Bio::Graphics::Glyph::protein - The "protein" glyph

- NAME
- SYNOPSIS
- DESCRIPTION

- OPTIONS

- BUGS
- SEE ALSO
- AUTHOR

# NAME

Bio::Graphics::Glyph::protein - The "protein" glyph

# SYNOPSIS

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

# 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 KD plot will use a window size of 9 residues, but this can be changed by specifying the kd_window option.

The feature may return either a protein sequence or a DNA sequence in response to the `seq()` method. However, if it returns a DNA sequence, then the feature must also return the correct phase and strand in order for the glyph to translate its open reading frame correctly!

## OPTIONS

The following options are standard among all Glyphs. See the Bio::Graphics::Glyph manpage 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)

      -hilite       Highlight color                undef (no color)

In addition to the common options, the following glyph-specific options are recognized:

      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"

# BUGS

Please report them.

# SEE ALSO

the Bio::Graphics::Panel manpage, the Bio::Graphics::Glyph manpage, the Bio::Graphics::Glyph::arrow manpage, the Bio::Graphics::Glyph::cds manpage, the Bio::Graphics::Glyph::crossbox manpage, the Bio::Graphics::Glyph::diamond manpage, the Bio::Graphics::Glyph::dna manpage, the Bio::Graphics::Glyph::dot manpage, the Bio::Graphics::Glyph::ellipse manpage, the Bio::Graphics::Glyph::extending_arrow manpage, the Bio::Graphics::Glyph::generic manpage, the Bio::Graphics::Glyph::graded_segments manpage, the Bio::Graphics::Glyph::heterogeneous_segments manpage, the Bio::Graphics::Glyph::line manpage, the Bio::Graphics::Glyph::pinsertion manpage, the Bio::Graphics::Glyph::primers manpage, the Bio::Graphics::Glyph::rndrect manpage, the Bio::Graphics::Glyph::segments manpage, the Bio::Graphics::Glyph::ruler_arrow manpage, the Bio::Graphics::Glyph::toomany manpage, the Bio::Graphics::Glyph::transcript manpage, the Bio::Graphics::Glyph::transcript2 manpage, the Bio::Graphics::Glyph::translation manpage, the Bio::Graphics::Glyph::triangle manpage, the Bio::DB::GFF manpage, the Bio::SeqI manpage, the Bio::SeqFeatureI manpage, the Bio::Das manpage, GD

# AUTHOR

Aaron J. Mackey, based on the "dna" glyphy by Lincoln Stein <lstein@cshl.org> and Peter Ashton <pda@sanger.ac.uk>.

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.

Bio::Graphics::Glyph::protein - The "protein" glyph