Odd problem with native jdk.1.4.1 and jalview

Odd problem with native jdk.1.4.1 and jalview

Post by Bruno Afon » Sat, 21 Jun 2003 04:27:26



Hey,

I am having a strange problem that I would like to share with you since
it appears to me to be a problem in the native jdk 1.4.1 :-)

The problem lies in a program to edit and view multiple alignments
(biology stuff, you don't really need to know what this is ;)

Here's how to reproduce it:

create a script.sh
cheetah% cat script.sh
-------
#!/bin/sh
cd ~
mkdir testdir
cd testdir
# grab jalview's latest and greatest
wget http://www2.ebi.ac.uk/~michele/jalview/dist/source-1.7.5b.tgz
tar -zxvf source-1.7.5b.tgz
javac jalview/AlignFrame.java
# grab the alignment file. :-)
wget http://bio98.ist.utl.pt/~bruno/mfsmdr12.aln
java jalview.AlignFrame mfsmdr12.aln File CLUSTAL
/usr/local/linux-sun-jdk1.4.1/bin/java jalview.AlignFrame mfsmdr12.aln
File CLUSTAL
-------

And now the problem:

The first time the app comes up, in the file dir, say to save postscript
to local file.
Sometimes I can't even open a dialog box with "browse" and I have never
ever been able to save the alignment. :-)

Now, this werks with java from linux jdk1.4.1... (the second time the
app comes up).

Ideas? I'm out of them :)

--
Bruno Miguel Afonso
Biological Eng. student.

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    I have Apache 1.3.24 [with the works] running in a jail. I tried to follow the article on getting the native JDK working but it requires linux emulation enabled, as does the 1.4 binary [obviously]. Has anyone gotten any sort of JDK running in a jail? I have only one server that needs to run dns, mail, db, ftp, and web and would rather not run the web services in the host environment.

Thanks
- aarong
--
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