<opt
  name="gbrowseconf"
  date="20040826"

  db_adaptor_class = "Bio::DB::GFF"
  db_adaptor = "lucene"
  db_dsn  = "${outputpath}/lucene/"
  db_user = "flybase"
  db_password = " "

  db_adaptor_class2 = "Bio::DB::Das::Chado"
  db_adaptor1 = "dbi::mysql"
  db_adaptor2 = "dbi::Pg"
  >
 
 <!-- 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[ 
# generated gbrowse config
[GENERAL]
description = ${species} ${rel}

## option GFF xxx adaptor 
db_adaptor = ${db_adaptor_class}
db_args    = -adaptor ${db_adaptor} 
             -dsn ${db_dsn}
user       = ${db_user}
passwd     = ${db_password}

## option Pg::Chado adaptor 
# db_adaptor    = Bio::DB::Das::Chado
# database      = ${db_dsn}
## option dbi::mysql adaptor 
# adaptor     = dbi::mysql
# database    = ${db_dsn}
## option lucene adaptor
#    db_adaptor = lucene
#    db_dsn  = "${outputpath}/lucene/"

default_name = ${default_location} 
default_range = 1-500000

examples = ${default_location}  ${examples}
 
header = 
  <h1>Genome Browser: <i>${species}</i>
  <br><small>Release ${rel}; ${date}</small>
  </h1>

footer = <hr>
	<table width="100%">
	<TR>
	<TD align="LEFT" class="databody">
	For the source code for this browser, see the <a href="http://www.gmod.org">
	Generic Model Organism Database Project.</a> 
	</TD>
	</TR>
	</table>
	<hr>
	<pre>$Id: gbrowseconf.xml,v 1.5 2007-10-17 01:01:29 dongilbert Exp $</pre>

plugins = BatchDumper TextMapDumper FeatureFastaDumper FastaDumper GFFDumper 

aggregators = processed_transcript  alignment

#fixme ...
uploads = 1

#fixme ...
default features =  gene scaffold

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

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

# where to link to when user clicks in detailed view
link          = AUTO

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

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

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

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


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

language = en


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

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

# Default glyph settings
[TRACK DEFAULTS]
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
label density = 25
bump density  = 100

overview label density = 160

### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks
[DNA/GC Content]
glyph        = dna
global feature = 1
height       = 40
do_gc        = 1
fgcolor      = red
axis_color   = blue

  ]]></header>
  
  <footer  title="footer"><![CDATA[
  ]]></footer> 
  </doc>


<!-- ============   GENERIC is template for unconfigured features  =========== -->
<fdef name="GENERIC"><![CDATA[
[GENERIC]
feature  = GENERIC
glyph    = segments
bgcolor  = lightslategray
fgcolor  = black
key      = GENERIC
citation = GENERIC
#category = Analysis
]]></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
category = Genomic
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
category = Genomic
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
category = Genomic
citation     = Gene and mRNA (transcript) features  
]]></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 
category = Genomic
]]></fdef>


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

<fdef name="tRNA"><![CDATA[
[tRNA]
feature  = tRNA
glyph = transcript2
label = 1
stranded     = 1
bgcolor      = white
fgcolor      = black
curatedexon  = slateblue
fontcolor    = slateblue
key          = tRNA
category = Genomic
]]></fdef>

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


<fdef name="point_mutation"><![CDATA[
[point_mutation]
feature  = point_mutation
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = point_mutation 
citation     = point_mutation 
category = Miscellany Genomic
]]></fdef>
 
<fdef name="protein_binding_site"><![CDATA[
[protein_binding_site]
feature  = protein_binding_site
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = protein_binding_site 
citation     = protein_binding_site 
category = Miscellany Genomic
]]></fdef>

<fdef name="rescue_fragment"><![CDATA[
[rescue_fragment]
feature  = rescue_fragment
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = rescue_fragment 
citation     = rescue_fragment 
category = Miscellany Genomic
]]></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 
category = Miscellany Genomic
]]></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 
category = Miscellany Genomic
]]></fdef>

<fdef name="enhancer"><![CDATA[
[enhancer]
feature  = enhancer
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = enhancer 
citation     = enhancer 
category = Miscellany Genomic
]]></fdef>

<fdef name="aberration_junction"><![CDATA[
[aberration_junction]
feature  = aberration_junction
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = aberration_junction 
citation     = aberration_junction 
category = Miscellany Genomic
]]></fdef>

<fdef name="regulatory_region"><![CDATA[
[regulatory_region]
feature  = regulatory_region
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = regulatory_region 
citation     = regulatory_region 
category = Miscellany Genomic
]]></fdef>

<fdef name="sequence_variant"><![CDATA[
[sequence_variant]
feature  = sequence_variant
strand_arrow  = 1
bgcolor       = lightslategray
fgcolor       = lightslategray
key           = sequence_variant 
citation     = sequence_variant 
category = Miscellany Genomic
]]></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 
category = Miscellany Genomic
]]></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 
category = Analysis
]]></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 
category = Analysis
]]></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 
category = Analysis
]]></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 
category = Analysis
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) 
category = Analysis
]]></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) 
category = Analysis
]]></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) 
category = Analysis
]]></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  
category = Analysis
]]></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  
category = Analysis
]]></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) 
category = Analysis
]]></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 
category = Analysis
]]></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 
category = Genome reagents
]]></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 
category = 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
category = "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 
category = Genome reagents
]]></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  
category = Genome reagents
]]></fdef>



</opt>
