[Biojava-l] Biocorba Demo and Iterator reset ?
Tue, 16 Jan 2001 10:17:09 +0000
On Mon, Jan 15, 2001 at 04:52:42PM +0000, Arnaud Kerhornou wrote:
> First just to let you know I ran the Biocorba demo with the new io
> proposal. With some modifications within the server code, it works fine.
> // SequenceFactory sFact = new SimpleSequenceFactory();
> SequenceBuilderFactory sfact = new
> FastaDescriptionLineParser.Factory (SimpleSequenceBuilder.FACTORY);
> // ...
> // SequenceIterator seqI = new StreamReader(seqDBI, sFormat, rParser,
> StreamReader seqI = new StreamReader (seqDBI, sFormat, rParser,
Cool. Do you have CVS write access (Matthew's probably the
person to ask if you want an account), or would you like me to
check this in?
> And I'd like to know if it's possible to reset an Iterator Object to
> start again an iteration from the beginning ?
No, I don't think iterators should have this functionality. An
iterator could encapsulate, for example, a stream of sequences
coming down an HTTP connection, and this can't be reset without
re-issuing the HTTP request. In both BioJava and BioCorba, the
corrent pattern if you want multiple iterations is to got a
SequenceDB (PrimarySeqDB), and create new iterators as required.
[As an aside, I've been working on the performance issues of
the BioJava IndexedSequenceDB over the weekend, and I'll add a
more efficient iterator() method to that.]