[GENERAL]
description = D. melanogaster (via Gadfly Release 2)
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor dbi::mysql
	        -dsn     dbi:mysql:database=fly;host=localhost
user          = nobody
pass          =

aggregators = transcript alignment
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 detaild view
link          = http://hedgehog.lbl.gov:8002/cgi-bin/annot/query?namesearch=$name

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

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

# max and default segment sizes for detailed view
max segment = 1000000
default segment = 100000

# zoom levels
zoom levels    = 100 500 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

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

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: 03.fly.conf,v 1.2 2003/06/29 23:18:46 lstein Exp $</pre>

# examples to show in the introduction
examples = 2L
	   2L:80,000..120,000
	   AE003590
	   Nrv2 Mipp1
	   gene:CG12178
	   transcript:CT33653
	   clone:BACR19F06
	   protein:P25160

# 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

#####################################################################
# the remainder of the sections configure particular features to show
#####################################################################

[TRANS]
feature      = transcript:gadfly
glyph        = transcript2
bgcolor      = turquoise
fgcolor      = black
height       = 10
description  = 1
key          = Predicted transcripts

[GENE]
feature      = gene:gadfly
glyph        = arrow
fgcolor      = red
linewidth    = 2
height       = 6
description  = 1
key          = Predicted genes

[EST]
feature       = alignment:groupest
feature_low   = similarity:groupest
bgcolor       = blue
glyph         = graded_segments
max_score     = 100
fgcolor       = black
height        = 6
connector     = dashed
key           = EST Alignments

[BLASTN]
feature       = alignment:blastn
feature_low   = similarity:blastn
glyph         = segments
bgcolor       = lightgray
fgcolor       = black
height        = 4
stranded      = 1
connector     = dashed
key           = BLASTN Hits

[BLASTX Hits]
feature       = alignment:blastx
bgcolor       = blue
glyph         = segments
fgcolor       = black
height        = 6
connector     = dashed
key           = BLASTX Hits
link          = http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=1&form=1&term=$name

[REP]
feature       = alignment:repeatmasker
glyph         = segments
bgcolor       = yellow
fgcolor       = black
height        = 5
stranded      = 1
connector     = dashed
key           = Repeatfinder Repeats

[CLO]
feature       = clone:clonelocator
fgcolor       = black
glyph         = anchored_arrow
height        = 7
key           = Clones

[SCAF]
feature       = Component:scaffold
fgcolor       = orange
glyph         = arrow
base          = 1
relative_coords  = 1
height        = 7
tick          = 2
key           = Scaffolds

[GAP]
feature       = Component:gap
fgcolor       = red
glyph         = arrow
height        = 7
double        = 1
tick          = 2
key           = Gaps

[DNA]
glyph        = dna
height       = 40
fgcolor      = red

[overview]
feature       = Component:scaffold
glyph         = drosophila_arrow
bgcolor       = lavender
label         = 1
height        = 5