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
>
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