[Biojava-l] biojava jar file

[Martin Moorhead]

Hi Thomas, Matthew and everybody in BioJava,

I have been using BioJava for the past 4 months in my Java development
work at Parallele Biosciences in San Francisco and I want to
congratulate everybody on BioJava for doing such an excellent job.

I am using the basic Sequences, Features, i/o and some visualizors. It's
so nice to have such well architected code to use as a platform. (e.g. I
do a lot of SNP stuff and the ambiguity symbols work very well).

[Thomas and Matthew might remember me from the (first?) biojava
bootcamp, when I was working at Viaken in Cambridge].

I am writing Java applications which I distribute to client PCs using
Java Web Start technology (like Applets but without the browser
incompatibility nuisances). [I noticed that DAS client is distributed
with Web Start].

Some of my applications require unrestricted security access to the host
PC (e.g. to run Blast locally) and hence I need to sign all the jars
that I distribute. This is where I have run into problems with the
biojava jar file. Somehow I am not able to properly sign all the entries
in the Biojava.jar file and I get the following error when I launch
through Java Web Start:

Missing signed entry in resource biojava.jar:

JNLPException[category: Download Error : Exception: null : LaunchDesc:
null ]
            at com.sun.javaws.security.SigningInfo.checkSigning(Unknown
Source)
            at
com.sun.javaws.cache.DownloadProtocol$RetrieveAction.actionDownload(Unkn
own Source)
            at com.sun.javaws.cache.DownloadProtocol.doDownload(Unknown
Source)
            at com.sun.javaws.cache.DownloadProtocol.getResource(Unknown
Source)
            at com.sun.javaws.LaunchDownload.downloadJarFiles(Unknown
Source)
            at com.sun.javaws.LaunchDownload.downloadEagerorAll(Unknown
Source)
            at com.sun.javaws.Launcher.downloadResources(Unknown Source)
            at com.sun.javaws.Launcher.handleApplicationDesc(Unknown
Source)
            at com.sun.javaws.Launcher.handleLaunchFile(Unknown Source)
            at com.sun.javaws.Launcher.run(Unknown Source)
            at java.lang.Thread.run(Thread.java:536)

I get this error when I use biojava-1.20.jar or biojava-1.21.jar but NOT
when I use biojava-1.11.jar! I also have no problem signing my own jars
or the other library jars I am using (xerces.jar etc.).
So, I am puzzled and wondering if anybody can help me with this problem?

Many thanks in advance.

Cheers, Martin Moorhead.

p.s. Is there an up to data list of projects that could be contributed
to BioJava? I looked on the web site and couldn't find any. We might
have some resources that we could contribute if the projects are
mutually beneficial. Is there a high level 'todo' list somewhere?