[Biojava-l] blast2html

Marc Dumontier dumontier at mshri.on.ca
Thu Nov 20 09:41:07 EST 2003


Thanks for your input

I found the route of less resistance was to add the -I parameter when
running blast, which will then include the gi from the original fasta.

I then just parse out the GI to include in my link


-----Original Message-----
From: Colin Hardman
To: Marc Dumontier
Cc: 'biojava-l at biojava.org'
Sent: 11/20/03 6:49 AM
Subject: Re: [Biojava-l] blast2html


    As I remember it the summary line from the blast output is split on
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,
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
> In HTMLRenderer, I'm trying to add a link to each row in my summary.
> The variable oHitSummary.oHitId.id contains the accession..well
> 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
> Thanks,
> Marc
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