Bio::Graphics::Glyph::Factory(3pm)

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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