[Biojava-l] Problems in biojava

[Thomas Down]

On Tue, Mar 05, 2002 at 12:42:36PM +0200, Eli Reuveni wrote:
>
> I tried to installed the library of biojava but had some errors
> in class "AlphabetManager" where some packages didn't found:
> 
> "AlphabetManager.java": Error #: 704 : cannot access directory org\w3c\dom 
> at line 30, column 1
> "AlphabetManager.java": Error #: 704 : cannot access directory 
> javax\xml\parsers at line 31, column 1
> "AlphabetManager.java": Error #: 704 : cannot access directory org\xml\sax 
> at line 32, column 1
> "AlphabetManager.java": Error #: 704 : cannot access directory 
> org\biojava\utils\bytecode at line 37, column 1
> 
> Please where can I get those packages?

You'll need the following packages to compile BioJava:

   xerces.jar            (XML parser)
   bytecode.jar         (Java bytecode generation library)
   jakarta-regexp.jar   (Regular expressions).

If you're downloading source code, all three of these
should already be included.  You should just need to install
ANT (if you haven't got it already), then type:

   ant package
   ant javadocs


Alternatively, you can download a pre-compiled library from:

   http://www.biojava.org/download/binaries/

(all the required libraries are also available from that
directory).

I do, however, notice that the error messages you're reporting
don't look like those produced by Sun's javac Java compiler.
What compiler are you using?


> and where can I get information for which kind of software
> is it better to choose Perl or Java since I just now starting the project.

I'm not sure if there's an exhaustive comparison of Perl and
Java from a bioinformatics perspective.  There's been a certain
amount of discussion on this mailing list which you might find
helpful -- look in the archives from a month or so back.
But in general, the choice should probably be based on which
language you feel most comforatable programming in.

One area where Java has a clear advantage over Perl is in
mathematics and sequence analysis, where computational speed
is important.


Hope this helps,

    Thomas.