image documentation.

Bio::Graphics::Glyph::image - A glyph that draws photographs & other images

No package variables defined.

base ' Bio::Graphics::Glyph::generic '

 use Bio::Graphics;
 use Bio::Seq;
 use Bio::SeqFeature::Generic;

 my $bsg = 'Bio::SeqFeature::Generic';

 my $seq    = Bio::Seq->new(-length=>1000);

 my $whole  = $bsg->new(-display_name => 'Clone82',
 		        -start        => 1,
		        -end          => $seq->length);

 my $image1 = $bsg->new(-start        => 100,
		        -end          => 300,
		        -display_name => 'Excretory System',
		        -tag=>{
			      image=>"http://www.flybase.org/anatomy/image-browser_files/excretory-system.gif"
			      }
		       );

 my $image2 = $bsg->new(-start        => 500,
		        -end          => 800,
		        -display_name => 'Expression Pattern',
		        -tag=>{
			      image=>"http://www.flybase.org/anatomy/image-browser_files/embryonic-expression-pattern.gif"
			      }
		       );

 my $panel = Bio::Graphics::Panel->new(-length    => $seq->length,
				       -width     => 800,
				       -truecolor => 1,
				       -key_style => 'between',
				       -pad_left  => 10,
				       -pad_right => 10,
				      );

 $panel->add_track($whole,
		   -glyph    => 'arrow',
		   -double   => 1,
		   -tick     => 2,
		   -label    => 1,
		   );

 $panel->add_track([$image1,$image2],
		   -glyph    => 'image',
		   -label    => 1,
		   -key       => 'Example images');

 binmode STDOUT;
 print $panel->png;

This glyph inserts an image into the track at the indicated feature
coordinates. The image can be in PNG, JPEG, GIF or GD format, and can
be either 8-bit or 24-bit ("truecolor"). The image can be located on
the local filesystem or located at a remote URL (provided that you
have the LWP module installed).
When working with photographic images, you may wish to have
Bio::Graphics::Panel create 24-bit (truecolor) images in order to
avoid running out of colors. The symptom of this is that images appear
posterized. To turn on truecolor images, pass the -truecolor option to
Bio::Graphics::Panel as shown in the synopsis. The following options are standard among all Glyphs. See
Bio::Graphics::Glyph for a full explanation.

  Option      Description                      Default
  ------      -----------                      -------

  -fgcolor      Foreground color	       black

  -outlinecolor	Synonym for -fgcolor

  -bgcolor      Background color               turquoise

  -fillcolor    Synonym for -bgcolor

  -linewidth    Line width                     1

  -height       Height of glyph		       10

  -font         Glyph font		       gdSmallFont

  -connector    Connector type                 0 (false)

  -connector_color
                Connector color                black

  -label        Whether to draw a label	       0 (false)

  -description  Whether to draw a description  0 (false)

  -hilite       Highlight color                undef (no color)

The following additional options are available to the "image" glyph:

  Option            Description                       Default
  ------            -----------                       -------

  -image            Specify the image path or URL     none
                    to use for this feature.

  -image_prefix     String to prepend to              none
                    each image path. You may prepend
                    a directory or a partial URL.

  -vertical_spacing Vertical distance from the box    20
                    that shows the physical span of
                    of the feature to the top of
                    the picture (in pixels).

  -glyph_delegate   Glyph to use for the part of      'generic'
                    the glyph that shows the physical
                    span of the feature.

