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.

   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