Re: Some (minimal?) Java help needed (Was: Bug#670353: ITP: fastqc -- quality control for next generation sequencing data)
Le 11/8/12 1:13 PM, Andreas Tille a écrit :
> 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")));
Looking at the code, I would expect to get something like:
new HelpDialog(application,new File(URLDecoder.decode("/usr/share/fastqc/Help","UTF-8")));
or
new HelpDialog(application,new File("/usr/share/fastqc/Help");
Olivier
>
> }
>
> catch (UnsupportedEncodingException e1) {
>
> e1.printStackTrace();
>
>
> but the result remained the same. Any idea?
>
> Kind regards
>
> Andreas.
>
>
--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
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Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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