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

[shalabh sharma]

Hey Adam,
                     Here are some example pictures of basic glyphs:

http://www.agcol.arizona.edu/software/java_gbrowse/Java_GBrowse/GBrowseConfiguration/gbrowse_configuration_content.htm

Shalabh


On Wed, Nov 12, 2008 at 12:29 PM, Lincoln Stein <lincoln.stein at gmail.com>wrote:

> 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
>>
>> -------------------------------------------------------------------------
>> This SF.Net email is sponsored by the Moblin Your Move Developer's
>> challenge
>> Build the coolest Linux based applications with Moblin SDK & win great
>> prizes
>> Grand prize is a trip for two to an Open Source event anywhere in the
>> world
>> http://moblin-contest.org/redirect.php?banner_id=100&url=/
>> _______________________________________________
>> Gmod-gbrowse mailing list
>> Gmod-gbrowse at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>>
>
>
>
> --
> Lincoln D. Stein
>
> Ontario Institute for Cancer Research
> 101 College St., Suite 800
> Toronto, ON, Canada M5G0A3
> 416 673-8514
> Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>
>
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724 USA
> (516) 367-8380
> Assistant: Sandra Michelsen <michelse at cshl.edu>
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's
> challenge
> Build the coolest Linux based applications with Moblin SDK & win great
> prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Gmod-gbrowse mailing list
> Gmod-gbrowse at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>