[GENERAL]
description =  test implementation of chado
db_adaptor    = Bio::DB::Das::Chado
db_args       = -dsn dbi:Pg:dbname=chado 
                -user scott
                -srcfeatureslice 1
                -organism yeast
                -version 1
                #-inferCDS 1

plugins = AttributeHiliter BatchDumper

# 'region' or 'contig' would be other typical choices,
# remember that in chado, the ref class must be part of 
# SOFA (as must all feature types)
#  IF you loaded your data from GFF--this must match the type
# (ie, the third column) of the reference feature in the GFF file
reference class  = chromosome

#Do not use aggregators with the chado adaptor
#aggregators = 

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

# advanced features
balloon tips    = 1
drag and drop = 1

# one hour
cache time    = 1

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

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

# 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

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

# examples to show in the introduction
examples = YAL031C
           YCR02*
           ChrV:100000-120000

# "automatic" classes to try when an unqualified identifier is given
#automatic classes = gene

language = en

# a footer
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: 07.chado.conf,v 1.8.6.3.2.1.2.3 2009/07/15 20:13:24 scottcain Exp $</pre>

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

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
label density = 25
bump density  = 100
# default pop-up balloon
balloon hover = <b>$name</b> is a $type spanning $ref from $start to $end. Click for more details.
link        = AUTO


### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks

[Genes]
feature      = gene
glyph        = arrow
base         = 1
ignore_sub_part = CDS intron
fgcolor      = red
height       = 5
linewidth    = 2
key          = Named gene
                                                                                
[CDS]
feature      = gene
sub_part     = CDS
glyph        = cds
height       = 20
key          = CDS
                                                                                
[tRNA]
feature      = tRNA
key          = tRNA
                                                                                
[SNP]
feature      = SNP
glyph        = triangle
key          = SNP
                                                                                
[STS]
feature      = STS
key          = STS

[Landmarks:overview]
feature      = region:landmark
glyph        = generic
fgcolor      = green
key          = Landmarks

[Translation]
glyph        = translation
global feature = 1
height       = 40
fgcolor      = purple
strand       = +1
translation  = 6frame
key          = 6-frame translation

[DNA/GC Content]
glyph        = dna
global feature = 1
height       = 40
do_gc        = 1
strand       = both
fgcolor      = red
axis_color   = blue

[Spacer region]
glyph        = generic
feature      = external_transcribed_spacer_region internal_transcribed_spacer_region
bgcolor      = sub {
                 my $feature = shift;
                 my $type = $feature->type;
                 if ($type eq 'internal_transcribed_spacer_region') {
                     return 'blue';
                 }
                 else {
                     return 'red';
                 }
               }
key           = Transcribed spacer regions

[Misc RNAs]
feature       = rRNA snoRNA snRNA ncRNA
glyph         = generic
key           = Misc RNAs
