[GENERAL]
description = H. Sapiens (via NCBI-annotation April 2002)
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor dbi::mysql
	        -dsn     dbi:mysql:database=human;host=localhost
user          = nobody
pass          =

aggregators = transcript
              transcript_density{bin:exon:NCBI}
              snp_density{bin:snp:NCBI}

plugins = SequenceDumper FastaDumper RestrictionAnnotator

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

# where to link to when user clicks in detailed view
link        = sub {
              my $feature = shift;
              my $name = $feature->name;
	      my $type = $feature->primary_tag;
	      my %sources = (snp => "http://www.ncbi.nih.gov/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=",
			     locus => "http://www.ncbi.nlm.nih.gov/LocusLink/LocRpt.cgi?l=",
			     component   => "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&term=",
			     sts     => "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Search&db=UniSTS&doptcmdl=UniSTS&term=",
			     transcript    => "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&term=");
	      my $link = $sources{$type} . $name;
	      return $link;
	  }

_link          = sub {
  		  my $feature = shift;
	          my $name = $feature->name;
		  if ($name =~ s/^TR://) {
	             return sprintf("http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-e+[SWALL-acc:%s]+-vn+2",$name);
		  } elsif ($name =~ s/^SW://) {
	             return sprintf("http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?-id+3LIc21HeBHW+-e+[SWALL:'%s']",$name);
                  } else {
                     return "/db/get?name=$name;class=Protein";
	          }
	      }

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

default features = 'RefSeq mRNAs'
                   'LocusLink genes'
                   'refSNPs'

# max and default segment sizes for detailed view
max segment     = 2000000
default segment = 250000

# eight numbers for the zoom levels - should be more flexible, sorry
zoom levels    = 100 500 1000 2000 5000 10000 20000 40000 100000 200000 500000 750000 1000000 2000000

# colors of the overview, detailed map and key
overview bgcolor = wheat
detailed bgcolor = lightblue
key bgcolor      = beige

# examples to show in the introduction
examples = Chr20 Chr9:80,000..180,000 NM_032757.1 AL117347.10 D1S2711 BRCA2 cyclin

# "automatic" classes to try when an unqualified identifier is given
automatic classes = SNP Locus Transcript
footer = <hr>
	<table width="100%">
	<TR>
	<TD align="LEFT" class="databody">
	For the source code for this browser, see the <a href="http://www.gmod.org">
	Generic Model Organism Database Project.</a>  For other questions, send
	mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
	</TD>
	</TR>
	</table>
	<hr>
	<pre>$Id: human.conf</pre>

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

[TRACK DEFAULTS]
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
fontcolor   = black
font2color  = blue
label density = 25
bump density  = 100

####################################################
# overview configuration
####################################################

[contig:overview]
feature       = contig:NCBI
glyph         = generic
fgcolor       = black
bgcolor       = blue
fillcolor     = blue
label         = 0
bump          = 1
label density = 10
height        = 4
key           = Contigs

[transcript:overview]
feature       = transcript_density
glyph         = xyplot
graph_type    = boxes
scale         = right
bgcolor       = red
fgcolor       = red
height        = 20
key           = Transcripts
 
####################################################
# track configuration
####################################################

[UniSTS Markers]
feature      = sts:NCBI
glyph        = triangle
connect      = 1
height       = 6
bgcolor      = red
fgcolor      = black
orient       = S
point        = 1
label        = 0

[LocusLink genes]
feature      = locus:NCBI
glyph        = arrow
base         = 1
fgcolor      = red
font2color   = red
linewidth    = 2
height       = 6
label        = 1
description  = 1
key          = LocusLink genes

[RefSeq mRNAs]
feature      = transcript:NCBI
glyph        = transcript
bgcolor      = dodgerblue
fgcolor      = black
height       = 10
key         = RefSeq Transcripts

[refSNPs]
feature       = snp:NCBI
glyph         = triangle
point         = 1
orient        = N
height        = 6
bgcolor       = blue
fgcolor       = blue
key           = refSNPs

[refSNPs:150000]
feature       = snp_density
glyph         = xyplot
graph_type    = boxes
scale         = right

[Components]
feature       = component:NCBI
glyph         = generic
height        = 4
fgcolor       = black
bgcolor       = black
stranded      = 1
strand_arrow  = 1

[NT contigs]
feature       = contig:NCBI
stranded      = 1
strand_arrow  = 1

[Clones]
feature       = clone:NCBI
fgcolor       = black
bgcolor       = white
glyph         = generic
height        = 5
stranded      = 1
strand_arrow  = 1

#[DNA]
#glyph        = dna
#height       = 40
#do_gc        = 1
#gc_bins      = 40
#tkcolor      = lightblue
#fgcolor      = red
#key          = DNA/GC Content
#axis_color   = blue