Ewan Birney

NAME

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

SYNOPSIS

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

DESCRIPTION

This glyph is used for drawing transcripts. It is like "transcript2" except that if the underlying feature is an Ace::Sequence object, the description is derived from some wormbase-specific fields, including info(), brief_identification() and locus(). Otherwise, the description is obtained from the notes() field.

In addition, this glyph can show different bgcolors depending on the direction of transcription.

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

In addition, the alignment glyph recognizes the following glyph-specific options:

  Option         Description                  Default
  ------         -----------                  -------

  -forwardcolor  Bgcolor for forward          Same as -bgcolor.
                    transcripts

  -reversecolor  Bgcolor for reverse          Same as -bgcolor.
                    transcripts

BUGS

Please report them.

SEE ALSO

Bio::Graphics::Panel, Bio::Graphics::Track, Bio::Graphics::Glyph::transcript2, Bio::Graphics::Glyph::anchored_arrow, Bio::Graphics::Glyph::arrow, Bio::Graphics::Glyph::box, Bio::Graphics::Glyph::primers, Bio::Graphics::Glyph::segments, Bio::Graphics::Glyph::toomany, Bio::Graphics::Glyph::transcript,

AUTHOR

Lincoln Stein <lstein@cshl.org>

Copyright (c) 2001 Cold Spring Harbor Laboratory

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.