Bio::Graphics::Glyph::UserrContributed Perl DoBio::Graphics::Glyph::generic(3)NAMEBio::Graphics::Glyph::generic - The "generic" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This is identical to the "box" glyph except that it will draw the
subparts of features that contain subfeatures. The subparts are not
connected -- use the "segments" glyph for that. "Generic" is the
default glyph used when not otherwise specified.
METHODS
This module overrides the maxdepth() method to return 0 unless the
-maxdepth option is provided explicitly. This means that any module
that inherits from generic will need to override maxdepth() again in
order to draw subfeatures. In general, those implementing multi-
segmented feature glyphs should inherit from
Bio::Graphics::Glyph::segments, which allows for one level of descent.
In addition, the following new methods are implemented:
labelfont(), descfont(), labelwidth(), descriptionwidth()
Return the font, width for the label or description.
label()
Return the glyph label text (printed above the glyph).
description()
Return the glyph description text (printed below the glyph).
draw_translation()
Draw the protein translation of the feature (assumes that the
feature is attached to a DNA sequence).
draw_sequence()
Draw the sequence of the feature (either DNA or protein).
OPTIONS
The following options are standard among all Glyphs. See
Bio::Graphics::Glyph for a full explanation.
Option Description Default
------------------------
-fgcolor Foreground color black
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Default font gdSmallFont
-label_font Font used for label gdSmallFont
-desc_font Font used for description gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-pad_top Top padding 0
-pad_bottom Bottom padding 0
-label Whether to draw a label 0 (false)
-label_position Where to draw the label "top" (default) or "left"
-description Whether to draw a description 0 (false)
-strand_arrow Whether to indicate 0 (false)
strandedness
-hilite Highlight color undef (no color)
-draw_dna If true, draw the dna residues 0 (false)
when magnification level
allows.
-canonical_strand If true, draw the dna residues 0 (false)
as they appear on the plus strand
even if the feature is on the minus
strand.
-pad_top and -pad_bottom allow you to insert some blank space between
the glyph's boundary and its contents. This is useful if you are
changing the glyph's height dynamically based on its feature's score.
BUGS
Please report them.
SEE ALSO
Bio::Graphics::Panel, Bio::Graphics::Glyph,
Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::cds,
Bio::Graphics::Glyph::crossbox, Bio::Graphics::Glyph::diamond,
Bio::Graphics::Glyph::dna, Bio::Graphics::Glyph::dot,
Bio::Graphics::Glyph::ellipse, Bio::Graphics::Glyph::extending_arrow,
Bio::Graphics::Glyph::generic, Bio::Graphics::Glyph::graded_segments,
Bio::Graphics::Glyph::heterogeneous_segments,
Bio::Graphics::Glyph::line, Bio::Graphics::Glyph::pinsertion,
Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::rndrect,
Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::ruler_arrow,
Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript,
Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::translation,
Bio::Graphics::Glyph::triangle, Bio::Graphics::Glyph::xyplot,
Bio::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR
Allen Day <day@cshl.org>, Lincoln Stein <lincoln.stein@gmail.com>
Copyright (c) 2001 Cold Spring Harbor Laboratory Copyright (c) 2010
Ontario Institute for Cancer Research
This library is free software; you can redistribute it and/or modify it
under the same terms as Perl itself. See DISCLAIMER.txt for
disclaimers of warranty.
perl v5.14.1 2011-07-22 Bio::Graphics::Glyph::generic(3)
