Bio::Graphics::Glyph::Factory.3pm

Langue: en

Version: 2009-06-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects

SYNOPSIS

See Bio::Graphics::Panel.

DESCRIPTION

This class is used internally by Bio::Graphics to generate new Glyph objects by combining a list of features with the user's desired configuration. It is intended to be used internally by Bio::Graphics.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Lincoln Stein

Email - lstein@cshl.org

SEE ALSO

Bio::Graphics::Panel

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with an ``_'' (underscore).

new

   Title   : new
   Usage   : $f = Bio::Graphics::Glyph::Factory->new(
                      -stylesheet => $stylesheet,
                      -glyph_map  => $glyph_map,
                      -options    => $options);
   Function : create a new Bio::Graphics::Glyph::Factory object
   Returns  : the new object
   Args     : $stylesheet is a Bio::Das::Stylesheet object that can
                  convert Bio::Das feature objects into glyph names and
                  associated options.
              $glyph_map is a hash that maps primary tags to glyph names.
              $options is a hash that maps option names to their values.
   Status   : Internal to Bio::Graphics
 
 

clone

   Title    : clone
   Usage    : $f2 = $f->clone
   Function : Deep copy of a factory object
   Returns  : a deep copy of the factory object
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

stylesheet

   Title    : stylesheet
   Usage    : $stylesheet = $f->stylesheet
   Function : accessor for stylesheet
   Returns  : a Bio::Das::Stylesheet object
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

glyph_map

   Title    : glyph_map
   Usage    : $map = $f->glyph_map
   Function : accessor for the glyph map
   Returns  : a hash mapping primary tags to glyphs
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

option_map

   Title    : option_map
   Usage    : $map = $f->option_map
   Function : accessor for the option map
   Returns  : a hash mapping option names to values
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

global_opts

   Title    : global_opts
   Usage    : $map = $f->global_opts
   Function : accessor for global options
   Returns  : a hash mapping option names to values
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

This returns a set of defaults for option values.

panel

   Title    : panel
   Usage    : $panel = $f->panel
   Function : accessor for Bio::Graphics::Panel
   Returns  : a Bio::Graphics::Panel
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

This returns the panel with which the factory is associated.

scale

   Title    : scale
   Usage    : $scale = $f->scale
   Function : accessor for the scale
   Returns  : a floating point number
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

This returns the scale, in pixels/bp for glyphs constructed by this factory.

font

   Title    : font
   Usage    : $font = $f->font
   Function : accessor for the font
   Returns  : a font name
   Args     : None
   Status   : Internal to Bio::Graphics
 
 

This returns a GD font name.

map_pt

   Title    : map_pt
   Usage    : @pixel_positions = $f->map_pt(@bp_positions)
   Function : map bp positions to pixel positions
   Returns  : a list of pixel positions
   Args     : a list of bp positions
   Status   : Internal to Bio::Graphics
 
 

The real work is done by the panel, but factory subclasses can override if desired.

map_no_trunc

   Title    : map_no_trunc
   Usage    : @pixel_positions = $f->map_no_trunc(@bp_positions)
   Function : map bp positions to pixel positions
   Returns  : a list of pixel positions
   Args     : a list of bp positions
   Status   : Internal to Bio::Graphics
 
 

Same as map_pt(), but it will NOT clip pixel positions to be within the drawing frame.

translate_color

   Title    : translate_color
   Usage    : $index = $f->translate_color($color_name)
   Function : translate symbolic color names into GD indexes
   Returns  : an integer
   Args     : a color name in format "green" or "#00FF00"
   Status   : Internal to Bio::Graphics
 
 

The real work is done by the panel, but factory subclasses can override if desired.

make_glyph

   Title    : make_glyph
   Usage    : @glyphs = $f->glyph($level,[$type,]$feature1,$feature2...)
   Function : transform features into glyphs.
   Returns  : a list of Bio::Graphics::Glyph objects
   Args     : a feature "level", followed by a list of FeatureI objects.
   Status   : Internal to Bio::Graphics
 
 

The level is used to track the level of nesting of features that have subfeatures. The option $type argument can be used to force the glyph type

feature_to_glyph

   Title    : feature_to_glyph
   Usage    : $glyph_name = $f->feature_to_glyph($feature)
   Function : choose the glyph name given a feature
   Returns  : a glyph name
   Args     : a Bio::Seq::FeatureI object
   Status   : Internal to Bio::Graphics
 
 

set_option

   Title    : set_option
   Usage    : $f->set_option($option_name=>$option_value)
   Function : set or change an option
   Returns  : nothing
   Args     : a name/value pair
   Status   : Internal to Bio::Graphics
 
 

options

   Title    : options
   Usage    : @option_names = $f->options
   Function : return all configured option names
   Returns  : a list of option names
   Args     : none
   Status   : Internal to Bio::Graphics