Provided by: libbio-graphics-perl_2.40-3_all bug

NAME

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

SYNOPSIS

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

DESCRIPTION

       This is identical to the "alignment" glyph, and is used for drawing features that consist
       of discontinuous segments.  The color intensity of each segment is proportionate to the
       score.

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

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

         -max_score  Maximum value of the          Calculated
                     feature's "score" attribute

         -min_score  Minimum value of the          Calculated
                     feature's "score" attribute

         -vary_fg    Vary the foreground color as  0 (false)
                     well as the background

         -merge_parts                             0 (false)
                     Whether to simplify the
                     alignment at low magnification

         -max_gap    Do not merge across gaps     Calculated
                     that exceed this threshold

       If max_score and min_score are not specified, then the glyph will calculate the local
       maximum and minimum scores at run time.  Since many scoring functions are exponential you
       may wish to take the log of your scores before passing them to this glyph.

   Simplifying the display of alignment features for large segments
       The "merge_parts" option is used for semantic zooming.  Specifically, if features are
       small and dense, they will not be displayed very well for large segments and the color-
       coding will be lost.  If merge-parts is set to a true value, adjacent alignment parts will
       be merged until a gap exceeding a calculated or user-specified value is encountered.
       Unless specified, the maximum gap allowed for merging adjacent features is calculated as
       (L/10000)*(L/500), where L = the length of the sequence displayed in the browser.  The
       exponentially increasing gap threshold allows more aggressive merging of alignment
       features as the size of the displayed sequence grows larger.

       The score of the merged feature is calculated as a weighted average.  For example,
       consider two adjacent HSPs that are each 400 bp in length and have scores of 60% and 70%.
       If the merge_parts option is set to a true value, the two HSPs would be merged in the
       display to a single 800 bp alignment block with an average score of 65%.

       The merge_parts option is turned off by default.

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.