[BioPython] BLAST parser updates

Cayte katel@worldpath.net
Wed, 22 Dec 1999 00:03:21 -0800

----- Original Message -----
From: Jeffrey Chang <jchang@SMI.Stanford.EDU>
To: <biopython@biopython.org>
Sent: Tuesday, December 21, 1999 12:54 PM
Subject: [BioPython] BLAST parser updates

> Hello Everybody,
> I've been working on an event-oriented parser for BLAST.  We have
> discussed it on this list.  I have written some documentation describing
> some ideas behind these types of parsers and have attached it to this
> email.  I'm hoping to use this design for other Biopython parsers as well.
> Please let me know what you think!
> Design Overview
> ---------------
> Parsers are built around an event-oriented design that includes
> Scanner and Consumer objects.
> Scanners take input from a data source and analyze it line by line,
> sending off an event whenever it recognizes some information in the
> data.  For example, if the data includes information about an organism
> name, the scanner may generate an "organism_name" event whenever it
> encounters a line containing the name.
> Consumers are objects that receive the events generated by Scanners.

   How do you deal with events coming in in the wrong order?  If a piece is
deleted from a file, for example, a new section could start before an old
section finishes.