--- name: "Bio::Graphics::Glyph::Factory" section: "3pm" platform: "linux" package: "libbio-graphics-perl" version: "2.40-6" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Graphics::Glyph::Factory" --- # Bio::Graphics::Glyph::Factory(3pm) Factory for Bio::Graphics::Glyph objects ## 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 ```