[Biojava-dev] Hi.. Calling Java from Perl

[Abhishek Pratap]

Yeah it is part of the development cycle. We need to integrate the
code some part of it is perl and some in Java.

>From your suggestions I feel I clearly have two options.
1. use a web service to talk between java and perl. This might not be
very efficient as we expect to make thousands of call per run.
2. Port the whole java code to bioperl.

#2 is scary but I might just have to do it.

Thanks again to all of you,
-Abhi

On Wed, Jul 29, 2009 at 4:56 PM, <ayates at ebi.ac.uk> wrote:
> That was my original point however it sounds from the original poster that
> the system which is in Perl needs to call out to an already implemented
> system in BioJava. In a perfect world this mismatch would never happen but
> hey we all know it can :)
>
> Andy
>
>> You could always use BioPerl instead :-)
>> http://www.bioperl.org/wiki/Main_Page
>>
>>
>>
>>
>> Russell Smithies
>>
>> Bioinformatics Applications Developer
>> T +64 3 489 9085
>> E  russell.smithies at agresearch.co.nz
>>
>> Invermay  Research Centre
>> Puddle Alley,
>> Mosgiel,
>> New Zealand
>> T  +64 3 489 3809
>> F  +64 3 489 9174
>> www.agresearch.co.nz
>>
>>
>>
>>> -----Original Message-----
>>> From: biojava-dev-bounces at lists.open-bio.org [mailto:biojava-dev-
>>> bounces at lists.open-bio.org] On Behalf Of Abhishek Pratap
>>> Sent: Wednesday, 29 July 2009 7:04 a.m.
>>> To: biojava-dev at lists.open-bio.org
>>> Subject: [Biojava-dev] Hi.. Calling Java from Perl
>>>
>>> Hi Guys
>>>
>>> Before I ask the question, let me introduce myself. I am Abhishek
>>> primarily a Bioinformatician and this is my first mail here. I
>>> realized sooner thn later that I have to use BioJava to make my life
>>> easier. :)
>>>
>>> So basically we have a lot of perl code where we would like to plugin
>>> some Biojava code and some inhouse written packages/classes. I am just
>>> wondering what is the best way to do so. Clearly I am not a java guy
>>> so please excuse me in case I am asking something which is very basic.
>>> I found couple of solutions after few googles but not sure which is
>>> the efficient one.
>>>
>>> Thanks,
>>> -Abhi
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>> =======================================================================
>> Attention: The information contained in this message and/or attachments
>> from AgResearch Limited is intended only for the persons or entities
>> to which it is addressed and may contain confidential and/or privileged
>> material. Any review, retransmission, dissemination or other use of, or
>> taking of any action in reliance upon, this information by persons or
>> entities other than the intended recipients is prohibited by AgResearch
>> Limited. If you have received this message in error, please notify the
>> sender immediately.
>> =======================================================================
>>
>> _______________________________________________
>> biojava-dev mailing list
>> biojava-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>
>
>