From 65d77c46d29bb514546ea7194374cdc9390556f4 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 12 May 2010 16:47:21 +0000
Subject: [PATCH] additions for MacOSX about, quit
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13814 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../components/alignment/BamFrame.java | 79 +++++++
.../components/alignment/BamOSXAdapter.java | 209 ++++++++++++++++++
.../artemis/components/alignment/BamView.java | 17 +-
3 files changed, 301 insertions(+), 4 deletions(-)
create mode 100644 uk/ac/sanger/artemis/components/alignment/BamFrame.java
create mode 100644 uk/ac/sanger/artemis/components/alignment/BamOSXAdapter.java
diff --git a/uk/ac/sanger/artemis/components/alignment/BamFrame.java b/uk/ac/sanger/artemis/components/alignment/BamFrame.java
new file mode 100644
index 000000000..a05bada92
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/BamFrame.java
@@ -0,0 +1,79 @@
+package uk.ac.sanger.artemis.components.alignment;
+
+import javax.swing.ImageIcon;
+import javax.swing.JFrame;
+import javax.swing.JOptionPane;
+
+
+ class BamFrame extends JFrame
+ {
+ private static final long serialVersionUID = 1L;
+ private String bamFile = null;
+
+ BamFrame()
+ {
+ super();
+ if(isMac())
+ initMac();
+ }
+
+ private void initMac()
+ {
+ try
+ {
+ // Generate and register the OSXAdapter, passing it a hash of all the
+ // methods we wish to
+ // use as delegates for various com.apple.eawt.ApplicationListener
+ // methods
+ Class splashClass = Class.forName("uk.ac.sanger.artemis.components.alignment.BamFrame");
+ BamOSXAdapter.setQuitHandler(this, splashClass.getDeclaredMethod(
+ "exitApp", (Class[]) null));
+ BamOSXAdapter.setAboutHandler(this, splashClass.getDeclaredMethod("about",
+ (Class[]) null));
+ // OSXAdapter.setPreferencesHandler(this,
+ // splashClass.getDeclaredMethod("preferences", (Class[])null));
+ BamOSXAdapter.setFileHandler(this, splashClass.getDeclaredMethod(
+ "loadFile", new Class[]
+ { String.class }));
+ }
+ catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+
+ protected void about()
+ {
+ ClassLoader cl = this.getClass().getClassLoader();
+ ImageIcon icon = new ImageIcon(cl.getResource("images/icon.gif"));
+
+ JOptionPane.showMessageDialog(this,
+ "BamView\nthis is free software and is distributed"
+ + "\nunder the terms of the GNU General Public License.",
+ "About", JOptionPane.INFORMATION_MESSAGE, icon);
+ }
+
+ protected void loadFile(final String bamFile)
+ {
+ this.bamFile = bamFile;
+ }
+
+ protected void exitApp()
+ {
+ int status = JOptionPane.showConfirmDialog(this, "Exit?",
+ "BamView", JOptionPane.OK_CANCEL_OPTION, JOptionPane.QUESTION_MESSAGE);
+ if(status == JOptionPane.CANCEL_OPTION)
+ return;
+ System.exit(0);
+ }
+
+ protected String getBamFile()
+ {
+ return bamFile;
+ }
+
+ private boolean isMac()
+ {
+ return System.getProperty("mrj.version") != null;
+ }
+ }
diff --git a/uk/ac/sanger/artemis/components/alignment/BamOSXAdapter.java b/uk/ac/sanger/artemis/components/alignment/BamOSXAdapter.java
new file mode 100644
index 000000000..2aaf01122
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/alignment/BamOSXAdapter.java
@@ -0,0 +1,209 @@
+package uk.ac.sanger.artemis.components.alignment;
+
+import java.lang.reflect.*;
+
+public class BamOSXAdapter implements InvocationHandler
+
+{
+ protected Object targetObject;
+ protected Method targetMethod;
+ protected String proxySignature;
+ static Object macOSXApplication;
+
+ // Each OSXAdapter has the name of the EAWT method it intends to listen for
+ // (handleAbout, for example),
+ // the Object that will ultimately perform the task, and the Method to be
+ // called on that Object
+ protected BamOSXAdapter(String proxySignature, Object target, Method handler)
+ {
+ this.proxySignature = proxySignature;
+ this.targetObject = target;
+ this.targetMethod = handler;
+ }
+
+ // Pass this method an Object and Method equipped to perform application
+ // shutdown logic
