[Bioperl-l] SOLVED Bio::Graphics::Panel make ruler have neg values

[Kevin Lam Koiyau]

I am so sorry for the truncated email accidentally hit reply.
if anyone is interested i have opted to change

change line 161 of arrow.pm in Perl/site/lib/Bio/Graphics/Glyph/arrow.pm
in linux its
/usr/lib/perl5/site_perl/5.8.5/Bio/Graphics/Glyph/arrow.pm


      $gd->string($font,$middle,$center+$a2-1,$label,$font_color)

to

      $gd->string($font,$middle,$center+$a2-1,$label-1000,$font_color)

just  for this one-off use.



strangely I found at line 112 for ver 1.51 bioperl in arrow.pm a hidden
option for coords offset?
    my $relative_coords_offset = $self->option('relative_coords_offset');
    $relative_coords_offset    = 1 unless defined $relative_coords_offset;
but entering the option -relative_coords_offset=>1000 in the arrow glyphs
didn't do anything...



Hi!
> oh it was in a slightly different header asking about the create image map
> feature.
> I am using the stable version 1.4 of bioperl now. In any case I have not
> added the sequence as a feature annotated seq. as I already have the bp
> where the TF binds (in 1-1050 numberings) so what I did was to just add
> graded segments based on the position.
> I saw that there is a scale function for the arrow glyp however, it is a
> multiply function, can it be hacked to take in a offset value (ie minus
> the
> scale by 1000?)
>
> cheers
> kevin
>
>
> Hi,
> >
> > For some reason I didn't see the first posting on this. In current
> bioperl
> > live, the ruler can have negative numberings - I use this routinely. You
> > need
> > to create a feature that starts in negative coordinates. What is
> happening
> > to
> > you when you try this?
> >
> > Lincoln
> >
> > On Wednesday 24 May 2006 21:59, Kevin Lam Koiyau wrote:
> > > Hi
> > > thanks for the help offered thus far!
> > > sigh I am trying to annotate TFBS on a -1000 to +50 bp promtoer seq
> > using
> > > bioperl. therefore i was asked to make the numberings as such (-1000)
> is
> > > there any way at all to do this in bioperl without changing the .pm
> > file?
> > >
> > > thanks guys..
> > > kevin
> > >
> > > _______________________________________________
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> > --
> > Lincoln D. Stein
> > Cold Spring Harbor Laboratory
> > 1 Bungtown Road
> > Cold Spring Harbor, NY 11724
> > (516) 367-8380 (voice)
> > (516) 367-8389 (fax)
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> > SANDRA MICHELSEN, AT michelse at cshl.edu
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