NAME¶
Bio::Graphics::Glyph::alignment - The "alignment" glyph
SYNOPSIS¶
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION¶
This is identical to the "graded_segments" glyph, and is used for
drawing features that consist of discontinuous segments. The color intensity
of each segment is proportionate to the score.
OPTIONS¶
The following options are standard among all Glyphs. See Bio::Graphics::Glyph
for a full explanation.
Option Description Default
------ ----------- -------
-fgcolor Foreground color black
-outlinecolor Synonym for -fgcolor
-bgcolor Background color turquoise
-fillcolor Synonym for -bgcolor
-linewidth Line width 1
-height Height of glyph 10
-font Glyph font gdSmallFont
-connector Connector type 0 (false)
-connector_color
Connector color black
-label Whether to draw a label 0 (false)
-description Whether to draw a description 0 (false)
-strand_arrow Whether to indicate 0 (false)
strandedness
-hilite Highlight color undef (no color)
In addition, the alignment glyph recognizes the following glyph-specific
options:
Option Description Default
------ ----------- -------
-max_score Maximum value of the Calculated
feature's "score" attribute
-min_score Minimum value of the Calculated
feature's "score" attribute
If max_score and min_score are not specified, then the glyph will calculate the
local maximum and minimum scores at run time.
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::DB::GFF, Bio::SeqI, Bio::SeqFeatureI, Bio::Das, GD
AUTHOR¶
Allen Day <day@cshl.org>.
Copyright (c) 2001 Cold Spring Harbor Laboratory
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.