AcePerl
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Ace/Graphics/Track.pm view on Meta::CPAN
my $collision = 0;
for my $old (@occupied) {
last if $old->right + 2 < $g->left;
next if $old->bottom < $pos;
next if $old->top > $bottom;
$collision = $old;
last;
}
last unless $collision;
if ($bump_direction > 0) {
$pos += $collision->height + 2; # collision, so bump
} else {
$pos -= $g->height + 2;
}
}
$g->move(0,$pos);
@occupied = sort { $b->right <=> $a->right } ($g,@occupied);
$rightmost = $g->right if $g->right > $rightmost;
}
}
# return list of glyphs -- only after they are laid out
sub glyphs { shift->{glyphs} }
# height is determined by the layout, and cannot be externally controlled
sub height {
my $self = shift;
return $self->{cache_height} if defined $self->{cache_height};
$self->layout;
my $glyphs = $self->{glyphs} or croak "Can't lay out";
return 0 unless @$glyphs;
my ($topmost) = sort { $a->top <=> $b->top } @$glyphs;
my ($bottommost) = sort { $b->bottom <=> $a->bottom } @$glyphs;
return $self->{cache_height} = $bottommost->bottom - $topmost->top;
}
sub make_factory {
my ($class,$type,@options) = @_;
Ace::Graphics::GlyphFactory->new($type,@options);
}
1;
__END__
=head1 NAME
Ace::Graphics::Track - PNG graphics of Ace::Sequence::Feature objects
=head1 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;
=head1 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.
=head1 METHODS
This section describes the class and object methods for
Ace::Graphics::Panel.
=head2 CONSTRUCTORS
There is only one constructor, the new() method. It is ordinarily
called by Ace::Graphics::Panel, and not in end-developer code.
=over 4
=item $track = Ace::Graphics::Track->new($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.
=back
=head2 OBJECT METHODS
Once a track is created, the following methods can be invoked.
=over 4
=item $track->add_feature($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.
=item $track->add_group($group)
This behaves the same as add_feature(), but requires that its argument
be an array reference containing a list of grouped features.
=item $track->draw($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.
=item $boxes = $track->boxes($left,$top)
=item @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.
=back
=head2 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
=head2 INTERNAL METHODS
The following methods are used internally, but may be useful for those
implementing new glyph types.
=over 4
=item $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.
=item $height = $track->height
Invokes layout() and returns the height of the track.
=item $glyphs = $track->glyphs
Returns the glyph cache. Returns undef before layout() and a
reference to an array of glyphs after layout().
=item $factory = $track->make_factory(@options)
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