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

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.

transparent_color

  Title    : transparent_color
  Usage    : $index = $f->transparent_color($opacity,$color_name)
  Function : translate symbolic color names into GD indexes, with
                an opacity value taken into account
  Returns  : an integer
  Args     : an opacity value from 0-1.0, plus 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