NAME

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

SYNOPSIS

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

DESCRIPTION

This glyph is used for drawing features that consist of discontinuous segments. Unlike "graded_segments" or "alignment", the segments are a uniform color and not dependent on the score of the segment.

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

  -draw_dna     If true, draw the dna residues 0 (false)
                 when magnification level
                 allows.

  -draw_target  If true, draw the dna residues 0 (false)
                 of the TARGET sequence when
                 magnification level allows.
                 SEE NOTE.

  -ragged_start When combined with -draw_target, 0 (false)
                 draw a few bases beyond the end
                 of the alignment.  SEE NOTE.

  -show_mismatch When combined with -draw_target, 0 (false)
                 highlights mismatched bases in
                 pink.  SEE NOTE.

The -draw_target and -ragged_start options only work with seqfeatures that implement the hit() method (Bio::SeqFeature::SimilarityPair). The -ragged_start option is mostly useful for looking for polyAs and cloning sites at the beginning of ESTs and cDNAs. Currently there is no way of activating ragged ends. The length of the ragged starts is hard-coded at 25 bp, and the color of mismatches is hard-coded as light pink.

BUGS

Please report them.

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, GD

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.