AcePerl

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Ace/Browser/TreeSubs.pm  view on Meta::CPAN

# A hack to allow access to external images.
# We use the name of the database as a URL to an external image.
# The URL will look like this:
#     /ace_images/external/database_name/foo.gif
# You must arrange for the URL to return the correct image, either with
# a CGI script, a symbolic link, or a redirection directive.
sub AceImageHackURL {
  my $image_name = shift;
  # correct some bad image file names in the database
  $image_name .= '.jpeg' unless $image_name =~ /\.(gif|jpg|jpeg|png|tiff|ps)$/;
  my $picture_path = Configuration->Pictures->[0];
  return join('/',$picture_path,Configuration->Name,'external',escape("$image_name"));
}


1;

Ace/Graphics/Panel.pm  view on Meta::CPAN

  return $self->{pens}{$linewidth} if $self->{pens}{$linewidth};

  my $pen = $self->{pens}{$linewidth} = GD::Image->new($linewidth,$linewidth);
  my @rgb = $self->rgb($color);
  my $bg = $pen->colorAllocate(255,255,255);
  my $fg = $pen->colorAllocate(@rgb);
  $pen->fill(0,0,$fg);
  $self->{gd}->setBrush($pen);
}

sub png {
  my $gd = shift->gd;
  $gd->png;
}

sub boxes {
  my $self = shift;
  my @boxes;
  my $offset = 0;
  my $pl = $self->pad_left;
  my $pt = $self->pad_top;
  for my $track (@{$self->{tracks}}) {
    my $boxes = $track->boxes($pl,$offset+$pt);

Ace/Graphics/Panel.pm  view on Meta::CPAN

  $panel->add_track(transcript => \@transcripts,
 		    -fillcolor =>  'wheat',
 		    -fgcolor   =>  'black',
                    -key       => 'Curated Genes',
 		    -bump      =>  +1,
 		    -height    =>  10,
 		    -label     =>  1);

  my $boxes = $panel->boxes;
  print $panel->png;

=head1 DESCRIPTION

The Ace::Graphics::Panel class provides drawing and formatting
services for Ace::Sequence::Feature objects or Das::Segment::Feature
objects.

Typically you will begin by creating a new Ace::Graphics::Panel
object, passing it the width of the visual display and the length of
the segment.  

You will then call add_track() one or more times to add sets of
related features to the picture.  When you have added all the features
you desire, you may call png() to convert the image into a PNG-format
image, or boxes() to return coordinate information that can be used to
create an imagemap.

Note that this modules depends on GD.

=head1 METHODS

This section describes the class and object methods for
Ace::Graphics::Panel.

Ace/Graphics/Panel.pm  view on Meta::CPAN

-connect_groups argument with a true value.  For example:

  $panel->add_track(segments => [[$abc_5,$abc_3],
				 [$xxx_5,$xxx_3],
				 [$yyy_5,$yyy_3]],
		    -connect_groups => 1);

=item $gd = $panel->gd

The gd() method lays out the image and returns a GD::Image object
containing it.  You may then call the GD::Image object's png() or
jpeg() methods to get the image data.

=item $png = $panel->png

The png() method returns the image as a PNG-format drawing, without
the intermediate step of returning a GD::Image object.

=item $boxes = $panel->boxes

=item @boxes = $panel->boxes

The boxes() method returns the coordinates of each glyph, useful for
constructing an image map.  In a scalar context, boxes() returns an
array ref.  In an list context, the method returns the array directly.

Ace/Graphics/Panel.pm  view on Meta::CPAN

=back

=head2 ACCESSORS

The following accessor methods provide access to various attributes of
the panel 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 prior to invoking
gd(), png() or boxes().  These three methods all invoke an internal
layout() method which places the tracks and the glyphs within them,
and then caches the result.

   Accessor Name      Description
   -------------      -----------

   width()	      Get/set width of panel
   spacing()	      Get/set spacing between tracks
   length()	      Get/set length of segment (bp)
   pad_top()	      Get/set top padding

Ace/Graphics/Track.pm  view on Meta::CPAN

   		                -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

examples/draw_seqmap.pl  view on Meta::CPAN

  $panel->add_track(\@features =>  $glyph,
		    -fillcolor =>  'green',
		    -fgcolor   =>  'black',
		    -bump      =>  +1,
		    -height    => 10,
		    -connect   => 1,
		    -label     => 1,
		   );
}
print $panel->png;