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.\" ========================================================================
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.IX Title "Bio::Graphics::Glyph::protein 3pm"
.TH Bio::Graphics::Glyph::protein 3pm "2019-11-25" "perl v5.30.0" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::Graphics::Glyph::protein \- The "protein" 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 protein sequences.  At high magnifications, this
glyph will draw the actual amino acids of the sequence.  At low
magnifications, the glyph will plot the Kyte-Doolite hydropathy.  By
default, the \s-1KD\s0 plot will use a window size of 9 residues, but this
can be changed by specifying the kd_window option.
.PP
The feature may return either a protein sequence or a \s-1DNA\s0 sequence in
response to the \fBseq()\fR method. However, if it returns a \s-1DNA\s0 sequence,
then the feature must also return the correct phase and strand in
order for the glyph to translate its open reading frame correctly!
.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)
\&
\&  \-hilite       Highlight color                undef (no color)
.Ve
.PP
In addition to the common options, the following glyph-specific
options are recognized:
.PP
.Vb 2
\&  Option      Description               Default
\&  \-\-\-\-\-\-      \-\-\-\-\-\-\-\-\-\-\-               \-\-\-\-\-\-\-
\&
\&  \-do_kd      Whether to draw the Kyte\-  true
\&              Doolittle hydropathy plot
\&              at low mags
\&
\&  \-kd_window  Size of the sliding window  9
\&              to use in the KD hydropathy 
\&              calculation.
\&
\&  \-axis_color Color of the vertical axes  fgcolor
\&              in the KD hydropathy plot
\&
\&  \-phase_style  The way phase is to be
\&                interpreted. One of            "012"
\&                "012" or "021"
.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"
Aaron J. Mackey, based on the \*(L"dna\*(R" glyphy by Lincoln Stein
<lstein@cshl.org> and Peter Ashton <pda@sanger.ac.uk>.
.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.