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.\" ========================================================================
.\"
.IX Title "Bio::Graphics::Glyph::cds 3pm"
.TH Bio::Graphics::Glyph::cds 3pm "2019-11-25" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Graphics::Glyph::cds \- The "cds" glyph
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
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.
.SS "\s-1OPTIONS\s0"
.IX Subsection "OPTIONS"
The following options are standard among all Glyphs.  See
Bio::Graphics::Glyph for a full explanation.
.PP
.Vb 2
\&  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)
.Ve
.PP
In addition, the cds glyph recognizes the following glyph-specific
options:
.PP
.Vb 2
\&  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
\&
\&  \-translation Number of lines of reading      3frame
\&               frames to show. One of
\&               "3frame", or "6frame".
\&               For 6frame, specify a height
\&               of at least 30 pixels.
\&
\&  \-sixframe   Draw a six\-frame staff           0 (false; usually draws 3 frame)
\&              This value overrides
\&              \-translation, which essentially
\&              does the same thing.
\&
\&  \-require_subparts
\&              Don\*(Aqt draw the reading frame 0   false
\&              unless it is a feature
\&              subpart.
\&
\&  \-sub_part   For objects with multiple        undef
\&              subpart types, defines which
\&              is the CDS part.
\&
\&  \-codontable   Codon table to use             1 (see Bio::Tools::CodonTable)
\&
\&  \-phase_style  The way phase is to be
\&                interpreted. One of            "012"
\&                "012" or "021"
\&  \-ignore_empty_phase                          false
\&              Only draw features that have
\&              their phase defined.
\&
\&  \-cds_only   Only draw features of type       false
\&              \*(AqCDS\*(Aq
.Ve
.PP
This glyph is more sensitive to the underlying data model than usual,
so there are a few additional options to use to help adapt the glyph
to different environments.
.PP
The \-require_subparts option is suggested when rendering spliced
transcripts which contain multiple \s-1CDS\s0 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.
.PP
The \-phase_style controls how the value returned by the \fBphase()\fR or
\&\fBframe()\fR methods is to be interpreted. The official interpretation is
that the phase value indicates the offset into the feature at which
the reading frame starts \*(-- e.g. a phase of \*(L"2\*(R" means the reading
frame starts after skipping two bases from the beginning of the
feature.  However, many \s-1GFF2\s0 format feature files interpret this field
to mean the position reading frame of the first base of the feature \*(--
e.g. a phase of \*(L"2\*(R" means that the reading frame starts after skipping
just one base from the beginning of the feature. Specify \*(L"012\*(R" to
interpret the phase field in the correct way, and \*(L"021\*(R" to interpret
the phase field in the legacy way. The default is \*(L"012.\*(R"
.PP
Here is how the option names were chosen:
.PP
.Vb 4
\&    * * *                  Base the reading frame starts on
\&    A B C A B C A B C...
\&    0 1 2                  PHASE REPRESENTED CORRECTLY
\&    0 2 1                  PHASE REPRESENTED IN THE LEGACY WAY
.Ve
.PP
Set the \-ignore_empty_phase option to true if you wish to skip
subfeatures that do not have a defined \fBphase()\fR or \fBframe()\fR. This is useful
if you are rendering exons that have both translated and untranslated
parts, and you wish to skip the untranslated parts.
.PP
Set the \-cds_only option to true if you wish to draw the glyph only
for subfeatures of type '\s-1CDS\s0'. This is recommended.
.SH "SUGGESTED STANZA FOR GENOME BROWSER"
.IX Header "SUGGESTED STANZA FOR GENOME BROWSER"
Using the \*(L"coding\*(R" aggregator, this produces a nice gbrowse display.
.PP
.Vb 10
\& [CDS]
\& feature      = coding
\& glyph        = cds
\& frame0f      = cadetblue
\& frame1f      = blue
\& frame2f      = darkblue
\& frame0r      = darkred
\& frame1r      = red
\& frame2r      = crimson
\& description  = 0
\& height       = 13
\& label        = CDS frame
\& key          = CDS
\& citation     = This track shows CDS reading frames.
.Ve
.SH "BUGS"
.IX Header "BUGS"
Please report them.
.SH "SEE ALSO"
.IX Header "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,
\&\s-1GD\s0
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lstein@cshl.org>
.PP
Copyright (c) 2001 Cold Spring Harbor Laboratory
.PP
This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.  See \s-1DISCLAIMER\s0.txt for
disclaimers of warranty.