# version 0.08 cross references all three web sites
# version 0.07 replaces "sgd" with "barc"
# version 0.09 changes Satt track to Loci
# version 0.10 adds QTL track
#              changes barc to various
#              took out links
#              change max view to 10,000,000
#              changed the comments and examples
# version 0.11 refers to Valine for further information
# version 0.12 changes D1A and D1B to D1AQ and D1BW
# version 0.13 adds Clones
#              description shortened to G. max
# version 0.14 adds 11 more Clones
# version 0.15 adds 75 contigs
# version 0.16 changes colors, glyphs, and examples
# version 0.17 for second FPC build; changes comments
# version 0.18 added Dr. DAL comments
# version 0.19 adds ontology graphic
# version 0.20 adds duplication track, inverts tracks, changes colors
# version 0.21 changes QTL's to brown, minimizes comments

[GENERAL]
description = G. max, Version 4, SIU 2003
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor dbi::mysqlopt 
	        -dsn     dbi:mysql:database=soybean;host=localhost
user          = nobody
pass          = 

aggregators = transcript alignment orf
# plugins = SequenceDumper FastaDumper RestrictionAnnotator

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

# Default glyph settings
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
label density = 1000
bump density  = 1000

# where to link to when user clicks in detaild view
# link          = http://genome-www4.stanford.edu/cgi-bin/SGD/locus.pl?locus=$name
# link          = http://soybase.agron.iastate.edu/SSR%20pages/$name.html

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

# default width of detailed view (pixels)
default width = 800
default features = Dups Loci Clone Ctg

# max and default segment sizes for detailed view
max segment     = 50000000
default segment = 10000000

# zoom levels
zoom levels    = 200 2000 5000 10000 20000 40000 100000 200000 500000 1000000 10000000 50000000

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

# examples to show in the introduction
examples = A1:9500000..10400000 
           A2:1..10000000
           B1:1..10000000
           B2:1..10000000
           C1:1..10000000
           C2:49000000..51000000
           D1AQ:19000000..23000000
           D1BW:1..10000000
           D2:1..10000000
           E:1..10000000
           F:1..10000000
           G:1..10000000
           H:1..10000000
           I:1..10000000
           J:1..10000000
           K:1..10000000
           L:1..10000000
           M:1..10000000
           N:1..10000000
           O:1..10000000
	   Queue:1..10000000

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Dups Loci Clone Ctg

# 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 general questions about this
        browser, send mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.  For
        questions about the SIUC soybean project, send mail to <a href="mailto:clangin@siu.edu">
        clangin@siu.edu</a>.
	</TD>
	</TR>
	</table>
	<hr>
	<pre>$Id: 01.soybean.conf,v 0.21 10/28/03 nlavu, clangin, lstein $</pre>

# Various places where you can insert your own HTML -- see configuration docs
html1 = <table><tr><td>&nbsp;</td></tr><tr><td align=center><a href="http://soybeangenome.siu.edu/soybean/ontology.html"><img src="http://bioinformatics.siu.edu/gif/ontology.gif" alt="Ontology" title="Ontology"></a></td><td><h2><em>This dataset is Version 4.  <a href="http://soybeangenome.siu.edu/index.html#methodology">Methodology and further information</a>.</em></h2></td></tr><tr>

</tr></table>
html2 = 
html3 = 
html4 = 
html5 = 
html6 = 

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

# [Dups]
# feature       = Dups:various
# glyph         = anchored_arrow
# fgcolor       = black
# font2color    = black
# linewidth     = 2
# height        = 6
# description   = 1
# key           = Duplications

[Ctg]
feature       = Ctg:various
glyph         = anchored_arrow
fgcolor       = blue
font2color    = lightblue
linewidth     = 2
height        = 6
description   = 1
key           = Contigs

[Clone]
feature       = Clone:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = lightgreen
linewidth     = 2
height        = 6
description   = 1
key           = Clones

[Loci]
feature       = Loci:various
glyph         = arrow
fgcolor       = red
font2color    = pink
linewidth     = 2
height        = 6
description   = 1
key           = Loci

[QTL]
feature       = QTL:various
glyph         = anchored_arrow
fgcolor       = brown
linewidth     = 2
height        = 6
description   = 1
key           = QTL