[BiO BB] Java API for BLAST?

[Joe Landman]

Hi Ahmed:

Ahmed Moustafa wrote:
> Hi Joe,
> 
> I thought of switching my project to Perl because I found BioPerl had 
> more functionalities and more "documentation" than BioJava but am trying 
> first to stay with Java, otherwise will go to BioPerl.

My apologies about not being clearer.  I am not suggesting a port to 
Perl, just hooking in the previously developed modules through some sort 
of inter-language call.  In Perl it is fairly easy to do with the 
Inline::* modules, and I believe it is fairly easy with Python and Java. 
   Thats it... not advocating re-inventing your program in a new 
language, just using what might be available in another language that 
can help.

Joe

> 
> Thanks!
> 
> Ahmed
> 
> On 12/9/2005 9:45 AM, Joe Landman wrote:
> 
>> Hi Ahmed:
>>
>>   You might look into hooking into the BioPerl bits from Java (RMI I 
>> think).  This shouldn't be too difficult.
>>
>> Joe
>>
>> Ahmed Moustafa wrote:
>>
>>> Hi All!
>>>
>>> Is there some sort of a Java package to do BLAST search (remote or 
>>> local)? I went through BioJava and I could not find something like 
>>> that, it seemed there was only a parser for the BLAST XML output.
>>>
>>> Thanks in advance!
>>>
>>> Ahmed
>>
>>
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Joseph Landman, Ph.D
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