# gbrowse config file for  genome maps

[GENERAL]
description = Drosophila melanogaster dmel_hetr32b_20041025 20041002
datapath    = /bio/argos/flybase/genomes/Drosophila_melanogaster/dmel_hetr32b_20041025/gnomap

browser title = Genome Browser
help = /maps/gbrowse

# adaptor     = flybase::gmod::FFFdb
adaptor     =  

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

# examples to show in the introduction
examples =  2h: 3h: 4h: U: Xh: Yh: 

header = Genome Browser
footer = <hr>
 Adapted from GBrowse of the <a href="http://www.gmod.org/">
 Generic Model Organism Database Project.</a>

debug = 0

plugins = BatchDumper FastaDumper

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

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

# Web site configuration info
stylesheet  = /templates/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 = bottom
key bgcolor = whitesmoke
grid = 1
overview bgcolor = whitesmoke


# # where to link to when user clicks in detaild view

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

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

# 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"
link =


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


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


[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 '' ; }


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


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


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


[match:blastx:aa_SP.hyp.dros]
feature  = match:blastx:aa_SP.hyp.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SP.hyp.dros
citation = match:blastx:aa_SP.hyp.dros
keygroup = "Analysis features"
link     =


[match:blastx:aa_SP.real.dros]
feature  = match:blastx:aa_SP.real.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SP.real.dros
citation = match:blastx:aa_SP.real.dros
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.dros]
feature  = match:blastx:aa_SPTR.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.dros
citation = match:blastx:aa_SPTR.dros
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.insect]
feature  = match:blastx:aa_SPTR.insect
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.insect
citation = match:blastx:aa_SPTR.insect
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.othinv]
feature  = match:blastx:aa_SPTR.othinv
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.othinv
citation = match:blastx:aa_SPTR.othinv
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.othvert]
feature  = match:blastx:aa_SPTR.othvert
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.othvert
citation = match:blastx:aa_SPTR.othvert
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.plant]
feature  = match:blastx:aa_SPTR.plant
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.plant
citation = match:blastx:aa_SPTR.plant
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.primate]
feature  = match:blastx:aa_SPTR.primate
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.primate
citation = match:blastx:aa_SPTR.primate
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.rodent]
feature  = match:blastx:aa_SPTR.rodent
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.rodent
citation = match:blastx:aa_SPTR.rodent
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.worm]
feature  = match:blastx:aa_SPTR.worm
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.worm
citation = match:blastx:aa_SPTR.worm
keygroup = "Analysis features"
link     =


[match:blastx:aa_SPTR.yeast]
feature  = match:blastx:aa_SPTR.yeast
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_SPTR.yeast
citation = match:blastx:aa_SPTR.yeast
keygroup = "Analysis features"
link     =


[match:blastx:aa_TR.real.dros]
feature  = match:blastx:aa_TR.real.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_TR.real.dros
citation = match:blastx:aa_TR.real.dros
keygroup = "Analysis features"
link     =


[match:blastx:aa_users_i.dros]
feature  = match:blastx:aa_users_i.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:blastx:aa_users_i.dros
citation = match:blastx:aa_users_i.dros
keygroup = "Analysis features"
link     =


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


[match:groupest:na_DGC.dros]
feature  = match:groupest:na_DGC.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:groupest:na_DGC.dros
citation = match:groupest:na_DGC.dros
keygroup = "Analysis features"
link     =


[match:groupest:na_EST.all_nr.dros]
feature  = match:groupest:na_EST.all_nr.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:groupest:na_EST.all_nr.dros
citation = match:groupest:na_EST.all_nr.dros
keygroup = "Analysis features"
link     =


[match:groupest:na_EST.complete.dros]
feature  = match:groupest:na_EST.complete.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:groupest:na_EST.complete.dros
citation = match:groupest:na_EST.complete.dros
keygroup = "Analysis features"
link     =


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


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


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


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


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


[match:sim4:P_U.fa]
feature  = match:sim4:P_U.fa
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:P_U.fa
citation = match:sim4:P_U.fa
keygroup = "Analysis features"
link     =


