<opt
  name="gbrowseconf"
  date="20040826"
  >
 
 <!-- need to call XML::Simple w/ ${variables} below in doc
 
  ${species} ${relfull} ${date}
  ${datapath}
  ${default_location} 
  ${chromosomes} == ${examples} ??
  readConfig( 'gbrowseconfig', { Variables => \%featvars });
 
 -->
 
  <title>Gbrowse conf generator</title>
  <about>
  </about>
  

<!-- add gbrowse.conf file parts here; as per blastfiles.doc -->
  <doc name="dummy"></doc>
  
  <doc name="gbrowse" path="gff/gbrowse.conf">
  <!-- no content tag here -->
  <header title="header"><![CDATA[ 
# gbrowse config file for  genome maps

[GENERAL]
description = ${species} ${rel}
datapath    = ${gnomapdir}

browser title = Genome Browser

adaptor     = flybase::gmod::FFFdb

default_name = ${default_location} 
# X:100000-200000
default_range = 1-500000

# examples to show in the introduction
# examples =  ${examples}
chromosomes = ${examples}
 
header = 
  <!--#include virtual="/templates/header.html" -->
  <h1>FlyBase Genome Browser: <i>${species}</i>
  <br><small>Release ${rel}; ${date}</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] ------------------------
  ]]></header>
  
  <footer  title="footer"><![CDATA[
  ]]></footer> 
  </doc>




<fdef name="GENERIC"><![CDATA[
[GENERIC]
feature  = GENERIC
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = GENERIC
citation = GENERIC
keygroup = "Analysis features"
]]></fdef>



<fdef name="rev_ruler"><![CDATA[
[rev_ruler]
glyph = ruler_arrow
label = 0
no_53_label = 1
label_align = center
tick = 1
no_tick_label = 0
units = K
link =
key  = Base ruler
keygroup = "  Genomic features"
]]></fdef>

<!-- ============   Genomic features  =========== -->
<fdef name="cytoband"><![CDATA[
[cytoband]
feature = cytoband
glyph = revcomp_arrow
both = 1
label_align = center
fgcolor = black
bgcolor = black
linewidth = 2
label = 1
label density = 10000
bump = 0
bump density = 0
key  = Cytologic band
keygroup = "  Genomic features"
citation     = Cytological bands on the polytene chromosomes
link = sub { my $f=shift; my $u=$ENV{REQUEST_URI};
	my $r= $f->ref.":".$f->to_FTstring;
	$u =~ s/\?.*$//; $u .= '?name='.$r.";doexpand=1";
	return $u;
	}
]]></fdef>



<fdef name="dna"><![CDATA[
[dna]
feature       = source
glyph         = dnabases
draw_dna      = 1
strand        = forward
label         = 0
label density = 0
key           = DNA sequence
keygroup = "  Genomic features"
link =
]]></fdef>

<fdef name="gene" feature="gene mRNA"><![CDATA[
[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 '' ; }
]]></fdef>


<fdef name="CDS"><![CDATA[
[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"
]]></fdef>


<fdef name="pseudogene"><![CDATA[
[pseudogene]
feature  = pseudogene
glyph = segments
strand_arrow  = 1
fgcolor       = orange
label = 1
key           = Pseudogene
keygroup = "  Genomic features"
]]></fdef>

<fdef name="tRNA"><![CDATA[
[tRNA]
feature  = tRNA
glyph = transcript2
label = 1
stranded     = 1
bgcolor      = white
fgcolor      = black
curatedexon  = slateblue
fontcolor    = slateblue
key          = tRNA
keygroup = "  Genomic features"
citation     = These are tRNA predictions made using Sean Eddy's tRNAscan program.
]]></fdef>

<fdef name="noncodingRNA" feature="ncRNA snoRNA snRNA miscRNA"><![CDATA[
[noncodingRNA]
feature      = ncRNA snoRNA snRNA miscRNA
glyph        = transcript2
bgcolor      = peachpuff
stranded     = 1
key          = Non-coding RNAs
citation     = Non-coding RNAs: ncRNA snoRNA snRNA miscRNA
keygroup = "  Genomic features"
]]></fdef>

<fdef name="transposable_element"><![CDATA[
[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 '' ; }
]]></fdef>



