Ace::Graphics::Track(3pm)				User Contributed Perl Documentation				 Ace::Graphics::Track(3pm)

NAME

       Ace::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 v5.14.2							    2001-09-17						 Ace::Graphics::Track(3pm)