Ace::Graphics::Track(3User Contributed Perl DocumentatiAce::Graphics::Track(3)NAMEAce::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects
SYNOPSIS
use Ace::Sequence;
use Ace::Graphics::Panel;
my $db = Ace->connect(-host=>'brie2.cshl.org',-port=>2005) or die;
my $cosmid = Ace::Sequence->new(-seq=>'Y16B4A',
-db=>$db,-start=>-15000,-end=>15000) or die;
my @transcripts = $cosmid->transcripts;
my $panel = Ace::Graphics::Panel->new(
-segment => $cosmid,
-width => 800
);
my $track = $panel->add_track('transcript'
-fillcolor => 'wheat',
-fgcolor => 'black',
-bump => +1,
-height => 10,
-label => 1);
foreach (@transcripts) {
$track->add_feature($_);
}
my $boxes = $panel->boxes;
print $panel->png;
DESCRIPTION
The Ace::Graphics::Track class is used by Ace::Graphics::Panel to lay
out a set of sequence features using a uniform glyph type. You will
ordinarily work with panels rather than directly with tracks.
METHODS
This section describes the class and object methods for
Ace::Graphics::Panel.
CONSTRUCTORS
There is only one constructor, the new() method. It is ordinarily
called by Ace::Graphics::Panel, and not in end-developer code.
$track = Ace::Graphics::Track->new($glyph_name,$features,@options)
The new() method creates a new track object from the provided glyph
name and list of features. The arguments are similar to those in
Ace::Graphics::Panel->new().
If successful new() will return a new Ace::Graphics::Track.
Otherwise, it will return undef.
If the specified glyph name is not a valid one, new() will throw an
exception.
OBJECT METHODS
Once a track is created, the following methods can be invoked.
$track->add_feature($feature)
This adds a new feature to the track. The feature can either be a
single object that implements the Bio::SeqFeatureI interface (such
as an Ace::Sequence::Feature or Das::Segment::Feature), or can be
an anonymous array containing a set of related features. In the
latter case, the track will attempt to keep the features in the
same horizontal band and will not allow any other features to
overlap.
$track->add_group($group)
This behaves the same as add_feature(), but requires that its
argument be an array reference containing a list of grouped
features.
$track->draw($gd,$left,$top)
Render the track on a previously-created GD::Image object. The
$left and $top arguments indicate the position at which to start
rendering.
$boxes = $track->boxes($left,$top)
@boxes = $track->boxes($left,$top)
Return an array of array references indicating glyph coordinates
for each of the render features. $left and $top indicate the
offset for the track on the image plane. In a scalar context, this
method returns an array reference of glyph coordinates. In a list
context, it returns the list itself.
See Ace::Graphics::Panel->boxes() for the format of the result.
ACCESSORS
The following accessor methods provide access to various attributes of
the track object. Called with no arguments, they each return the
current value of the attribute. Called with a single argument, they
set the attribute and return its previous value.
Note that in most cases you must change attributes before the track's
layout() method is called.
Accessor Name Description
------------------------
scale() Get/set the track scale, measured in pixels/bp
lineheight() Get/set the height of each glyph, pixels
width() Get/set the width of the track
bump() Get/set the bump direction
INTERNAL METHODS
The following methods are used internally, but may be useful for those
implementing new glyph types.
$glyphs = $track->layout
Layout the features, and return an anonymous array of
Ace::Graphics::Glyph objects that have been created and correctly
positioned.
Because layout is an expensive operation, calling this method
several times will return the previously-cached result, ignoring
any changes to track attributes.
$height = $track->height
Invokes layout() and returns the height of the track.
$glyphs = $track->glyphs
Returns the glyph cache. Returns undef before layout() and a
reference to an array of glyphs after layout().
$factory = $track->make_factory(@options)
Given a set of options (argument/value pairs), returns a
Ace::Graphics::GlyphFactory for use in creating the glyphs with the
desired settings.
BUGS
Please report them.
SEE ALSO
Ace::Sequence,Ace::Sequence::Feature,Ace::Graphics::Panel,
Ace::Graphics::GlyphFactory,Ace::Graphics::Glyph
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.
perl v5.14.1 2001-09-17 Ace::Graphics::Track(3)