<fdef name="transposable_element_insertion_site"><![CDATA[
[transposable_element_insertion_site]
feature  = transposable_element_insertion_site
glyph         = pinsertion
bgcolor       = darkturquoise
fgcolor       = darkturquoise
bump          = 1
label         = 0
key           = Transgene insertion site
citation     = Transgene insertion site (annotation DB ; Chado)
keygroup = "  Genomic features"
]]></fdef>


<!-- ============  Misc. Genomic features  =========== -->

<fdef name="polyA_site"><![CDATA[
[polyA_site]
feature  = polyA_site
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = polyA_site 
citation     = polyA_site (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>


<fdef name="point_mutation"><![CDATA[
[point_mutation]
feature  = point_mutation
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = point_mutation 
citation     = point_mutation (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
 
 
[protein_binding_site]
feature  = protein_binding_site
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = protein_binding_site 
citation     = protein_binding_site (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>

<fdef name="rescue_fragment"><![CDATA[
[rescue_fragment]
feature  = rescue_fragment
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = rescue_fragment 
citation     = rescue_fragment (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>

<fdef name="mature_peptide"><![CDATA[
[mature_peptide]
feature  = mature_peptide
glyph = segments
strand_arrow  = 1
bgcolor = palegoldenrod
fgcolor       = orange
label = 1
key  = mature_peptide
citation     = mature_peptide (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
  }
]]></fdef>

<fdef name="signal_peptide"><![CDATA[
[signal_peptide]
feature  = signal_peptide
glyph = segments
strand_arrow  = 1
bgcolor = palegoldenrod
fgcolor       = orange
label = 1
key  = signal_peptide
citation     = signal_peptide (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>

<fdef name="enhancer"><![CDATA[
[enhancer]
feature  = enhancer
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = enhancer 
citation     = enhancer (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>

<fdef name="aberration_junction"><![CDATA[
[aberration_junction]
feature  = aberration_junction
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = aberration_junction 
citation     = aberration_junction (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>

<fdef name="regulatory_region"><![CDATA[
[regulatory_region]
feature  = regulatory_region
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = regulatory_region 
citation     = regulatory_region (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>

<fdef name="sequence_variant"><![CDATA[
[sequence_variant]
feature  = sequence_variant
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = sequence_variant 
citation     = sequence_variant (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
link = sub {
  my $v=shift->name(); $v=~s/\-\d+.*$/\*/; $v=~s/\+/\?/g; return '/cgi-bin/fbannq.html?synonym='.$v;  
 }
]]></fdef>


<fdef name="DNA_motif" feature="DNA_motif RNA_motif"><![CDATA[
[DNA_motif]
feature  = DNA_motif RNA_motif
bgcolor       = plum
fgcolor       = plum
secondary     = RNA_motif
secondary_bgcolor = mediumseagreen
secondary_fgcolor = mediumseagreen
strand_arrow  = 1
bump          = 1
label         = 0
key           = DNA / RNA motif
citation     = DNA_motif and RNA_motif (annotation DB ; Chado)
keygroup = "  Misc. Genomic features"
]]></fdef>





<!-- ============  Analysis  =========== -->
<fdef name="transcription_start_site"><![CDATA[
[transcription_start_site]
feature  = transcription_start_site
glyph         = promoter
bgcolor       = purple
fgcolor       = purple
bump          = 1
label         = 0
key = Promoter prediction
citation     = Transcription promoter prediction (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>


<fdef name="processed_transcript"><![CDATA[
[processed_transcript]
feature  = processed_transcript
glyph         = processed_transcript
bgcolor       = plum
fgcolor       = plum
height       = 4
bump          = 1
label         = 0
key           = Processed transcript
citation     = processed_transcript (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>


<fdef name="protein"><![CDATA[
[protein]
feature  = protein
bgcolor       = salmon
fgcolor       = salmon
height       = 3
strand_arrow  = 1
bump          = 1
label         = 1
key           = Protein BLAST alignment
citation     = protein from BLAST alignments (annotation DB ; Chado)
keygroup = "Analysis 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 =~ /^C[GR]/ ){ return '/cgi-bin/fbannq.html?acc='.$d; }
 }
 if ($f->name() =~ /^(\w+):(\w+)/){ return '/cgi-bin/fbannq.html?DBX='.$f->name; }
 return '' ; }
   #above DBX should go to swissprot et al web db
]]></fdef>

