[Biojava-l] Quick EMBL Loading?

Schreiber, Mark mark.schreiber@agresearch.co.nz
Tue, 30 Apr 2002 08:31:51 +1200


I have done some work on the Serialization issue and I'm pretty
confident that you can safely serialize a sequence by sending it to an
object output stream which creates a binary stream which you can write
to a file. Not exactly a flat file but it retains the object structure.

- mark

> -----Original Message-----
> From: pootle monster [mailto:pootle_monster@hotmail.com] 
> Sent: Monday, 29 April 2002 9:31 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Quick EMBL Loading?
> I am using the method below to load an EMBL file
> BufferedReader br = new BufferedReader(new 
> FileReader(emblFile)); stream = SeqIOTools.readEmbl(br); 
> while (stream.hasNext()){
>   seq = stream.nextSequence();
> }
> The problem is that this takes about 10 seconds
> I often use the same EMBL files and only want the CDS Features
> I feel that there must be a quicker way to do this
> As Sequence is Serializable can I save the Sequence to a flat 
> file and load that instead? is that possible? would this be 
> quicker? would it be more efficient if I removed the features 
> I did not want?
> I realise a database might be the way to go - but I dont want 
> to go that way 
> at the moment.
> Simon
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