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contrib/SynView/MAL11/MAL11.conf  view on Meta::CPAN 

[GENERAL]
description   = P. falciparum chromosome 11
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor memory
				-dir    '/var/www/html/gbrowse/databases/MAL11'

aggregators = transcript alignment orf
plugins = BatchDumper FastaDumper RestrictionAnnotator FilterTest

# Web site configuration info
stylesheet  = /gbrowse/gbrowse.css
buttons     = /gbrowse/images/buttons
js          = /gbrowse/js
tmpimages   = /gbrowse/tmp

# where to link to when user clicks in detailed view
link          = AUTO

# what image widths to offer
image widths  = 450 640 800 1024

# default width of detailed view (pixels)
default width = 800
default features = Genes

# The class of the feature that is used as the reference for all others
# "Sequence" is the default - change it if you use something else
reference class = Sequence

# max and default segment sizes for detailed view
max segment     = 500000
default segment = 50000

# zoom levels
zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000

# whether to show the sources popup menu (0=false, 1=true; defaults to true)
show sources   = 1

# colors of the overview, detailed map and key
overview bgcolor = lightgrey
detailed bgcolor = lightgoldenrodyellow
key bgcolor      = beige

# examples to show in the introduction
examples = MAL11:370,500..410,000

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Symbol Gene Clone

### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
# inside the <head></head> section
head = 

# at the top...
header =

# a footer
footer = 

# Various places where you can insert your own HTML -- see configuration docs
html1 = 
html2 = 
html3 = 
html4 = 
html5 = 
html6 = 

postgrid = sub {
             my ($gd, $panel) = @_; 
			 $gd->alphaBlending(0); 
			 $gd->saveAlpha(1); 
			 $panel->boxes(); # causes the layout to be calculated 
			 use Tie::IxHash; 
			 my %orthologs; 
			 my %location; 
			 my %drawn; 
			 my %newdrawn; 
			 for my $track (@{$panel->{tracks}}) { 
			   for my $part (@{$track->{parts}}) { 
			     my $feature = $part->{feature}; 
				 next unless $feature->isa("Bio::SeqFeatureI"); 
				 my @orthologs = $feature->get_tag_values("Ortholog"); 
				 next unless @orthologs; 
				 my $gene = $feature->name; 
				 for my $ortholog (@orthologs) { 
				   unless (exists $orthologs{$ortholog}) { 
				     tie(%{$orthologs{$ortholog}}, "Tie::IxHash"); 
				   } 
				   $orthologs{$ortholog}->{$gene}++; 
				 } 
				 my $yoffset = $panel->track_position($track); 
				 my $padleft = $panel->pad_left(); 
				 my ($x1, $y1, $x2, $y2) = $part->bounds(); 
				 $x1 += $padleft; 
				 $x2 += $padleft; 
				 $y1 += $yoffset - 2;



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