Bio::Graphics::Glyph::Factory(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::Factory(3pm)
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
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::Factory(3pm)