Set -vertical_spacing to 0 to completely suppress the diagonal
lines that connect the physical span of the feature to the image. The path to the image can be specified in two ways. First, you can
place it in the feature itself using a tag named "image". Second, you
can specify it as a track option using a callback:

  $panel->add_track(\@features,
                    -glyph=>'image',
                    -image => sub { my $feature = shift;
                                    my $image_path = do_something();
                                    return $image }
                    );

You can of course give -image a constant string, in which case each
feature will show the same image.
The image can be a file on the local operating system or a
URL. However, URL fetching will only work if the LWP module is
installed on your system. Otherwise the glyph will fail with an error
message.
If the image is a relative path (it does not begin with a slash or a
URL protocol), then the contents of -image_prefix will be prepended to
it. This allows you to specify images that are relative to a
particular directory or a partial URL. Example:

  $panel->add_track(\@features,
                    -glyph => 'image',
                    -image_prefix => 'http://www.flybase.org/anatomy/image-browser_files',
                   );

This specifies that each feature's "image" tag is to be appended to
the partial FlyBase URL, thereby saving space. The image glyph consists of two parts: an upper part that shows the
extent of the feature in base pair coordinates, and a lower part that
shows the image. No scaling of the image is done; its height and width
are fixed.
By default the upper part uses the "generic" glyph, which is a simple
rectangle filled with the bgcolor and outlined with the fgcolor. To
use a different glyph in the upper part, specify the -glyph_delegate
option, giving the name of the glyph you wish to use. For instance, to
use the "span" glyph:

  $panel->add_track(\@features,
                    -glyph          => 'image',
                    -glyph_delegate => 'span'
                   );

This feature does not work with all glyphs, and in particular requires
a recent CVS checkout of Bio::Perl to work properly with the "arrow",
"span" and "primers" glyphs (support for the feature did not make it
into version 1.5).

sub new {

  my $self  = shift->SUPER::new(@_);
  $self->{image} = $self->get_image();
  return $self;

}

sub get_image {

  my $self    = shift;
  my ($format,$image)   = eval { $self->image_data };
  unless ($image) {
    warn $@ if $@;
    return;
  }
  my $gd      =   $format eq 'image/png'  ? GD::Image->newFromPngData($image,1)
                : $format eq 'image/jpeg' ? GD::Image->newFromJpegData($image,1)
		: $format eq 'image/gif'  ? GD::Image->newFromGifData($image)
		: $format eq 'image/gd'   ? GD::Image->newFromGdData($image)
		: $format eq 'image/gd2'  ? GD::Image->newFromGd2Data($image)
		: $self->throw("This module cannot handle images of type $format");
  return $gd;

}

sub _guess_format {

  my $self = shift;
  my $path = shift;
  return 'image/png'   if $path =~ /\.png$/i;
  return 'image/jpeg'  if $path =~ /\.jpe?g$/i;
  return 'image/gif'   if $path =~ /\.gif(87)?$/i;
  return 'image/gd'    if $path =~ /\.gd$/i;
  return 'image/gd2'   if $path =~ /\.gd2$/i;
  my ($extension) = $path =~ /\.(\w+)$/;  #cop-out
  return $extension;

}

sub image_path {

  my $self = shift;
  my $feature  = $self->feature  or $self->throw("no feature!");
  my $dirname  = $self->image_dir;
  my $basename = $self->option('image');

  # can't get it from callback, so try looking for an 'image' attribute
  if (!$basename && $feature->can('has_tag') && $feature->has_tag('image')) {
    ($basename)  = $feature->get_tag_values('image');
  }

  return unless $basename;
  return $basename             if $basename =~ m!^\w+:/!;  # looks like a URL
  return $basename             if $basename =~ m!^/!;      # looks like an abs path
  return "$dirname/$basename";

}

sub image_data {

  my $self = shift;
  my $path = $self->image_path;

  if ($path =~ m!^\w+:/!) { # looks like a URL
    require LWP::UserAgent;
    my $ua = LWP::UserAgent->new(env_proxy => 1);
    my $response = $ua->get($path);
    if ($response->is_success) {
      return ($response->content_type,$response->content);
    } else {
      $self->throw($response->status_line);
    }


  } else {
    my $content_type = $self->_guess_format($path);
    open F,$path or $self->throw("Can't open $path: $!");
    binmode F;
    my $data;
    $data .= $_ while read(F,$_,1024);
    close F;
    return ($content_type,$data);
  }