+ // The method passed should return a boolean stating whether or not the quit
+ // should occur
+ public static void setQuitHandler(Object target, Method quitHandler)
+ {
+ setHandler(new BamOSXAdapter("handleQuit", target, quitHandler));
+ }
+
+ // Pass this method an Object and Method equipped to display application info
+ // They will be called when the About menu item is selected from the
+ // application menu
+ public static void setAboutHandler(Object target, Method aboutHandler)
+ {
+ boolean enableAboutMenu = (target != null && aboutHandler != null);
+ if(enableAboutMenu)
+ setHandler(new BamOSXAdapter("handleAbout", target, aboutHandler));
+
+ // If we're setting a handler, enable the About menu item by calling
+ // com.apple.eawt.Application reflectively
+ try
+ {
+ Method enableAboutMethod = macOSXApplication.getClass()
+ .getDeclaredMethod("setEnabledAboutMenu",
+ new Class[] { boolean.class });
+ enableAboutMethod.invoke(macOSXApplication, new Object[] { Boolean
+ .valueOf(enableAboutMenu) });
+ }
+ catch(Exception ex)
+ {
+ System.err.println("OSXAdapter could not access the About Menu");
+ ex.printStackTrace();
+ }
+ }
+
+ // Pass this method an Object and a Method equipped to display application
+ // options
+ // They will be called when the Preferences menu item is selected from the
+ // application menu
+ public static void setPreferencesHandler(Object target, Method prefsHandler)
+ {
+ boolean enablePrefsMenu = (target != null && prefsHandler != null);
+ if(enablePrefsMenu)
+ setHandler(new BamOSXAdapter("handlePreferences", target, prefsHandler));
+
+ // If we're setting a handler, enable the Preferences menu item by calling
+ // com.apple.eawt.Application reflectively
+ try
+ {
+ Method enablePrefsMethod = macOSXApplication.getClass()
+ .getDeclaredMethod("setEnabledPreferencesMenu",
+ new Class[] { boolean.class });
+ enablePrefsMethod.invoke(macOSXApplication, new Object[] { Boolean
+ .valueOf(enablePrefsMenu) });
+ }
+ catch(Exception ex)
+ {
+ System.err.println("OSXAdapter could not access the About Menu");
+ ex.printStackTrace();
+ }
+ }
+
+ // Pass this method an Object and a Method equipped to handle document
+ // events from the Finder. Documents are registered with the Finder via
+ // the CFBundleDocumentTypes dictionary in the application Info.plist
+ public static void setFileHandler(Object target, Method fileHandler)
+ {
+ setHandler(new BamOSXAdapter("handleOpenFile", target, fileHandler)
+ {
+ // Override OSXAdapter.callTarget to send information on the
+ // file to be opened
+ public boolean callTarget(Object appleEvent)
+ {
+ if(appleEvent != null)
+ {
+ try
+ {
+ Method getFilenameMethod = appleEvent.getClass().getDeclaredMethod(
+ "getFilename", (Class[]) null);
+ String filename = (String) getFilenameMethod.invoke(appleEvent,
+ (Object[]) null);
+ this.targetMethod.invoke(this.targetObject,
+ new Object[] { filename });
+ }
+ catch(Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return true;
+ }
+ });
+ }
+
+ // setHandler creates a Proxy object from the passed OSXAdapter and adds it as
+ // an ApplicationListener
+ public static void setHandler(BamOSXAdapter adapter)
+ {
+ try
+ {
+ Class applicationClass = Class.forName("com.apple.eawt.Application");
+ if(macOSXApplication == null)
+ macOSXApplication = applicationClass.getConstructor((Class[]) null)
+ .newInstance((Object[]) null);
+
+ Class applicationListenerClass = Class
+ .forName("com.apple.eawt.ApplicationListener");
+ Method addListenerMethod = applicationClass.getDeclaredMethod(
+ "addApplicationListener", new Class[] { applicationListenerClass });
+ // Create a proxy object around this handler that can be reflectively added as an Apple ApplicationListener
+ Object osxAdapterProxy = Proxy.newProxyInstance(BamOSXAdapter.class
+ .getClassLoader(), new Class[] { applicationListenerClass }, adapter);
+ addListenerMethod.invoke(macOSXApplication,
+ new Object[] { osxAdapterProxy });
+ }
