[Bioperl-l] Can I get different Graphics::Panel colours fordifferent HSP frames within the same blast hit?

Marcus Claesson m.claesson at student.ucc.ie
Thu Dec 9 13:26:52 EST 2004

Thanks for your answers guys!

That hack seems to do it. However, my program will be used by people
installing it themselves so I have to stick with the standard non-hacked
version of bioperl.

Cheers though,

On Thu, 2004-12-09 at 16:51, Crabtree, Jonathan wrote:
> Hi Aaron-
> > There's another solution that shouldn't involve code patches: see the 
> > documentation in Panel (short answer: all_callbacks: 1)
> Perhaps I'm being obtuse, but I don't see how turning all_callbacks on
> helps you with the -bgcolor issue.  It seems like
> Bio::Graphics::Glyph::graded_segments::draw need to be called on the
> parent feature in order to get the correct min/max score range.  To wit:
>   my ($min_score,$max_score) = $self->minmax(\@parts);
> And since the call that sets $fill = $self->bgcolor is outside the loop
> that sets the colors of the individual @parts (the HSPs in this case),
> there's no way you can then get a different (base) color for each part
> unless you do what I did, and move the assignment to $fill inside the
> loop.
> Now I'm not saying there isn't some other way to assign the HSPs their
> own colors, just that if you want to use the graded_segments glyph to do
> so then you need a slightly different implementation of its draw method.
> Besides, all solutions involve code patches; it's just a question of
> which code you feel like patching ;)
> Jonathan

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