[Bioperl-l] [Gmod-gbrowse] example pictures of all the glyphs?

[Lincoln Stein]

There are a pair of scripts in bioperl which generate png images of some of
the more esoteric glyphs, but the list of glyphs is not complete, as their
names are hard-coded. Perhaps these scripts can be used as the basis for a
more general script that traverses the Bio/Graphics/Glyph subdirectory,
loads each glyph it finds, and draws it.
For what it's worth, the scripts are located here:

  $BIOPERL/scripts/biographics/bp_glyphs1-demo.PLS
  $BIOPERL/scripts/biographics/bp_glyphs2-demo.PLS

On the todo list is a way for glyphs to self-document their parameters. To
do this, glyphs will need to support two new methods:

 sub parameters()
     return a hashref consisting of all the options they recognize as keys,
which in turn points to a hashref containing a human readable description of
the option, and a machine-readable description of the type of data that can
be passed. Here's the concept:

{
    height => {description => 'height of the glyph in pixels',
               range       => 'integer(1..100)'
               },
    fgcolor => {description => 'color of the outline of the glyph',
                range       => 'color'
               },
    bump     => {description => 'true if features should not overlap',
                 range       => 'boolean'
                },
    sort      => {description => 'sort order',
                  range       => '{by_name,by_score,by_position}'
}


This is all conceptual. In fact the range should use some sort of Perl
prototyping, such as the one used by Class::Struct.

In any case, this would let us achieve two things. One is to generate a page
illustrating glyph types, as you originally asked about. The other is to
enable sophisticated editing of gbrowse track configurations by the user.

Lincoln
On Wed, Nov 12, 2008 at 11:42 AM, Adam Witney <awitney at sgul.ac.uk> wrote:

>
> I was just wondering if there are any example pictures of all the
> available glyphs somewhere?
>
> thanks
>
> adam
>
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-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
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Cold Spring Harbor Laboratory
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