Bio::Graphics::RendererI(3pm) User Contributed Perl Documentation Bio::Graphics::RendererI(3pm)NAME
Bio::Graphics::RendererI - A renderer for the Bio::Graphics class that renders Bio::SeqFeature::CollectionI objects onto
Bio::Graphics::Panels using configuration information provided by a Bio::Graphics::ConfiguratorI.
SYNOPSIS
# Get a renderer somehow, called $renderer
# create a new panel and render contents a feature collection onto it
my $config = new ConfigIO( $config_file )->getConfig();
my $features = $data_provider->getCollection();
my ( $tracks_rendered, $panel ) = $renderer->render( $features, $prefs );
DESCRIPTION
Renderer of Bio::SeqFeature::CollectionIs (collections of features) onto a Bio::Graphics::Panel using a Bio::Graphics::ConfiguratorI for
general and track-specific rendering options.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR
Paul Edlefsen <paul@systemsbiology.org>.
Copyright (c) 2003 Institute for Systems Biology
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.
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
render
Title : render
Usage : ( $rendered, $panel ) =
$renderer->render( $collection, $configurator [, $panel ] );
Function: Renders the SeqFeatures in the given collection onto a
Bio::Graphics::Panel (if no panel is given, one will be
created), using the given Bio::Graphics::ConfiguratorI for general
and track-specific rendering options.
Returns : In a scalar context returns the number of tracks rendered.
In a list context, returns a two-element list containing
the number of features rendered and the panel.
Args : A Bio::SeqFeature::CollectionI and a Bio::Graphics::ConfiguratorI
and optionally a Bio::Graphics::Panel.
Status : Public
perl v5.14.2 2012-02-20 Bio::Graphics::RendererI(3pm)
Check Out this Related Man Page
Bio::Graphics::Glyph::pinsertion(3pm) User Contributed Perl Documentation Bio::Graphics::Glyph::pinsertion(3pm)NAME
Bio::Graphics::Glyph::pinsertion - The "Drosophila P-element Insertion" glyph
SYNOPSIS
See L<Bio::Graphics::Panel> and L<Bio::Graphics::Glyph>.
DESCRIPTION
This glyph was designed to show P-element insertions in the Drosophila genome, but in fact is suitable for any type of zero-width feature.
Also see the triangle glyph.
OPTIONS
In addition to the generic options, this glyph recognizes:
Option Name Description Default
-----------------------------
-insertion_width Width of glyph in pixels 3
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
Allen Day <day@cshl.org>, Shengqiang Shu <sshu@bdgp.lbl.gov>
Copyright (c) 2001 Cold Spring Harbor Laboratory, BDGP
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.
perl v5.14.2 2012-02-20 Bio::Graphics::Glyph::pinsertion(3pm)