[Biojava-l] NCBI xml parser

[Pierre-Yves]

Dear list,

I am trying to find my way around parsing ncbi blast xml.
I am using a small library which performs the blast online [1] and
returns a FileReader of the xml.
I can convert the FileReader to a string and print it, it seems fine.
(I used the default input shown on [1]).

So I am now trying to parse it automatically. I looked at [2] and [3]
but I could not get them working. I then found this message from this
mailing list [4] and thus went to use BlastXMLParserFacade.
It returns me an "org.xml.sax.SAXException: illegal frame number
encountered. (0)".

So my question is then: which method should I use ?

Thanks in advance,

Best regards,

Pierre



[1] http://users.encs.concordia.ca/~f_kohant/ncbiblast/
[2] http://biojava.org/wiki/BioJava:CookBook:Blast:Echo
[3]
http://biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book
[4] http://osdir.com/ml/java.bio.general/2005-06/msg00018.html