[GENERAL]
description   = Volvox Example Database
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
		-dir '/disk/www/html/gbrowse/databases/volvox'

plugins     = Aligner RestrictionAnnotator GFFDumper

drag and drop       = 1
balloon tips        = 1
titles are balloons = 1

# list of tracks to turn on by default
default features = ExampleFeatures

# examples to show in the introduction
examples = ctgA

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

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

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

# feature to show on startup
initial landmark = ctgA:1..10000

# max and default segment sizes for detailed view
max segment     = 50000
default segment = 5000

# zoom levels
zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 50000

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

label density = 25
bump density  = 100

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

# other customization options...

# HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS
# inside the <head></head> section
head = 

# at the top...
header =

# a footer
footer = <hr /><pre>$Id: volvox_final.conf,v 1.6.6.2.2.4.2.1 2008/03/26 13:36:37 lstein Exp $</pre>

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

category tables = 'ArrayExpts' 'strain-A strain-B strain-C' 'temperature anaerobic aerobic'

########################
# Default glyph settings
########################


[TRACK DEFAULTS]
glyph         = generic
height        = 10
bgcolor       = lightgrey
fgcolor       = black
font2color    = blue
label density = 25
bump density  = 100
# where to link to when user clicks in detailed view
link          = AUTO

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

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = orange
height       = 10
key          = Example Features

[NameTest]
feature      = protein_coding_primary_transcript polypeptide
glyph        = generic
stranded     = 1
bgcolor      = green
height       = 10
key          = Name test track

[Motifs]
feature      = polypeptide_domain
glyph        = span
height       = 5
description  = 1
balloon hover = <h2>Gene $name</h2>
balloon click = <h2>Gene $name</h2>
       <a href='http://www.google.com/search?q=$name'>Search Google</a><br>
       <a href='http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&term=$name'>Search NCBI</a><br>
key          = Example motifs

[Alignments]
feature      = match
glyph        = segments
category     = Alignments
key          = Example alignments

[Genes]
feature      	   = gene
glyph              = gene
bgcolor            = peachpuff
label_transcripts  = 1
draw_translation   = 1
category           = Genes
key                = Protein-coding genes

[ReadingFrame]
feature            = mRNA
glyph              = cds
ignore_empty_phase = 1
category           = Genes
key                = Frame usage

[CDS]
feature      	   = CDS:predicted mRNA:exonerate
glyph              = gene
bgcolor            = white
category           = Genes
key                = Predicted genes

[Transcript]
feature      	   = mRNA:exonerate
glyph              = so_transcript
description        = 1
bgcolor            = beige
category           = Genes
key                = Exonerate predictions

[Clones]
feature      = BAC
glyph        = segments
bgcolor      = yellow
connector    = dashed
strand_arrow = 1
description  = 1
key          = Fingerprinted BACs

[TransChip1]
feature        = microarray_oligo
glyph          = wiggle_density
#glyph          = wiggle_xyplot
#graph_type     = linepoints
#point_symbol   = disc
#point_radius   = 3
height         = 30
bgcolor        = blue
category       = Genes
description    = 1
key            = Transcriptional Profile

[TransChip2]
feature        = microarray_oligo
glyph          = wiggle_xyplot
#graph_type     = linepoints
#point_symbol   = disc
#point_radius   = 3
height         = 30
bgcolor        = blue
category       = Genes
description    = 1
key            = Transcriptional Profile


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

[Translation]
glyph          = translation
global feature = 1
height         = 40
fgcolor        = purple
start_codons   = 0
stop_codons    = 1
translation    = 6frame
key            = 6-frame translation

[EST]
feature          = EST_match:est
height           = 6
glyph            = segments
draw_target      = 1
show_mismatch    = 1
canonical_strand = 1
bgcolor      = sub {
		my $feature = shift;
		my $name    = $feature->display_name;
		if ($name =~ /\.5$/) {
		   return 'red';
		} else {
		   return 'orange';
		}
	}
group_pattern     = /\.[53]$/
key               = ESTs

[Traces]
feature      = read
glyph        = trace
fgcolor      = black
bgcolor      = orange
strand_arrow = 1
height       = 6
description  = 1
a_color      = green
c_color      = blue
g_color      = black
t_color      = red
trace_height = 80
trace_prefix = http://localhost/gbrowse/tutorial/data_files/
key          = Traces

########################
# Plugin configuration
########################

[Aligner:plugin]
alignable_tracks   = EST
upcase_tracks      = CDS Motifs
upcase_default     = CDS

[Motifs:overview]
feature      = polypeptide_domain
glyph        = span
height       = 5
description  = 1
label        = 1
key          = Motifs

