[Gmod-gbrowse-cmts] Generic-Genome-Browser/libnew/Bio/Graphics/Browser DataSource.pm, 1.22, 1.23 RenderPanels.pm, 1.27, 1.28 Karyotype.pm, 1.1, NONE

[Lincoln S. <ls...@us...>]

Update of /cvsroot/gmod/Generic-Genome-Browser/libnew/Bio/Graphics/Browser
In directory sc8-pr-cvs2.sourceforge.net:/tmp/cvs-serv6977/libnew/Bio/Graphics/Browser

Modified Files:
	DataSource.pm RenderPanels.pm 
Removed Files:
	Karyotype.pm 
Log Message:
basic hits-on-karyotype class added -- not complete

--- Karyotype.pm DELETED ---

Index: RenderPanels.pm
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/libnew/Bio/Graphics/Browser/RenderPanels.pm,v
retrieving revision 1.27
retrieving revision 1.28
diff -C2 -d -r1.27 -r1.28
*** RenderPanels.pm	18 Aug 2008 16:53:38 -0000	1.27
--- RenderPanels.pm	20 Aug 2008 00:12:10 -0000	1.28
***************
*** 242,246 ****
          my $width  = $data->width;
          my $height = $data->height;
!         my $url    = $self->generate_image($gd);
  
          # for debugging
--- 242,246 ----
          my $width  = $data->width;
          my $height = $data->height;
!         my $url    = $self->source->generate_image($gd);
  
          # for debugging
***************
*** 357,361 ****
      # to the center of the page!
      my $pad     = $self->render_image_pad();
!     my $pad_url = $self->generate_image($pad);
      my $pad_img = img({-src   => $pad_url,
  		       -width => $pad->width,
--- 357,361 ----
      # to the center of the page!
      my $pad     = $self->render_image_pad();
!     my $pad_url = $self->source->generate_image($pad);
      my $pad_img = img({-src   => $pad_url,
  		       -width => $pad->width,
***************
*** 645,649 ****
      eval { $panel->finished }; # should quash memory leaks when used in conjunction with bioperl 1.4
  
!     my $url    = $self->generate_image($gd);
      my $height = $y2 - $y1 + 1;
  
--- 645,649 ----
      eval { $panel->finished }; # should quash memory leaks when used in conjunction with bioperl 1.4
  
!     my $url    = $self->source->generate_image($gd);
      my $height = $y2 - $y1 + 1;
  
***************
*** 1791,1795 ****
      };
  }
-       
  
  sub hilite_fill {
--- 1791,1794 ----
***************
*** 1805,1850 ****
  }
  
- =head2 generate_image
- 
-   ($url,$path) = $render_panels->generate_image($gd)
- 
- Given a GD::Image object, this method calls its png() or gif() methods
- (depending on GD version), stores the output into the temporary
- directory given by the "tmpimages" option in the configuration file,
- and returns a two element list consisting of the URL to the image and
- the physical path of the image.
- 
- =cut
- 
- sub generate_image {
-   my $self   = shift;
-   my $image  = shift;
- 
-   my $source = $self->source;
- 
-   my $extension = $image->can('png') ? 'png' : 'gif';
-   my $data      = $image->can('png') ? $image->png : $image->gif;
-   my $signature = md5_hex($data);
- 
-   warn ((CGI::param('ref')||'')   . ':' .
- 	(CGI::param('start')||'') . '..'.
- 	(CGI::param('stop')||'')
- 	,
- 	" sig $signature\n") if DEBUG;
- 
-   # untaint signature for use in open
-   $signature =~ /^([0-9A-Fa-f]+)$/g or return;
-   $signature = $1;
- 
-   my ($uri,$path) = $source->globals->tmpdir($source->name.'/img');
-   my $url         = sprintf("%s/%s.%s",$uri,$signature,$extension);
-   my $imagefile   = sprintf("%s/%s.%s",$path,$signature,$extension);
-   open (F,">$imagefile") || die("Can't open image file $imagefile for writing: $!\n");
-   binmode(F);
-   print F $data;
-   close F;
-   return $url;
- }
- 
  1;
  
--- 1804,1807 ----

Index: DataSource.pm
===================================================================
RCS file: /cvsroot/gmod/Generic-Genome-Browser/libnew/Bio/Graphics/Browser/DataSource.pm,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** DataSource.pm	14 Aug 2008 18:28:49 -0000	1.22
--- DataSource.pm	20 Aug 2008 00:12:10 -0000	1.23
***************
*** 10,13 ****
--- 10,14 ----
  use File::Path 'mkpath';
  use Data::Dumper 'Dumper';
+ use Digest::MD5 'md5_hex';
  use Carp 'croak';
  use Socket 'AF_INET','inet_aton';  # for inet_aton() call
***************
*** 773,776 ****
--- 774,811 ----
  }
  
+ =head2 generate_image
+ 
+   ($url,$path) = generate_image($gd);
+ 
+ Given a GD::Image object, this method calls its png() or gif() methods
+ (depending on GD version), stores the output into the temporary
+ directory given by the "tmpimages" option in the configuration file,
+ and returns a two element list consisting of the URL to the image and
+ the physical path of the image.
+ 
+ =cut
+ 
+ sub generate_image {
+   my $self   = shift;
+   my $image  = shift;
+ 
+   my $extension = $image->can('png') ? 'png' : 'gif';
+   my $data      = $image->can('png') ? $image->png : $image->gif;
+   my $signature = md5_hex($data);
+ 
+   # untaint signature for use in open
+   $signature =~ /^([0-9A-Fa-f]+)$/g or return;
+   $signature = $1;
+ 
+   my ($uri,$path) = $self->globals->tmpdir($self->name.'/img');
+   my $url         = sprintf("%s/%s.%s",$uri,$signature,$extension);
+   my $imagefile   = sprintf("%s/%s.%s",$path,$signature,$extension);
+   open (my $f,'>',$imagefile) || die("Can't open image file $imagefile for writing: $!\n");
+   binmode($f);
+   print $f $data;
+   close $f;
+   return $url;
+ }
+ 
  1;