diff variant_effect_predictor/Bio/Graphics/Glyph/alignment.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Graphics/Glyph/alignment.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,124 @@
+package Bio::Graphics::Glyph::alignment;
+
+use strict;
+
+use Bio::Graphics::Glyph::graded_segments;
+use vars '@ISA';
+@ISA = 'Bio::Graphics::Glyph::graded_segments';
+
+1;
+
+__END__
+
+=head1 NAME
+
+Bio::Graphics::Glyph::alignment - The "alignment" glyph
+
+=head1 SYNOPSIS
+
+  See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
+
+=head1 DESCRIPTION
+
+This is identical to the "graded_segments" glyph, and is used for
+drawing features that consist of discontinuous segments.  The
+color intensity of each segment is proportionate to the score.
+
+=head2 OPTIONS
+
+The following options are standard among all Glyphs.  See
+L<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
+  ------      -----------                  -------
+
+  -max_score  Maximum value of the	   Calculated
+              feature's "score" attribute
+
+  -min_score  Minimum value of the         Calculated
+              feature's "score" attribute
+
+If max_score and min_score are not specified, then the glyph will
+calculate the local maximum and minimum scores at run time.
+
+
+=head1 BUGS
+
+Please report them.
+
+=head1 SEE ALSO
+
+L<Bio::Graphics::Panel>,
+L<Bio::Graphics::Glyph>,
+L<Bio::Graphics::Glyph::arrow>,
+L<Bio::Graphics::Glyph::cds>,
+L<Bio::Graphics::Glyph::crossbox>,
+L<Bio::Graphics::Glyph::diamond>,
+L<Bio::Graphics::Glyph::dna>,
+L<Bio::Graphics::Glyph::dot>,
+L<Bio::Graphics::Glyph::ellipse>,
+L<Bio::Graphics::Glyph::extending_arrow>,
+L<Bio::Graphics::Glyph::generic>,
+L<Bio::Graphics::Glyph::graded_segments>,
+L<Bio::Graphics::Glyph::heterogeneous_segments>,
+L<Bio::Graphics::Glyph::line>,
+L<Bio::Graphics::Glyph::pinsertion>,
+L<Bio::Graphics::Glyph::primers>,
+L<Bio::Graphics::Glyph::rndrect>,
+L<Bio::Graphics::Glyph::segments>,
+L<Bio::Graphics::Glyph::ruler_arrow>,
+L<Bio::Graphics::Glyph::toomany>,
+L<Bio::Graphics::Glyph::transcript>,
+L<Bio::Graphics::Glyph::transcript2>,
+L<Bio::Graphics::Glyph::translation>,
+L<Bio::Graphics::Glyph::triangle>,
+L<Bio::DB::GFF>,
+L<Bio::SeqI>,
+L<Bio::SeqFeatureI>,
+L<Bio::Das>,
+L<GD>
+
+=head1 AUTHOR
+
+Allen Day E<lt>[e-mail]<gt>.
+
+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.
+
+=cut