# gbrowse config file for  genome maps

[GENERAL]
description = Drosophila pseudoobscura r1.04
datapath    = /bio/argos/flybase/genomes/Drosophila_pseudoobscura/dpse_r10_20041216/gnomap

browser title = Genome Browser

adaptor     = flybase::gmod::FFFdb

default_name = 2:1..100000 
# X:100000-200000
default_range = 1-500000

# examples to show in the introduction
# examples =  2: 2L: 2R: 2_groupMISC: 3: 3L: 3R: 3_groupMISC: 4: 4_group1: 4_group2: 4_group3: 4_group4: 4_group5: 4_groupMISC: 5_groupMISC: U: X: XL_group1a: XL_group1e: XL_group3a: XL_group3b: XL_groupMISC: XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9: XR_groupMISC: 
chromosomes = 2: 2L: 2R: 2_groupMISC: 3: 3L: 3R: 3_groupMISC: 4: 4_group1: 4_group2: 4_group3: 4_group4: 4_group5: 4_groupMISC: 5_groupMISC: U: X: XL_group1a: XL_group1e: XL_group3a: XL_group3b: XL_groupMISC: XR_group3a: XR_group5: XR_group6: XR_group8: XR_group9: XR_groupMISC: 
 
header = 
  <!--#include virtual="/templates/header.html" -->
  <h1>FlyBase Genome Browser: <i>Drosophila pseudoobscura</i>
  <br><small>Release r1.04; 20041216</small>
  </h1>

footer = <hr>
 Adapted from GBrowse of the <a href="http://www.gmod.org/">
 Generic Model Organism Database Project.</a>
  <!--#include virtual="/templates/footer.html" -->

plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper 
# GFFDumper - not as good as BatchDumper
# OligoFinder  - requires Bio::DB::GFF sql calls

uploads = 1

#fixme ...
default features = rev_ruler cytoband gene  tRNA noncodingRNA  pseudogene
  syntenic_region  scaffold BAC transposable_element 
primary_feature = gene
scale_feature = cytoband

dumpviews = FastA GenBank GFF FFF
dataviews = "Default" "Collapse All" "Expand All" 

# Web site configuration info
help        = /common/perl/gbrowse_fb/htdocs
stylesheet  = /common/perl/gbrowse_fb/gbrowse.css
buttons     = /common/perl/gbrowse_fb/images/buttons
tmpimages   = /tmp/gbrowse_fb

# max and default segment sizes for detailed view
max segment     = 1000001
default segment = 100000

## base range to expand around gene given ID lookup
expand_by = 20000

zoom levels = 100 200 1000 2000 5000 10000 20000 40000 100000 200000 500000 1000000

searchhelp = Search using Chromosome:base_start..end or FlyBase Gene ID.

#panel property
pad_left    = 20
pad_right   = 30
key_style = between
key bgcolor = whitesmoke
overview bgcolor = whitesmoke
grid = 1

# put reversed features on same track or below ?
mix_strand = 1

# # where to link to when user clicks in detaild view
# # default dummy link to get popup title view
link = sub { return "#"; }

# link = sub {
#  my $f= shift;
#  my $d= $f->primary_id() if $f->can('primary_id');
#  $d= $f->source() unless($d);
#  if ($d) {
#  if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; }
#  elsif ($d =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
#  elsif ($d =~ /\-\w+/ ){ return '/cgi-bin/fbannq.html?'.$d; }
#  }
#  if ($f->name()) { return '/cgi-bin/fbsymq.html?'.$f->name(); }
#  return '' ; }

title = sub { my $f= shift;
	return $f->class .":". $f->info . " ". $f->seq_id .':'.$f->start."..".$f->end;
	}

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


# Default glyph settings
glyph       = generic
height      = 5
bgcolor			= palegoldenrod
fgcolor     = cyan
boxcolor 		= blue
label density = 20
bump density  = 50
overview label density = 160

image widths  = 450 640 800 950 1024
default width = 800
width				= 800

#---------- end [GENERAL] ------------------------
  
[CDS]
feature  = CDS
glyph = segments
stranded     = 1
translation  = 1frame
bgcolor = palegoldenrod
fgcolor = goldenrod
label = 1
key  = CDS
citation     = Protein coding sequence (CDS or translation; annotation DB ; Chado)
keygroup = "  Genomic features"


[chromosome_arm]
feature  = chromosome_arm
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = chromosome_arm
citation = chromosome_arm
keygroup = "Analysis features"


[gene]
feature       = gene mRNA
glyph         = transcript2
bgcolor       = lightblue
fgcolor       = blue
secondary     = mRNA
secondary_bgcolor = mediumblue
secondary_fgcolor = mediumblue
highlight_color = red
higlighted = 1
label = 1
label density = 50
key           = Gene Model
keygroup = "  Genomic features"
citation     = Gene and mRNA (transcript) features  (annotation DB ; Chado)
link = sub {
 my $f= shift;
 my $d= $f->primary_id() if $f->can('primary_id');
 $d= $f->source() unless($d);
 if ($d) {
 if ($d =~ /(FB\w\w\d+)/){ return '/cgi-bin/fbidq.html?'.$1; }
 elsif ($d =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
 }
 if ($f->name()) { return '/cgi-bin/fbgenq.html?symbol='.$f->name(); }
 return '' ; }


[gene:genewise]
feature  = gene:genewise
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = gene:genewise
citation = gene:genewise
keygroup = "Analysis features"


[gene:genscan]
feature  = gene:genscan
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = gene:genscan
citation = gene:genscan
keygroup = "Analysis features"


[gene:twinscan]
feature  = gene:twinscan
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = gene:twinscan
citation = gene:twinscan
keygroup = "Analysis features"


[golden_path]
feature  = golden_path
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = golden_path
citation = golden_path
keygroup = "Analysis features"


[golden_path_fragment]
feature  = golden_path_fragment
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = golden_path_fragment
citation = golden_path_fragment
keygroup = "Analysis features"


[intron]
feature  = intron
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = intron
citation = intron
keygroup = "Analysis features"


[mRNA]
feature  = mRNA
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = mRNA
citation = mRNA
keygroup = "Analysis features"


[mRNA:genewise]
feature  = mRNA:genewise
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = mRNA:genewise
citation = mRNA:genewise
keygroup = "Analysis features"


[mRNA:genscan]
feature  = mRNA:genscan
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = mRNA:genscan
citation = mRNA:genscan
keygroup = "Analysis features"


[mRNA:twinscan]
feature  = mRNA:twinscan
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = mRNA:twinscan
citation = mRNA:twinscan
keygroup = "Analysis features"


[match:blastn:na_dbEST.dpse]
feature  = match:blastn:na_dbEST.dpse
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastn:na_dbEST.dpse
citation = match:blastn:na_dbEST.dpse
keygroup = "Analysis features"


[match:blastz]
feature  = match:blastz
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastz
citation = match:blastz
keygroup = "Analysis features"


[orthologous_region]
feature  = orthologous_region
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = orthologous_region
citation = orthologous_region
keygroup = "Analysis features"


[source]
feature  = source
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = source
citation = source
keygroup = "Analysis features"


[supercontig]
feature  = supercontig
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = supercontig
citation = supercontig
keygroup = "Analysis features"


[syntenic_region]
feature  = syntenic_region
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = syntenic_region
citation = syntenic_region
keygroup = "Analysis features"