Search results for "distribution:Bio-Graphics bio::graphics"
Bio::Graphics - Generate GD images of Bio::Seq objects
Please see Bio::Graphics::Panel for the full interface. Also try the script glyph_help.pl for quick help on glyphs and their options....
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Util - non-object-oriented utilities used in Bio::Graphics modules
CJFIELDS/Bio-Graphics-2.40
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16 Dec 2016 04:50:36 UTC
Bio::Graphics::Panel - Generate GD images of Bio::Seq objects
The Bio::Graphics::Panel class provides drawing and formatting services for any object that implements the Bio::SeqFeatureI interface, including Ace::Sequence::Feature and Das::Segment::Feature objects. It can be used to draw sequence annotations, ph...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph - Base class for Bio::Graphics::Glyph objects
Bio::Graphics::Glyph is the base class for all glyph objects. Each glyph is a wrapper around an Bio:SeqFeatureI object, knows how to render itself on an Bio::Graphics::Panel, and has a variety of configuration variables. End developers will not ordin...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Wiggle - Binary storage for dense genomic features
IMPORTANT NOTE: This implementation is still not right. See http://genomewiki.ucsc.edu/index.php/Wiggle for a more space-efficient implementation. This module stores "wiggle" style quantitative genome data for display in a genome browser application....
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Feature - A simple feature object for use with Bio::Graphics::Panel
This is a simple Bio::SeqFeatureI-compliant object that is compatible with Bio::Graphics::Panel. With it you can create lightweight feature objects for drawing. All methods are as described in Bio::SeqFeatureI with the following additions: The new() ...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
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.
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....
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Pictogram - generate SVG output of Pictogram display for consensus motifs
A module for generating SVG output of Pictogram display for consensus motifs. This method of representation was describe by Burge and colleagues: (Burge, C.B.,Tuschl, T., Sharp, P.A. in The RNA world II, 525-560, CSHL press, 1999) This is a simple mo...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::ex - the "ex", or "crossed box" glyph
This is a box with an 'X' inside glyph. 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 ...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::dot - The "dot" glyph
This glyph draws an ellipse the width of the scaled feature passed, and height a possibly configured height (See Bio::Graphics::Glyph). OPTIONS The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. Opti...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::dna - The "dna" glyph
This glyph draws DNA sequences. At high magnifications, this glyph will draw the actual base pairs of the sequence (both strands). At low magnifications, the glyph will plot the GC content. By default, the GC calculation will use non-overlapping bins...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::box - The "box" glyph
This is the most basic glyph. It draws a filled box and optionally a label. It does *NOT* draw subparts, and so is useful for semantic zooming when one is zoomed out too far to see substructure. OPTIONS The following options are standard among all Gl...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::FeatureDir - A directory of feature files and conf files
This class implements most of the methods of Bio::Graphics::FeatureFile, but stores the data files and features in a directory indexed by the Bio::DB::SeqFeature::Store::berkeleydb adaptor. Therefore it is fast. Methods POD ERRORS Hey! The above docu...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::hat - The "hat" glyph
This glyph draws an inverted V parallel to the sequence segment. It is different from other glyphs in that it is designed to work with DAS tracks. The inverted V is drawn BETWEEN subparts as if you specified a connector type of "hat". OPTIONS This gl...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::cds - The "cds" glyph
This glyph draws features that are associated with a protein coding region. At high magnifications, draws a series of boxes that are color-coded to indicate the frame in which the translation occurs. At low magnifications, draws the amino acid sequen...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::line - The "line" glyph
This glyph draws a line parallel to the sequence segment. It is different from other glyphs in that it is designed to work with DAS tracks. The line is drawn BETWEEN the subparts, as if you specified a connector type of "line". OPTIONS This glyph tak...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::wave - The "wave" glyph
This glyph draws a sine wave with an optional circle in the beginning. The wave can also become a straight line. OPTIONS In addition to the common options, the following glyph-specific options are recognized: Option Description Default ------ -------...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::oval - The "oval" glyph
This glyph draws an oval instead of a box. It is an alias for the "ellipse" glyph. OPTIONS The following options are standard among all Glyphs. See Bio::Graphics::Glyph for a full explanation. Option Description Default ------ ----------- ------- -fg...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::FeatureBase - Compatibility module
CJFIELDS/Bio-Graphics-2.40
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16 Dec 2016 04:50:36 UTC
Bio::Graphics::FeatureFile - A set of Bio::Graphics features, stored in a file
The Bio::Graphics::FeatureFile module reads and parses files that describe sequence features and their renderings. It accepts both GFF format and a more human-friendly file format described below. Once a FeatureFile object has been initialized, you c...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC