[Biojava-l] Help with Chromatogram applet

[Mark Schreiber]

Hi -

You need to sign the jar (and possibly the applet) to give it access
outside the 'sandbox'.

To do this get a recent copy of the biojava source code and jar from
http://www.spice-3d.org/cruise/

To sign biojava.jar using a self signed certificate do:

ant sign

to verify that a biojava.jar has a valid signature do:

jarsigner -verify biojava.jar

For more info, google something like applet security, signing jars or
java sandbox.

- Mark

On 9/6/07, gtg477y at mail.gatech.edu <gtg477y at mail.gatech.edu> wrote:
> Hi all,
>
> It seems I might not be the first person to ask about this, but I am working on
> a chromatogram applet. I am trying to open chromatogram files using
> ChromatogramFactory. I first tried it in a stand alone app, and it worked fine,
> but when I try to use the ChromatogramFactory.create method in an applet, it
> gives me the following message:
>
>  Exception in thread "AWT-EventQueue-1" java.security.AccessControlException:
> access denied (java.io.FilePermission 3422_A01.ab1 read)
>
>  at
> java.security.AccessControlContext.checkPermission(AccessControlContext.java:264)
>  at java.security.AccessController.checkPermission(AccessController.java:427)
>  at java.lang.SecurityManager.checkPermission(SecurityManager.java:532)
>  at java.lang.SecurityManager.checkRead(SecurityManager.java:871)
>  at java.io.FileInputStream.<init>(FileInputStream.java:100)
>  at
> org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:69)
>  at ChromatogramApplet.paint(ChromatogramApplet.java:19)
>  at sun.awt.RepaintArea.paintComponent(RepaintArea.java:248)
>  at sun.awt.RepaintArea.paint(RepaintArea.java:224)
>  at sun.awt.windows.WComponentPeer.handleEvent(WComponentPeer.java:254)
>  at java.awt.Component.dispatchEventImpl(Component.java:4060)
>  at java.awt.Container.dispatchEventImpl(Container.java:2024)
>  at java.awt.Component.dispatchEvent(Component.java:3819)
>  at java.awt.EventQueue.dispatchEvent(EventQueue.java:463)
>  at
> java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
>  at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
>  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
>  at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
>  at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
>
>
> I'm pretty new to Java, so I don't know what a lot of it means, but I assume
> that for some reason I don't have permission to access the file from an applet.
> Is that pretty much correct? Is there any way to get around this? Or should I
> perhaps use a different class to open the files?
>
> --
>
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