[Biojava-l] blast2html

Colin Hardman colin.hardman at cambridgeAntibody.com
Thu Nov 20 06:49:31 EST 2003


    As I remember it the summary line from the blast output is split on white
space with the first token put into hitid - this will make it's way into
oHitSummary.oHitId.id in Blast2HTML

If you want to change this then you need to implement your own
SummaryLineHelperIF in org.biojava.bio.program.sax, but I don't think you will
need to.

As the actual format of this line depends on how, and from what source, you
built the blast indexes the HTMLRenderer delegates the link generation to the
DatabaseURLGenerator interface.
If your blast result has a summary line line the following

 gi|4557284|ref|NM_000646.1|[4557284]  some text description.....
eg from http://www.ncbi.nlm.nih.gov/RefSeq/RSfaq.html

you are going to need to parse it in your own DatabaseURLGenerator -
HTMLRenderer gets hold of these using a URLGeneratorFactory to get the list -
ths first returned in the list is used to create the link in the summary, the
others ( if they exist ) are added as extra links in the details.

for an example look at NcbiDatabaseURLGenerator & DefaultURLGeneratorFactory in

If you write one to parse the above format it might be useful to add it to the
repository - even make it the default.

Hope that helps,

Colin Hardman

Marc Dumontier wrote:

> hi,
> I'm trying to modify the Blasr2HTML code in
> org.biojava.bio.program.blast2html to add some links to my blast output.
> In HTMLRenderer, I'm trying to add a link to each row in my summary.
> The variable oHitSummary.oHitId.id contains the accession..well something
> like (ref|NP_011554.1|) , I was wondering if the Blast2HTMLHandler saves GI
> information, since the link i need to create needs the GI as the argument.
> Thanks,
> Marc
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