[Biojava-l] How to handle the big size of FASTA file?

[Kalle Näslund]

Matthew Pocock wrote:

>Hi,
>
>Java runs with an implementation specific default
>memory size. You can alter this using the Xmx switch.
>For example,
>
>java -Xmx100mb com.bar.Foo
>
>will run the com.bar.Foo class in a VM that can grow
>to 100 mb in size.
>
>Matthew
>
> --- hjAN <hjan at if.kaist.ac.kr> wrote: > Dear all
>members,
>  
>
>>The FASTA file of any one human chromosome is in
>>general over 100Mbytes.
>>Therefore, 'OutOfMemoryException' happens when I
>>handle that file with Sequence interface. 
>>
>>Is there any way to handle the big size of FASTA
>>file? 
>>
>>Sincerely,
>>AN, Hyeong-Jun
>>    
>>
>>>_______________________________________________
>>>      
>>>
>>Biojava-l mailing list  -  Biojava-l at biojava.org
>>http://biojava.org/mailman/listinfo/biojava-l
>> 
>>    
>>
>
>__________________________________________________
>Yahoo! Plus
>For a better Internet experience
>http://www.yahoo.co.uk/btoffer
>_______________________________________________
>Biojava-l mailing list  -  Biojava-l at biojava.org
>http://biojava.org/mailman/listinfo/biojava-l
>  
>
And, in case you are using biojava 1.2, a switch to 1.3 or
CVS source builds might be appropriate.

Thats becaset newer biojava contains some classes that stores large
sequences in packed form in memory, this reduces memory
useage a lot. If i understood things correctly, with 1.3/CVS
this happens magicaly for you. So you just open the sequence
as usual, and if it is larger then some certain size, it will be
loaded to memory in a packed format.

Hope this helps aswell, Kalle