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 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)

  -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.

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

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