<fdef name="repeat_region"><![CDATA[
[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 =
]]></fdef>

<fdef name="mRNA_genscan"><![CDATA[
[mRNA_genscan]
feature   = mRNA_genscan
glyph         = segments
strand_arrow  = 1
bgcolor       = tan
fgcolor       = brown
connector     = solid
bump          = 1
label         = 0
key           = Genscan prediction
citation     = Genscan (gene prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>

<fdef name="mRNA_piecegenie"><![CDATA[
[mRNA_piecegenie]
feature   = mRNA_piecegenie
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
label         = 0
key           = Genie prediction 
citation     = PieceGenie (gene prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>

<fdef name="match_fgenesh"><![CDATA[
[match_fgenesh]
feature   = match_fgenesh
glyph         = segments
strand_arrow  = 1
bgcolor       = tan
fgcolor       = brown
connector     = solid
bump          = 1
label         = 0
key           = fgenesh prediction 
citation     = match_fgenesh (gene prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>

<fdef name="match_HDP"><![CDATA[
[match_HDP]
feature   = match_HDP
glyph         = segments
strand_arrow  = 1
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
label         = 0
key           =HDP prediction 
citation     = HDP  (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>

<fdef name="match_RNAiHDP"><![CDATA[
[match_RNAiHDP]
feature   = match_RNAiHDP
glyph         = segments
strand_arrow  = 1
bgcolor       = tan
fgcolor       = brown
connector     = solid
bump          = 1
label         = 0
key           = RNAiHDP prediction 
citation     = RNAiHDP  (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>


<fdef name="tRNA_trnascan"><![CDATA[
[tRNA_trnascan]
feature   = tRNA_trnascan
glyph = transcript2
bgcolor       = yellow
fgcolor       = brown
connector     = solid
bump          = 1
label         = 0
key           = tRNAscan prediction
citation     = tRNAscan (tRNA prediction) (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>

<fdef name="transposable_element_pred"><![CDATA[
[transposable_element_pred]
feature  = transposable_element_pred
bgcolor       = tan
fgcolor       = brown
label = 1
glyph         = anchored_arrow
key           = Transposon prediction
citation     = Transposon prediction (annotation DB ; Chado)
keygroup = "Analysis features"
]]></fdef>

<!-- ============  Genome reagents  =========== -->
<fdef name="oligonucleotide"><![CDATA[
[oligonucleotide]
feature  = oligonucleotide
glyph         = generic
bgcolor       = tomato
fgcolor       = tomato
height       = 4
bump          = 0
bump density  = 1
label         = 0
label density = 0
key           = Affy Oligo
citation     = oligonucleotide (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub { my $f= shift;
 return ($f->name())?'/cgi-bin/fbannq.html?oligo='.$f->name() : ''; }
]]></fdef>


<fdef name="EST" feature="EST cDNA_clone"><![CDATA[
[EST]
feature       = EST cDNA_clone
glyph         = segments
strand_arrow  = 1
bgcolor       = lightgreen
fgcolor       = green
secondary     = cDNA_clone
secondary_bgcolor = mediumseagreen
secondary_fgcolor = mediumseagreen
key           = cDNA + EST 
citation     = cDNA_clone and EST (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub {
  my $v=shift->name();  $v=~s/[:.].*(prime|contig).*$//;  $v=~s/^(GB)[:]//;  
  return 'http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&doptcmdl=GenBank&tool=FlyBase&term='.$v;  
 }
]]></fdef>


<fdef name="blast"><![CDATA[
[blast]
feature       = blast
glyph         = alignment
bgcolor       = darkorchid
fgcolor       = darkorchid
bump          = 1
label         = 1
key           = Blast hit
height        = 8
citation      = BLAST alignment hit
keygroup = "hidden"
]]></fdef>

<fdef name="BAC"><![CDATA[
[BAC]
feature  = BAC
glyph         = extending_arrow
no_arrows     = 1
base          = 0
bgcolor       = lightslategray
fgcolor       = lightslategray
linewidth     = 2
bump          = 1
label         = 1
key           = Tiling BAC
citation     = BAC (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub { my $f= shift;
 return ($f->name())?'/cgi-bin/fbannq.html?DBX='.$f->name() : ''; }
]]></fdef>

