Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects

- NAME
- SYNOPSIS
- DESCRIPTION
- FEEDBACK

- Mailing Lists
- Reporting Bugs

- AUTHOR - Lincoln Stein
- SEE ALSO
- APPENDIX

- new
- clone
- stylesheet
- glyph_map
- option_map
- global_opts
- panel
- scale
- font
- map_pt
- map_no_trunc
- translate_color
- make_glyph
- feature_to_glyph
- set_option
- options

# NAME

Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects

# SYNOPSIS

See the Bio::Graphics::Panel manpage.

# 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

the Bio::Graphics::Panel manpage

# 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.

## 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

Bio::Graphics::Glyph::Factory - Factory for Bio::Graphics::Glyph objects