[Biojava-l] blast xml parser

[Ewan Birney]

A view from bioperl:


I would claim that you do need layered levels of abstraction. The event
parsing SAX model is something we are very jealous of in bioperl because
we understand its flexibility and the ease of writing seriously
lean-and-mean parsers by experts. 

maintaince of parsers is one of our headaches over time.

However we would always maintain the object-level representation of
BLAST/HMMER parsing results - although this is one mapping to in-memory
objects, for at least 50% of use cases this is fine, and we cna guarentee
that the fine details of how this objects interact with the rest of the
package work.

These are ideal for small scale uses and throw-away scripts, as well as
actually being an ok fit with large scale cases (BPLite is, as the name
implies, Lite on the code and parsing). Scaling is mainly achieved by
having on set of objects per result - not ideal but good enough


So I guess both views of "parsing BLAST" are correct. They are just
nested.


ewan

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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