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Bio-Graphics-2.33
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Graphics::Glyph::Factory

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