<!--
name="golden_path"   
alt_name0 = "golden_path_region" 
alt_name1 = "golden_path_fragment" 
alt_name2 = "databank_scaffold"
alt_name3 = "scaffold"
alt_name4 = "supercontig"
-->
<fdef name="scaffold" feature="scaffold  golden_path_fragment segment"><![CDATA[
[scaffold]
## aug04 - renamed to SO equivalent golden_path; 
## sep04 - golden_path_fragment is better, or supercontig ?
feature  = scaffold golden_path_fragment 
glyph         = anchored_arrow
no_arrows     = 1
base          = 0
fgcolor       = black
bgcolor       = black
linewidth     = 2
bump          = 1
label         = 1
height        = 4
key           = GenBank Scaffold
citation     = genbank submission unit, a golden_path_fragment  (annotation DB ; Chado)
keygroup = " Genome reagents"
link = sub { my $f= shift;
 return ($f->name())?'/cgi-bin/fbannq.html?ARM='.$f->name() : ''; }
]]></fdef>



<!-- ============  Cytology mapped  =========== -->

<fdef name="cytobreakpoint_other"><![CDATA[
[cytobreakpoint_other]
feature       = cytobreakpoint_other
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #8888FF
bump          = 1
label         = 1
key						= Other breakpoints (cytol.)
citation     	= Other breakpoints (cytology mapped)
height        = 4
keygroup 			= "Cytology mapped features"
]]></fdef>

<fdef name="cytodeleted_segment"><![CDATA[
[cytodeleted_segment]
feature       = cytodeleted_segment
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #ff00aa
bump          = 1
label         = 1
key						= Deleted segments (cytol.)
citation     	= Deleted segments (cytology mapped)
height        = 2
keygroup 			= "Cytology mapped features"
]]></fdef>

<fdef name="cytoduplicated_segment"><![CDATA[
[cytoduplicated_segment]
feature       = cytoduplicated_segment
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #88FF88
bump          = 1
label         = 1
key						= Duplicated segments (cytol.)
citation     	= Duplicated segments (cytology mapped)
height        = 2
keygroup 			= "Cytology mapped features"
]]></fdef>

<fdef name="cytobreakpoint_inv"><![CDATA[
[cytobreakpoint_inv]
feature       = cytobreakpoint_inv
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
connector_color = #FF9900
bump          = 1
label         = 1
key						= Inversion breakpoints (cytol.)
citation     	= Inversion breakpoints (cytology mapped)
height        = 4
keygroup 			= "Cytology mapped features"
]]></fdef>

<fdef name="cytobreakpoint_ttp"><![CDATA[
[cytobreakpoint_ttp]
feature       = cytobreakpoint_ttp
glyph         = cytobar
bgcolor       = lightslategray
fgcolor       = lightslategray
connector 		= dashed
bump          = 1
label         = 1
key						= Translocations & Transpositions (cytol.)
citation     	= Translocation & Transposition breakpoints (cytology mapped)
height        = 4
keygroup 			= "Cytology mapped features"
]]></fdef>

<fdef name="cytoins"><![CDATA[
[cytoins]
feature       = cytoins
glyph         = cytobar
connector_color = #ffbb00
bgcolor       = lightslategray
fgcolor       = lightslategray
connector = dashed
bump          = 1
label         = 1
key	= Transgene insertion (cytol.)
citation     = Chromosomal Insertion (cytologically mapped; CytoSearch DB)
height        = 2
keygroup 			= "Cytology mapped features"
]]></fdef>

<fdef name="cytogene"><![CDATA[
[cytogene]
feature       = cytogene
glyph         = cytobar
connector = dashed
connector_color = #ffaa00
bgcolor       = lightslategray
fgcolor       = lightslategray
connector = dashed
bump          = 1
label         = 1
key           = Gene (recomb. only)
citation      = Genes mapped by cytology/recombination data only (possible orphans; cytologically mapped; CytoSearch DB)
height        = 4
keygroup = "Cytology mapped features"
]]></fdef>

</opt>
