase = event.getStart();
- BamView.this.endBase = event.getEnd();
-
- int width = feature_display.getMaxVisibleBases();
- setZoomLevel(width);
- repaint();
- }
- else
- {
- setDisplay(event.getStart(),
- event.getStart()+feature_display.getMaxVisibleBases(), event);
- repaint();
- }
+ displayAdjustmentWork(event);
+ if(waitingFrame != null)
+ waitingFrame.setVisible(false);
return null;
}
};
worker.start();
}
+ /**
+ * Carry out the display agjustment event action.
+ * @param event
+ */
+ private void displayAdjustmentWork(final DisplayAdjustmentEvent event)
+ {
+ if(event.getType() == DisplayAdjustmentEvent.SCALE_ADJUST_EVENT)
+ {
+ laststart = -1;
+ lastend = -1;
+ BamView.this.startBase = event.getStart();
+ BamView.this.endBase = event.getEnd();
+
+ int width = feature_display.getMaxVisibleBases();
+ setZoomLevel(width);
+ repaint();
+ }
+ else
+ {
+ setDisplay(event.getStart(),
+ event.getStart()+feature_display.getMaxVisibleBases(), event);
+ repaint();
+ }
+ }
+
public void selectionChanged(SelectionChangeEvent event)
{
repaint();
@@ -2265,7 +2308,7 @@ public class BamView extends JPanel
if(popup == null)
{
popup = new JPopupMenu();
- createViewMenu(popup);
+ createMenus(popup);
}
if(gotoMateMenuItem != null)
@@ -2317,6 +2360,7 @@ public class BamView extends JPanel
private JTextArea textArea = new JTextArea();
PopupMessageFrame()
{
+ super();
getRootPane().putClientProperty("Window.alpha", new Float(0.8f));
textArea.setWrapStyleWord(true);
textArea.setEditable(false);
@@ -2324,6 +2368,25 @@ public class BamView extends JPanel
getContentPane().add(textArea);
}
+ PopupMessageFrame(String msg)
+ {
+ this();
+ textArea.setFont(textArea.getFont().deriveFont(14.f));
+ textArea.setText(msg);
+ setTitle(msg);
+ pack();
+ }
+
+ protected void showWaiting()
+ {
+ Point p = mainPanel.getLocationOnScreen();
+ p.x += (mainPanel.getWidth() - PopupMessageFrame.this.getWidth())/2;
+ p.y += mainPanel.getHeight()/2;
+ setLocation(p);
+ setVisible(true);
+ requestFocus();
+ }
+
protected void show(String title, String msg, int ypos, long aliveTime)
{
setTitle(title);
--
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