Search results for "dist:Bio-Graphics Bio::SeqI"
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::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::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
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::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::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::span - The "span" glyph
This glyph draws a span that looks like this: |-----------------------------| If one or both ends go off the edges of the panel, they are truncated: ----------------------| left end off picture |---------------------------- right end off picture ----...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::flag - the "flag" glyph
This glyph draws a flag with a text next to it. OPTIONS In addition to the common options, the following glyph-specific options are recognized: Option Description Default ------ ----------- ------- -text Text to draw next to the flag ori -width Width...
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::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::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::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::track - The "track" glyph
This glyph is used internally by Bio::Graphics::Panel for laying out tracks. It should not be used explicitly....
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::gene - A GFF3-compatible gene glyph
This glyph is used for drawing genes that may have alternatively-spliced transcripts. The various isoforms are stacked on top of each other and given a single label and description that apply to the entire stack. Each individual transcript's name is ...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::hidden - The "hidden" glyph
This glyph does nothing. It is used by DAS rendering to draw an empty space between components of a compound feature. OPTIONS This glyph takes only the standard options. See Bio::Graphics::Glyph for a full explanation. Option Description Default ----...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::arrow - the "arrow" glyph
This glyph draws arrows. Depending on options, the arrows can be labeled, be oriented vertically or horizontally, or can contain major and minor ticks suitable for use as a scale. OPTIONS The following options are standard among all Glyphs. See Bio::...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::image - A glyph that draws photographs & other images
This glyph inserts an image into the track at the indicated feature coordinates. The image can be in PNG, JPEG, GIF or GD format, and can be either 8-bit or 24-bit ("truecolor"). The image can be located on the local filesystem or located at a remote...
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC
Bio::Graphics::Glyph::toomany - The "too many to show" glyph
This glyph is intended for features that are too dense to show properly. Mostly a placeholder, it currently shows a filled oval. If you choose a bump of 0, the ovals will overlap, to give a cloud effect. OPTIONS There are no glyph-specific options....
CJFIELDS/Bio-Graphics-2.40 - 16 Dec 2016 04:50:36 UTC