[GENERAL]
description   = Volvox Example Database
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor memory
	        -dir     '/var/www/gbrowse2/databases/volvox'

aggregators = match
	      BAC{left_end_read,right_end_read/BAC}
	      processed_transcript
	      coding
	      tprofile{tlevel}

plugins = Aligner RestrictionAnnotator

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

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

### 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_withPhylo.conf,v 1.1 2008-10-22 18:54:40 lstein Exp $</pre>

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

# 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

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

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

# 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

########################
# 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     = Examples
key          = Example features

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

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

[Alignments:30000]
glyph        = box
label        = 0

[Alignments:45000]
glyph        = box
bump         = 0

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

[Transcripts]
feature      = processed_transcript gene
glyph        = processed_transcript
bgcolor      = peachpuff
description  = 1
category     = Genes
key          = Protein-coding genes

[CDS]
feature      = coding
glyph        = cds
category     = Genes
key          = Frame usage

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

[TransChip]
feature        = tprofile
glyph          = xyplot
graph_type     = boxes
height         = 50
min_score      = 0
max_score      = 1000
scale          = right
category       = Genes
key            = Transcriptional Profile

[TransChip:region]
feature        = tprofile
glyph          = xyplot
graph_type     = boxes
height         = 50
min_score      = 0
max_score      = 1000
bgcolor        = blue
scale          = right
key            = Profile

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

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

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

[Traces]
feature      = trace
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
show_border  = 1

[PhyloAlignment]
glyph         = phylo_align
global feature = 1
height       = 40
draw_clado_left = 0
species_spacing = 1.2
species_spacing_score = 5
hide_label = 0
fgcolor      = darkblue
errcolor     = red
axis_color   = darkorange
mid_axis_color = yellow
clado_bg     = peachpuff
bg_color     = white
targ_color   = yellowgreen
ref_color    = palegoldenrod
key          = Phylogenetic Alignment
reference    = volvox
#tree_step_width = 5
tree_file    = /Users/mokada/development/gsoc/head/htdocs/gbrowse/databases/volvox/species.tre
tree_format  = newick

