Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects See Bio::Graphics::Panel. 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.

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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email - lstein@cshl.org Bio::Graphics::Panel 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.

glyph
Title : glyph Usage : @glyphs = $f->glyph($level,$feature1,$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.

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