[match:sim4:gad_mrna.r3]
feature  = match:sim4:gad_mrna.r3
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:gad_mrna.r3
citation = match:sim4:gad_mrna.r3
keygroup = "Analysis features"
link     =


[match:sim4:na_ARGsregion.dros]
feature  = match:sim4:na_ARGsregion.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_ARGsregion.dros
citation = match:sim4:na_ARGsregion.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_DGC.dros]
feature  = match:sim4:na_DGC.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_DGC.dros
citation = match:sim4:na_DGC.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_DGC.in_process.dros]
feature  = match:sim4:na_DGC.in_process.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_DGC.in_process.dros
citation = match:sim4:na_DGC.in_process.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_EST.all_nr.dros]
feature  = match:sim4:na_EST.all_nr.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_EST.all_nr.dros
citation = match:sim4:na_EST.all_nr.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_EST.complete.dros]
feature  = match:sim4:na_EST.complete.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_EST.complete.dros
citation = match:sim4:na_EST.complete.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_STS.dros]
feature  = match:sim4:na_STS.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_STS.dros
citation = match:sim4:na_STS.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_cDNA.dros]
feature  = match:sim4:na_cDNA.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_cDNA.dros
citation = match:sim4:na_cDNA.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_gadfly.dros.RELEASE2]
feature  = match:sim4:na_gadfly.dros.RELEASE2
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_gadfly.dros.RELEASE2
citation = match:sim4:na_gadfly.dros.RELEASE2
keygroup = "Analysis features"
link     =


[match:sim4:na_gb.dmel]
feature  = match:sim4:na_gb.dmel
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_gb.dmel
citation = match:sim4:na_gb.dmel
keygroup = "Analysis features"
link     =


[match:sim4:na_gb.dros]
feature  = match:sim4:na_gb.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_gb.dros
citation = match:sim4:na_gb.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_pe.dros]
feature  = match:sim4:na_pe.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_pe.dros
citation = match:sim4:na_pe.dros
keygroup = "Analysis features"
link     =


[match:sim4:na_snRNA.dros]
feature  = match:sim4:na_snRNA.dros
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:na_snRNA.dros
citation = match:sim4:na_snRNA.dros
keygroup = "Analysis features"
link     =


[match:sim4:r3_noncoding.FASTA]
feature  = match:sim4:r3_noncoding.FASTA
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:sim4:r3_noncoding.FASTA
citation = match:sim4:r3_noncoding.FASTA
keygroup = "Analysis features"
link     =


[match:tblastx:P_U.fa]
feature  = match:tblastx:P_U.fa
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:tblastx:P_U.fa
citation = match:tblastx:P_U.fa
keygroup = "Analysis features"
link     =


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


[match:tblastx:na_unigene.rodent]
feature  = match:tblastx:na_unigene.rodent
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = match:tblastx:na_unigene.rodent
citation = match:tblastx:na_unigene.rodent
keygroup = "Analysis features"
link     =


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


[pseudogene]
feature  = pseudogene
glyph = segments
strand_arrow  = 1
fgcolor       = orange
label = 1
key           = Pseudogene
keygroup = "  Genomic features"


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


[repeat_region]
feature   = repeat_region
bgcolor       = darkorchid
fgcolor       = darkorchid
height        = 3
connector     = solid
bump          = 1
strand_arrow  = 0
label         = 0
key           = Repeat region
citation     = repeat_region (annotation DB ; Chado)
keygroup = "Analysis features"
link =


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


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


[transposable_element]
feature  = transposable_element
bgcolor       = magenta
fgcolor       = magenta
label = 1
glyph         = anchored_arrow
key           = Natural transposon
citation     = Natural transposon (annotation DB ; Chado)
keygroup = "  Genomic features"
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 =~ /^TE/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
 }
 if ($f->name()) { return '/cgi-bin/fbinsq.html?symbol='.$f->name(); }
 return '' ; }