# note: for this configuration to work, you will need to launch gbrowse slave
# servers on ports 8100 & 8101 on localhost.

[GENERAL]
description   = Volvox Example Database
database      = volvox1

aggregators = match
	      BAC{left_end_read,right_end_read/BAC}
	      processed_transcript
	      coding
	      tprofile{tlevel}
	      qtl{signal/peak}
	      chromosome{chromosome_band,centromere/contig}

plugins = Aligner RestrictionAnnotator ProteinDumper TestFinder

initial landmark = ctgA:1..10000

# the extra left padding makes it easier to see the mRNA labels,
# which are printed on the left by the new "gene" glyph
pad_left  = 60
pad_right = 30

# list of tracks to turn on by default
default features = ExampleFeatures
	           Motifs:overview
                   TransChip:region
		   Transcripts
		   Transcripts:overview

reference class  = Contig

# examples to show in the introduction
examples = ctgA

# "automatic" classes to try when an unqualified identifier is given
automatic classes = My_feature Motif Binding_site Match

show track categories = 0

### HTML TO INSERT AT VARIOUS STRATEGIC LOCATIONS ###
html2 = This is overridden

# max and default segment sizes for detailed view
max segment     = 100000
default segment = 5000

# size of the "region panel"
region segment = 20000

# zoom levels
zoom levels    = 100 200 1000 2000 5000 10000 20000 40000 50000 75000 100000

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

default varying = 1

# DAS reference server
das mapmaster = SELF



########################
# Named databases
########################

[volvox1:database]
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor memory
	        -dsn    $ENV{GBROWSE_DOCS}/databases/volvox/

[volvox2:database]
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor memory
	        -gff    $ENV{GBROWSE_DOCS}/databases/volvox2

[volvox3:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
	        -dsn    $ENV{GBROWSE_DOCS}/databases/volvox3

[volvox4:database]
db_adaptor    = Bio::DB::SeqFeature::Store
db_args       = -adaptor memory
	        -dsn    $ENV{GBROWSE_DOCS}/databases/volvox4



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

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

########################
# 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      = my_feature
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
category     = Genes
das category = example
citation     = These are undifferentiated features that are displayed using the generic glyph
   with a bgcolor of blue.
key          = Example features

[Motifs]
feature      = motif
glyph        = span
height       = 5
description  = 1
das category = example
category     = Proteins
key          = Example motifs

[Clones]
feature      = BAC
glyph        = segments_new
bgcolor      = yellow
strand_arrow = 1
description  = 1
das category = example
category     = Alignments
key          = Fingerprinted BACs

[Transcripts]
feature      = processed_transcript gene
glyph        = processed_transcript
bgcolor      = peachpuff
category     = Genes
key          = Protein-coding genes

[Transcripts:overview]
feature      = processed_transcript gene
glyph        = processed_transcript
bgcolor      = peachpuff
height       = 12
category     = Genes
key          = Protein-coding genes

[CDS]
feature      = coding
glyph        = cds
category     = Genes
phase_style  = 012
translation  = 3frame
key          = Frame usage

[Variation]
feature      = variation
glyph        = triangle
point        = 1
orient       = N
description = 1
restrict    = Order deny,allow
              deny from all
              allow from .cshl.edu .ebi.ed.uk
              require valid-user
key         = Variations

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

[Translation]
glyph          = translation
global feature = 1
height         = 40
fgcolor        = purple
start_codons   = 0
stop_codons    = 1
codontable     = 2
category       = Proteins
translation  = 6frame
key          = 6-frame translation

[Translation:30000]
hide = 1

[Motifs:overview]
feature      = motif
glyph        = span
height       = 5
description  = 0
label        = 1
key          = Motifs

[motif:details]
translation = sub {
		my $value = shift;
		$value =~ s/(\S{1,60})/$1\n/g;
		"<pre>$value</pre>";
	}
Note  = <a href="http://www.google.com/search?q=$value">$value</a>

[ProteinDumper:plugin]
geneticcode=12

[BindingSites]
database      = volvox2
feature       = binding_site
key           = Binding Sites

[builtin:karyotype]
chromosome    = chromosome
chrom_height  = 120
chrom_width   = 16
fgcolor       = black
bgcolor       = gneg:white gpos25:silver gpos50:gray gpos:gray
                gpos75:darkgray gpos100:black gvar:var stalk:#666666
arcradius     = 7
key           = You should never see this

[CleavageSites]
database      = volvox3
feature       = cleavage_site
key           = Cleavage Sites

[Alignments]
database       = volvox2
remote renderer = http://localhost:8100
feature      = match
glyph        = segments
category     = Alignments
das category = example
key          = Example alignments

[Alignments:30000]
glyph        = box

[Alignments:45000]
glyph        = box
label        = 0
bump         = 0

[EST]
database      = volvox4
remote renderer = http://localhost:8101
feature      = EST_match
glyph        = segments
height       = 8
draw_target   = 1
true_target = 0
label_position = left
# draw_dna = 1
show_mismatch = 1
realign = 1
canonical_strand = 1
bgcolor      = sub {
		my $feature = shift;
		my $name    = $feature->display_name;
		if ($name =~ /\.5$/) {
		   return 'red';
		} else {
		   return 'orange';
		}
	}
box_subparts = 0
group_pattern = /\.[53]$/
category     = Alignments
key          = ESTs

[EST:200]
label_position = top

# this one uses a slave renderer
[TransChip]
database       = volvox2
feature        = tprofile
remote renderer = http://localhost:8100
glyph          = xyplot
graph_type     = boxes
height         = 50
bgcolor        = orange
min_score      = 0
max_score      = 1000
scale          = right
category       = Genes
key            = Transcriptional Profile

# this one uses the main renderer
[TransChip:region]
database      = volvox2
feature        = tprofile
glyph          = xyplot
graph_type     = boxes
height         = 50
min_score      = 0
max_score      = 1000
bgcolor        = blue
scale          = right
key            = Profile



