# version SoyV4R4.000 - copied and adapted from version 0.023
#                .001 - Added track for reversed contigs

[GENERAL]
description = G. max, Version 4, Round 4, SIU 2004
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor dbi::mysqlopt 
	        -dsn     dbi:mysql:database=SoyV4R4;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 = 110
bump density  = 110

# 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 = aLoci bLoci gLoci 
                   aClones b1Clones b2Clones b2sClones RevClones gClones gsClones
                   gContigs bContigs RevContigs sContigs 
                   Confirmed QTL QTLGENE EST MPT Sequence RelatedG RelatedGenes

# max and default segment sizes for detailed view
max segment     = 100000000
default segment = 10000000

# zoom levels
zoom levels    = 200 2000 5000 10000 20000 40000 100000 200000 500000 1000000 10000000 75000000

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

# examples to show in the introduction
examples = mlgA1
           mlgA2
           mlgB1
           mlgB2
           mlgC1
           mlgC2
           mlgD1AQ
           mlgD1BW
           mlgD2
           mlgE
           mlgF
           mlgG
           mlgH
           mlgI
           mlgJ
           mlgK
           mlgL
           mlgM
           mlgN
           mlgO
	   mlgQueue:5..100000000

# "automatic" classes to try when an unqualified identifier is given
automatic classes = aLoci bLoci gLoci 
                    aClones b1Clones b2Clones b2sClones RevClones gClones gsClones
                    gContigs bContigs RevContigs sContigs 
                    Confirmed QTL QTLGene EST MPT Sequence RelatedG RelatedGenes
# 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: SoyV4R4.conf,v 0.000 5/03/04 clangin, nlavu, 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, Round 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

[gContigs]
feature       = gContigs:various
glyph         = anchored_arrow
fgcolor       = blue
font2color    = blue
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Gamma Contigs

[bContigs]
feature       = bContigs:various
glyph         = anchored_arrow
fgcolor       = blue
font2color    = blue
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Beta Contigs

[RevContigs]
feature       = RevContigs:various
glyph         = anchored_arrow
fgcolor       = blue
font2color    = blue
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Reversed Contigs

[gClones]
feature       = gClones:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = green
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Gamma Clones

[b2Clones]
feature       = b2Clones:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = green
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Beta 2 Clones

[RevClones]
feature       = RevClones:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = green
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Reverse Beta 2 Clones

[gLoci]
feature       = gLoci:various
glyph         = arrow
fgcolor       = red
font2color    = tomato
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Gamma Loci

[sContigs]
feature       = sContigs:various
glyph         = anchored_arrow
fgcolor       = slateblue
font2color    = slateblue
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Spread Contigs

[gsClones]
feature       = gsClones:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = green
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Spread Gamma Clones

[b2sClones]
feature       = b2sClones:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = green
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Spread Beta 2 Clones

[b1Clones]
feature       = b1Clones:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = green
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Beta 1 Clones

[aClones]
feature       = aClones:various
glyph         = anchored_arrow
fgcolor       = green
font2color    = green
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Alpha Clones

[bLoci]
feature       = bLoci:various
glyph         = arrow
fgcolor       = red
font2color    = tomato
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Beta Loci

[aLoci]
feature       = aLoci:various
glyph         = arrow
fgcolor       = red
font2color    = tomato
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Alpha Loci

[QTL]
feature       = QTL:various
glyph         = anchored_arrow
fgcolor       = brown
font2color    = brown
linewidth     = 2
height        = 6
description   = 1
link          = http://soybase.ncgr.org/cgi-bin/ace/generic/pic/soybase?name=$name&class=QTL
key           = QTL

[QTLGene]
feature       = QTLGene:various
glyph         = anchored_arrow
fgcolor       = palevioletred
font2color    = palevioletred
linewidth     = 2
height        = 6
description   = 1
link          = http://soybase.ncgr.org/cgi-bin/ace/generic/pic/soybase?name=$name&class=Gene
key           = QTL Gene

[EST]
feature       = EST:various
glyph         = anchored_arrow
fgcolor       = darkgoldenrod
font2color    = darkgoldenrod
linewidth     = 2
height        = 6
description   = 1
link = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=($name)&db=Nucleotide
key           = EST

[MTP]
feature       = MTP:various
glyph         = anchored_arrow
fgcolor       = darkblue
font2color    = darkblue
linewidth     = 2
height        = 6
description   = 1
link = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=($name)&db=Nucleotide
key           = MTP

[Sequence]
feature       = Sequence:various
glyph         = anchored_arrow
fgcolor       = black
font2color    = black
linewidth     = 2
height        = 6
description   = 1
link = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=($name)&db=Nucleotide
key           = Sequence

[RelatedG]
feature       = RelatedG:various
glyph         = anchored_arrow
fgcolor       = maroon
font2color    = maroon
linewidth     = 2
height        = 6
description   = 1
link = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=($name)&db=Nucleotide
key           = Related G. max

[RelatedGenes]
feature       = RelatedGenes:various
glyph         = anchored_arrow
fgcolor       = purple
font2color    = purple
linewidth     = 2
height        = 6
description   = 1
link = http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&term=($name)&db=Nucleotide
key           = Related Genes

[Confirmed]
feature       = Confirmed:various
glyph         = arrow
fgcolor       = magenta
font2color    = magenta
linewidth     = 2
height        = 6
description   = 1
link          = http://bioinformatics.siu.edu:60/cgi-bin/detail?$name&$id&$class&$method&$source&$ref&$description&$start&$end&$segstart&$segend
link_target   = _blank
title         = AUTO
key           = Confirmed Locations