[Biojava-l] Query

Ola Spjuth ola.spjuth at farmbio.uu.se
Thu May 31 15:26:49 UTC 2007


Look into the Bioclipse project (http://www.bioclipse.net). It is a  
graphical workbench that has integrated other tools such as ClustalW  
and Blast. Duplicating such an integration for HMMER seems like a  
straightforward task. Somewhat limited CLI is even done at runtime in  
the Bioclipse preferences, but it could very well be extended.


    .../Ola Spjuth

On May 31, 2007, at 17:10 , Tom Oinn wrote:

> rohit reja wrote:
>> Hello all,
>> I am working on HMMER which runs on a command line interface(CLI).
>> Now i want to create and integrate a GUI to execute the commands  
>> on the  CLI
>> .
>> How can we do this using java .?
> This isn't really a BioJava question (this list is for discussion  
> of the
> BioJava project and its usage) but...
> You can use the system Runtime class in Java to exec external tools,
> your application will have to construct the command line then create a
> Process object from this command line which has streams from which you
> can manipulate stdin and stdout for the process. Google for 'Java
> Runtime exec' for plenty more information.
> Hint - the process will block unless you consume both stdout and  
> stderr
> streams, blocking when the buffer for those streams (which is OS and
> Java version dependant) is full. If you get odd behaviour with the
> application sometimes hanging this is probably why!
> Cheers,
> Tom
>> Please reply ASAP.
> ps - don't ask people to reply ASAP, it just annoys people! The
> assumption if you ask a question on a mailing list is that you'd  
> like an
> answer :)
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