GBrowse

 view release on metacpan or  search on metacpan

Changes  view on Meta::CPAN

  * Fix track-level genbank and fasta dumping.
  * Fix (mostly) the batch and sequence dumping plugins.

2.47
  * Fix bugs in demo mode.
  * Fix session locking bug; FastCGI performance subjectively improved.
  * Revert to using inline imagemaps when not running in an accelerated environment.
  * Require Bio::Graphics version 2.26, so that transparency is supported.

2.46
  * Support for transparent overlay tracks. These will appear as a user settable formatting option	
    for any track with subtracks. To make this default for a track set "bump = overlap" and consider
    setting "color_series = 1" in order for background colors to be assigned automatically;
  * When downloading vista tracks, default download format to "vista_wiggle".
  * Fix signal handling under FastCGI in order to kill runaway rendering processes
    when server restarted.

2.45
  * Restore h_feat & h_region functionality to gbrowse_img.
  * Fix gbrowse_img documentation to point to correct example URLs on WormBase.
  * Fix persistent grey screen when clicking on snapshot thumbnail.

docs/pod/PLUGINS_HOWTO.pod  view on Meta::CPAN

=item 2. finders

These plugins accept input from the user and return a list of
genomic regions. The main browser displays the found regions and
allows the user to select among them. Example: BLAST search.

=item 3. annotators

These plugins receive the genomic segment object and return a list
of features which are overlayed on top of the detailed view.
Example: restriction site annotator.

=item 4. highlighters

These plugins receive each feature in turn before it is rendered and
can return a color name in order to highlight the background of the
feature with that color.

=item 5. filters

htdocs/js/snapshotManager.js  view on Meta::CPAN

			return false;
		} else {
			return true;
		}
	} else {
		return false;
	}
 },

      /* this code has nothing to do with snapshots
       * but is instead a hack for xyplot overlays
       * disable it for now
 linkTrackLegend:
  function(){
	var subtrack_groups = $$('.subtrack_group');

	subtrack_groups.each(function(subtrack_group) {
		var subtracks = subtrack_group.childElements();
		if(subtracks.size() > 1){
		    subtracks.each(function(subtrack) {
			    var label = subtrack.down().down().innerHTML;

lib/Bio/Graphics/Browser2/Plugin.pm  view on Meta::CPAN

=item 2) finders

These plugins accept input from the user and return a
list of genomic regions.  The main browser displays the found regions
and allows the user to select among them. Example: BLAST search.

=item 3) annotators 

These plugins receive the genomic segment object and either 1) return 
a list of features which are overlayed on top of the detailed view 
(Example: restriction site annotator) or 2) update the database with 
new or modified features and return nothing (Example: basic editor)

=item 4) trackfilters

These plugins can be used to reduce the complexity of sites that have
many tracks, by providing search and filtering functions for the track
table. When a trackfilter is active, its form-based user interface is
positioned directly above the tracks table, and changes to the for
cause the list of tracks to be updated dynamically.

lib/Bio/Graphics/Browser2/RenderPanels.pm  view on Meta::CPAN

    my $pad_img = img(
        {   -src    => $pad_url,
            -width  => $pad->width,
            -border => 0,
            -id     => "${label}_pad",
	    -class  => 'track_image',
            -style  => $collapsed ? "display:inline" : "display:none",
        }
    );

    my $overlay_div = '';

    # Add arrows for panning to details scalebar panel
    if ($is_scalebar && $is_detail) {
	my $style    = 'opacity:0.35;position:absolute;border:none;cursor:pointer';
        my $pan_left   =  img({
	    -style   => $style . ';left:5px',
	    -class   => 'panleft',
	    -src     => "$buttons/panleft.png",
	    -onClick => "Controller.scroll('left',0.5)"
	});

lib/Bio/Graphics/Browser2/RenderPanels.pm  view on Meta::CPAN

	my $pan_right  = img({
	    -style   => $style . ';right:5px',
	    -class   => 'panright',
	    -src     => "$buttons/panright.png",
	    -onClick => "Controller.scroll('right',0.5)",
	});

	my $scale_div = div( { -id => "detail_scale_scale",
			       -style => "position:absolute; top:12px", }, "" );

        $overlay_div = div( { -id => "${label}_overlay_div",
			      -style => "position:absolute; top:0px; width:100%; left:0px", }, $pan_left . $pan_right . $scale_div);
    }

    my $inner_div = div( { -id => "${label}_inner_div",-class=>'inner_div' }, $img . $pad_img ); #Should probably improve this


    my $subtrack_labels = join '',map {
	my ($label,$left,$top,undef,undef,$color) = @$_;
	$left -= $source->global_setting('pad_left') + PAD_DETAIL_SIDES;
	$left = 3 if $left < 3;
	my ($r,$g,$b,$a) = $color =~ /rgba\((\d+),(\d+),(\d+),([\d.]+)/;
	$a = 0.60 if $a > 0.75;
	my $fgcolor = $a <= 0.5 ? 'black' : ($r+$g+$b)/3 > 128 ? 'black' : 'white';
	div({-class=>'subtrack',-style=>"top:${top}px;left:${left}px;color:$fgcolor;background-color:rgba($r,$g,$b,$a)"},$label);
    } @$titles;

    my $html = div({-class=>'centered_block',
		 -style=>"position:relative;overflow:hidden"
		},
         ($show_titlebar ? $titlebar : '' ) . $popmenu .  $subtrack_labels . $inner_div . $overlay_div ) . ( $map_html || '' );
    return $html;
}

sub if_not_ipad {
    my $self = shift;
    my @args = @_;
    my $agent = CGI->user_agent || '';
    my $probably_ipad = $agent =~ /Mobile.+Safari/i;
    return if $probably_ipad;
    return @args;