}

sub pad_left {

  my $self = shift;
  my $pad          = $self->SUPER::pad_left;
  my $image        = $self->{image} or return $pad;
  my $width_needed = ($image->width - $self->width)/2;
  return $pad > $width_needed ? $pad : $width_needed;

}

sub pad_right {

  my $self = shift;
  my $pad          = $self->SUPER::pad_right;
  my $image        = $self->{image} or return $pad;
  my $width_needed = ($image->width - $self->width)/2;
  return $pad > $width_needed ? $pad : $width_needed;

}

sub pad_bottom {

  my $self   = shift;
  my $pb     = $self->SUPER::pad_bottom;
  my $image  = $self->{image} or return $pb;
  $pb       += $self->vertical_spacing;
  $pb       += $image->height;
  return $pb;

}

sub vertical_spacing {

  my $self  = shift;
  my $vs    = $self->option('vertical_spacing');
  return $vs if defined $vs;
  return VERTICAL_SPACING;

}

sub draw_description {

  my $self = shift;
  my ($gd,$left,$top,$partno,$total_parts) = @_;
  $top += $self->{image}->height+$self->vertical_spacing if $self->{image};
  $self->SUPER::draw_description($gd,$left,$top,$partno,$total_parts);

}

sub image_dir {

  my $self = shift;
  return $self->option('image_prefix');

}

sub draw_component {

  my $self  = shift;
  my $gd    = shift;
  my($x1,$y1,$x2,$y2) = $self->bounds(@_);

  my $delegate = $self->option('glyph_delegate') || 'generic';
  if ($delegate eq 'generic') {
    $self->SUPER::draw_component($gd,@_);
  } else {
    eval "require Bio::Graphics::Glyph::$delegate";
    local @ISA = ("Bio::Graphics::Glyph::$delegate");
    my $method = "Bio::Graphics::Glyph::${delegate}::draw_component";
    $self->$method($gd,@_);
  }

  my $image  = $self->{image} or return;

  my $fgcolor = $self->fgcolor;
  my $bgcolor = $self->bgcolor;
  my $height  = $self->option('height');
  my $half    = 4;
  my $vs      = $self->vertical_spacing;

  my $delta = (($x2-$x1) - $image->width)/2;
  my($x,$y) = ($x1+$delta,$y1+$vs+$self->height);
  if ($gd->can('copy')) {
    $gd->copy($image,$x,$y,0,0,$image->width,$image->height) ;
  } else {
    my $gray = $self->panel->translate_color('gray');
    $gd->filledRectangle($x,$y,$x+$image->width,$y+$image->height,$gray);
  }

  if ($vs > 0) {
    $gd->line($x1,$y2+2,$x1,$y2+$half,$fgcolor);
    $gd->line($x2,$y2+2,$x2,$y2+$half,$fgcolor);
    $gd->line($x1,$y2+$half,$x,$y-$half,$fgcolor);
    $gd->line($x2,$y2+$half,$x+$image->width-1,$y-$half,$fgcolor);
    $gd->line($x,$y-$half,$x,$y-2,$fgcolor);
    $gd->line($x+$image->width-1,$y-$half,$x+$image->width-1,$y-2,$fgcolor);
  }

}

General documentation

This glyph does not work with GD::SVG. If you try to render it onto a
GD::SVG panel, the image will be shown as a gray box. This will be
fixed in a future version of GD::SVG.

Lincoln Stein <lstein@cshl.org>, Todd Harris <harris@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.

new	No description	Code
get_image	No description	Code
_guess_format	No description	Code
image_path	No description	Code
image_data	No description	Code
pad_left	No description	Code
pad_right	No description	Code
pad_bottom	No description	Code
vertical_spacing	No description	Code
draw_description	No description	Code
image_dir	No description	Code
draw_component	No description	Code