Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
Hi Olivier,
On Thu, Nov 08, 2012 at 11:17:33AM +0100, Olivier Sallou wrote:
> > This sounds somehow obvious and works (even if I wonder why my manual
> > call at command line which exactly did what you suggested was (and is)
> > failing).
> It seems that the exec call loose the ENV{CLASSPATH} set by the perl
> program where dependencies are set. As classpath is correctly set in the
> manifest, calling the -jar works perfectly.
> If you call on command line: java -cp
> /usr/share/fastqc/fastqc.jar:path_tobam.jar:path_to-bzip2.jar
> uk.ac.babraham.FastQC.FastQCApplication, it works fine too.
I guess this might be an effect of beeing fastqc.jar not in
/usr/share/java where all *.jar files should end up. Whatever, thanks
for enlightening me.
I commited the packaging stuff that creates a fastqc that properly starts
now to SVN. Everybody please give it a test with your sequences.
Unfortunately there seems one remaining issue with the Help system:
If I try the menu item
"Help" -> "Contents..."
I get the following:
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
at uk.ac.babraham.FastQC.FastQCMenuBar.actionPerformed(FastQCMenuBar.java:135)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:374)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:829)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:873)
at java.awt.Component.processMouseEvent(Component.java:6389)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3268)
at java.awt.Component.processEvent(Component.java:6154)
at java.awt.Container.processEvent(Container.java:2045)
at java.awt.Component.dispatchEventImpl(Component.java:4750)
at java.awt.Container.dispatchEventImpl(Container.java:2103)
at java.awt.Component.dispatchEvent(Component.java:4576)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4633)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4297)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4227)
at java.awt.Container.dispatchEventImpl(Container.java:2089)
at java.awt.Window.dispatchEventImpl(Window.java:2518)
at java.awt.Component.dispatchEvent(Component.java:4576)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:672)
at java.awt.EventQueue.access$400(EventQueue.java:96)
at java.awt.EventQueue$2.run(EventQueue.java:631)
at java.awt.EventQueue$2.run(EventQueue.java:629)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116)
at java.awt.EventQueue$3.run(EventQueue.java:645)
at java.awt.EventQueue$3.run(EventQueue.java:643)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:642)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
I tried to find the reason for this pretty useless error log and assumed
that the reason migth possibly be the implicite PATH to the Help dir and
replaced it with an explicite PATH
--- a/uk/ac/babraham/FastQC/FastQCMenuBar.java
+++ b/uk/ac/babraham/FastQC/FastQCMenuBar.java
@@ -132,7 +132,7 @@ public class FastQCMenuBar extends JMenu
}
else if (command.equals("help_contents")) {
try {
- new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("Help").getFile(),"UTF-8")));
+ new HelpDialog(application,new File(URLDecoder.decode(ClassLoader.getSystemResource("/usr/share/fastqc/Help").getFile(),"UTF-8")));
}
catch (UnsupportedEncodingException e1) {
e1.printStackTrace();
but the result remained the same. Any idea?
Kind regards
Andreas.
--
http://fam-tille.de
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