[Biojava-l] BLAST/Java interface
Fri, 23 Aug 2002 10:52:36 +1200
Matthew and Keith,
Might this be a case for encapsulation of some of the common parsing
tasks in a single easy to use object or tools class. Most of the time if
you want to quickly parse a blast output you don't want have to
understand the entire event driven parsing framework. Much like creating
a DNA sequence with DNATools. Most of the ugliness is handled for you
and you don't really need to know whats going on.
Is it possible to have a class that contains an internal Process object
that points to the blast binary(s) (whose path could be passed as a File
reference). This object could then take seach strings as an InputStream
and return results as an OutputStream abstracting away the need to
understand whats happening under the hood.
Just a thought.
> -----Original Message-----
> From: Matthew Pocock [mailto:firstname.lastname@example.org]
> Sent: Friday, 23 August 2002 9:12 a.m.
> To: nathan whitehouse
> Cc: email@example.com
> Subject: Re: [Biojava-l] BLAST/Java interface
> Hi Nathan,
> The solution depends on wether you want to do the processing of the
> blast report client or server side. It sounds like you are using
> servlets. If that's the case, then you can drop biojava.jar in as a
> dependancy in your servlets .war (in the lib directory?) and use the
> excelent blast handeling code from CAT. There's a tutorial at
> ml to get
> you started. You could stream the result to the applet as an XML
> document and then parse that client-side with a SAX handler,
> or perhaps
> send over serialized simple-stupid objects - presumably you have an
> object model for blast hits in the applet portion already. If the
> servlet is spitting out static pages, then it's relatively easy to
> consume the blast XML and emit a well formatted web page,
> either using
> your own code or using XSLT.
> If the parsing needs to be done in the client-side applet, then I
> sudgest you grab the source-code version of biojava (from
> anonymous CVS
> - http://cvs.biojava.org/) and try pulling the xml parser package out
> into its own small jar. It would be bad to send the whole of
> biojava to
> the client unless you are using webstart and have a guaranteed good
> connection to the clients (e.g. not over the web).
> I hope that gives you some ideas. There are other ways to
> skin this cat,
> so if none of this hits the spot, post back a slightly more detailed
> idea of what you are doing and we may be able to give a more focussed
> Good luck,
> ps if you have problems with the blast parser not handeling
> your version
> of blast then we can work together to sort this out
> nathan whitehouse wrote:
> > Hello people at BioJava,
> > I'm modifying an existing Java applet-servlet used
> > by this lab.
> > People want us to add BLAST to this applet.
> > Anybody know of a good way to do this?
> > Are there convenient BLAST libraries to call from
> > the servlet? We've talked about calling a C or C++
> > library using the JNI. I've looked around and it
> > seems that there's no modularized BLAST lying around
> > that would make this easy.
> > The simple way to do it is just call BLASTAll from
> > the shell with its arguments. But this is a hack; I
> > want to know if there is a better way to pass objects
> > in and out of BLAST.
> > Thanks!
> > Nathan
> > Nathan Whitehouse
> > Shaulsky Lab
> > Baylor College of Medicine
> > Houston, Texas, USA
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