[Biojava-l] Blast2HTMLHandler.java bug

[Colin Hardman]

Hi Simon,

Your fix is correct with the addition that you also need to remove the line
272
in the Summary endElement code else the last item will be duplicated.

} else if ( poElementName.equals( "Summary" ) ) {
   oRenderer.writeCurrentSummary( oHitSummary ) ;
   oRenderer.endSummaryTable();
}

becomes

} else if ( poElementName.equals( "Summary" ) ) {
   oRenderer.endSummaryTable();
}

I've made the changes in biojava-live.

Thanks,

Colin


Simon Foote wrote:

> Hi Simon,
>
> I've found a bug in the Blast2HTMLHandler code.  In the hit summary
> section that it produces, the score and expect values are shifted by 1
> result.  Thus, the first hit has the score & expect from the 2nd and so on.
>
> I fixed it as follows (not sure if this is correct way, but it seems to
> work):
>
> - removed the else part of the if statement at lines 173-178: (in
> startElement method)
>     } else {
>               oRenderer.writeCurrentSummary( oHitSummary );
>     }
> - added to endElement method above line 273:
>     } else if ( poElementName.equals( "HitSummary" ) ) {
>         oRenderer.writeCurrentSummary( oHitSummary );
>
> Regards,
> Simon Foote
>