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.