Bio::Graphics::Glyph::cds 1.4

Bio::Graphics::Glyph::cds module contains the "cds" glyph.

SYNOPSIS

See L< Bio::Graphics::Panel > and L< Bio::Graphics::Glyph >.

This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the frame in which the translation occurs. At low magnifications, draws the amino acid sequence of the resulting protein. Amino acids that are created by a splice are optionally shown in a distinctive color.

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
------ ----------- -------

-frame0f Color for first (+) frame background color

-frame1f Color for second (+) frame background color

-frame2f Color for third (+) frame background color

-frame0r Color for first (-) frame background color

-frame1r Color for second (-) frame background color

-frame2r Color for third (-) frame background color

-gridcolor Color for the "staff" lightslategray

-sixframe Draw a six-frame staff 0 (false; usually draws 3 frame)

-require_subparts
Dont draw the reading frame 0 (false)
unless it is a feature
subpart.

-codontable Codon table to use 1 (see Bio::Tools::CodonTable)

The -require_subparts option is suggested when rendering spliced transcripts which contain multiple CDS subparts. Otherwise, the glyph will hickup when zoomed way down onto an intron between two CDSs (a phantom reading frame will appear). For unspliced sequences, do *not* use -require_subparts.