[Biojava-l] Quick EMBL Loading?

[Matthew Pocock]

Hi Simon,

10 sec? That's bad. Do you have any -Xprof numbers to indicate where the 
time is being wasted? The worst-case scenario is that 9.5 sec of this is 
VM and BioJava initialization, but the profile should tell us what is 
going on.

Matthew

pootle monster wrote:
> 
> 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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