+ catch(ClassNotFoundException cnfe)
+ {
+ System.err.println(
+ "This version of Mac OS X does not support the Apple EAWT. ApplicationEvent handling has been disabled ("
+ + cnfe + ")");
+ }
+ catch(Exception ex)
+ { // Likely a NoSuchMethodException or an IllegalAccessException loading/invoking eawt.Application methods
+ System.err.println("Mac OS X Adapter could not talk to EAWT:");
+ ex.printStackTrace();
+ }
+ }
+
+ // Override this method to perform any operations on the event
+ // that comes with the various callbacks
+ // See setFileHandler above for an example
+ public boolean callTarget(Object appleEvent)
+ throws InvocationTargetException, IllegalAccessException
+ {
+ Object result = targetMethod.invoke(targetObject, (Object[]) null);
+ if(result == null)
+ return true;
+
+ return Boolean.valueOf(result.toString()).booleanValue();
+ }
+
+ // InvocationHandler implementation
+ // This is the entry point for our proxy object; it is called every time an ApplicationListener method is invoked
+ public Object invoke(Object proxy, Method method, Object[] args)
+ throws Throwable
+ {
+ if(isCorrectMethod(method, args))
+ {
+ boolean handled = callTarget(args[0]);
+ setApplicationEventHandled(args[0], handled);
+ }
+ // All of the ApplicationListener methods are void; return null regardless of what happens
+ return null;
+ }
+
+ // Compare the method that was called to the intended method when the OSXAdapter instance was created
+ // (e.g. handleAbout, handleQuit, handleOpenFile, etc.)
+ protected boolean isCorrectMethod(Method method, Object[] args)
+ {
+ return (targetMethod != null && proxySignature.equals(method.getName()) && args.length == 1);
+ }
+
+ // It is important to mark the ApplicationEvent as handled and cancel the default behavior
+ // This method checks for a boolean result from the proxy method and sets the event accordingly
+ protected void setApplicationEventHandled(Object event, boolean handled)
+ {
+ if(event != null)
+ {
+ try
+ {
+ Method setHandledMethod = event.getClass().getDeclaredMethod(
+ "setHandled", new Class[] { boolean.class });
+ // If the target method returns a boolean, use that as a hint
+ setHandledMethod.invoke(event,
+ new Object[] { Boolean.valueOf(handled) });
+ }
+ catch(Exception ex)
+ {
+ System.err
+ .println("OSXAdapter was unable to handle an ApplicationEvent: "
+ + event);
+ ex.printStackTrace();
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/components/alignment/BamView.java b/uk/ac/sanger/artemis/components/alignment/BamView.java
index 99c6e5a3e..0a7b21aac 100644
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -210,6 +210,7 @@ public class BamView extends JPanel
int nbasesInView)
{
super();
+
setBackground(Color.white);
this.bamList = bamList;
this.nbasesInView = nbasesInView;
@@ -2861,19 +2862,27 @@ public class BamView extends JPanel
{
SAMRecord sam1;
SAMRecord sam2;
- }
-
+ }
+
public static void main(String[] args)
{
- List<String> bam = new Vector<String>();;
+ BamFrame frame = new BamFrame();
+ if(args.length == 0 && frame.getBamFile() != null)
+ args = new String[]{ frame.getBamFile() };
+
+ List<String> bam = new Vector<String>();
String reference = null;
if(args.length == 0)
{
+ System.setProperty("default_directory", System.getProperty("user.dir"));
FileSelectionDialog fileSelection = new FileSelectionDialog(null, true);
bam = fileSelection.getBamFiles();
reference = fileSelection.getReferenceFile();
if(reference == null || reference.equals(""))
reference = null;
+
+ if(bam == null || bam.size() < 1)
+ System.exit(0);
}
else if(!args[0].startsWith("-"))
{
@@ -2916,7 +2925,7 @@ public class BamView extends JPanel
}
final BamView view = new BamView(bam, reference, nbasesInView);
- JFrame frame = new JFrame("BamView v"+view.getVersion());
+ frame.setTitle("BamView v"+view.getVersion());
// translucent
//frame.getRootPane().putClientProperty("Window.alpha", new Float(0.9f));
--
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