[GENERAL]

## data indexing command:
# perl -Ilib bin/lucene_bulk_load_gff.pl --java lib/java/ --create \
#  --data databases/aphid/genometemp --fasta databases/aphid/*genome.fa.gz \
#  databases/aphid/*.gff databases/aphid/*.gff.gz

description = Pea aphid 2008-06
header= <h1><small> <a href="http://insects.eugenes.org/DroSpeGe/">DroSpeGe</a> view of</small>
	Pea aphid <i>Acyrthosiphon pisum</i> genome (2008.06)</h1>

db_adaptor    = Bio::DB::GFF
db_args       = -adaptor lucene -dsn ../databases/aphid/scaffold;est;prot;pred;pred2;predevg
#      -dsn /bio/argos/work/ggb169/databases/aphid/scaffold;est;prot;pred;pred2
 
# example multi-indices, relative to DOCUMENT_ROOT
#   -dsn ../databases/drosmel/genome;chrs;wig0;tfa0

aggregators =  processed_transcript alignment 

default_name = SCAFFOLD2001:1..50000 
examples =  SCAFFOLD2001:1..50000 
 SCAFFOLD4501 SCAFFOLD9501 SCAFFOLD11501 SCAFFOLD13000 SCAFFOLD4503 SCAFFOLD14500 SCAFFOLD11502 SCAFFOLD7501
 SCAFFOLD16230 SCAFFOLD15000 SCAFFOLD15730 SCAFFOLD15230 SCAFFOLD6003 SCAFFOLD11000 SCAFFOLD2001

default features = evm gnomon aug4 pasagene  exrnasv exrtcas exrdaph

instructions section = closed
display_settings section = closed
upload_tracks section = closed

plugins = BatchDumper FeatureFastaDumper FastaDumper GFFDumper ProteinDumper
#[BatchDumper:plugin]
#[GFFDumper:plugin]
#[ProteinDumper:plugin]
#  my $furl= $surl."\?name=$fid;pid=1;plugin=ProteinDumper;plugin_do=1";

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

default width = 800

zoom levels = 100 200 1000 2500 5000 10000 25000 50000  75000
    100000 150000 200000 300000 500000 1000000

# advanced features
balloon tips  = 0
drag and drop = 1
cache time    = 1  # one hour

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

# what image widths to offer
image widths  = 450 640 800 1024

html4 = sub {
  my ($segment, $settings) = @_; return unless($segment);
  # APHIDBASE at INRA Rennes ; https://genoweb.irisa.fr/Insect/aphid/index.htm
  my %aurl= ( AphidBase_INRA => "http://genouest.org/cgi-bin/gbrowse/gbrowse/aphidbase/"
	);
  my $loc= $segment->seq_id() .":".$segment->start()."-".$segment->end();
  my $links="";
  foreach my $label (sort keys %aurl) { 
  my $url= $aurl{$label};
  $links.= "<a href='$url?name=$loc' target='altmap'>$label:$loc</a> &nbsp; .. "; 
  }
  my $ht="<center><h3 class='searchtitle'>View also at $links</h3></center>\n";
  $ht= '<h4><font color="#CC1111">'.
  '16-jun-2008 NOTICE: there is a SCAFFOLD-ID mismatch between NCBI Gnomon gene models and '.
  'the genome assembly used here. This will be corrected shortly by '.
  'changing scaffold IDs to new ones.  The gene models can be used, but scaffold IDs '.
  'in GFF location files will change soon.  </font></h4> ' .$ht;
  return $ht;
  }

title = sub { my $f= shift;
  my $loc= $f->seq_id .':'.$f->start."..".$f->end;
  my $ftype= ($f->can("method")) ? $f->method : $f->type;
  if ($ftype =~ /^match/) { $ftype= $f->source(); }
  $ftype =~ s/processed_transcript/tr/;
  my ($nm,$id);
  if($f->can("attributes")) {
    ($nm)= grep( /^\w/, $f->attributes('Name'), $f->attributes('Alias'), $f->attributes('ID'), $f->name);
    ($id)= ($f->attributes('ID'),$f->attributes('Parent'),$f->display_name()); # add Parent
  } else { $nm= $f->display_name(); }
  if($id && $nm !~ /$id/){ $nm.=" ($id)";}
  if($f->can("score")) { my $sc= $f->score; if($sc=~/\d/){ $sc=int($sc) if($sc>1); $nm .= " p=$sc";}  }
  return "$ftype:$nm $loc";
  }

[TRACK DEFAULTS]
height      = 6
bump density  = 50
# all labels are computed IDs, useless
label density  = 1
glyph    = processed_transcript
thin_utr = 1


### TRACK CONFIGURATION ####

# config for typesource
#feature = cDNA_match:pasaasm_acyr
#feature = cDNA_match:pasaval_acyr
#feature = mRNA:AUGUSTUS.4
#feature = mRNA:Chainer
#feature = mRNA:Gnomon
#feature = mRNA:SNAP
#feature = mRNA:EVM
#feature = mRNA:exonr_daph5
#feature = mRNA:exonr_nasv5
#feature = mRNA:pasagene_acyr
#feature = scaffold:acyr1

#feature = mRNA:exonr_tcas3

[cDNAasm]
feature = alignment:pasaasm_acyr
glyph   = alignment 
bgcolor  = lavender
key      = cDNA assembly: PASA
category= EST

[Name:DETAILS]
URL = sub {
  my($tag,$d)= @_;
  if ($d =~ /(asmbl_\w+)/){
    return 'http://server2.eugenes.org/cgi-bin/PASA/cgi-bin/cdnaasmbl_report.cgi'
        .'?db=pasa_acyr&compare_id=1&cdna_acc='.$1;
    }
  if ($d =~ /daphnia_g(\w+)/){
    return 'http://wfleabase.org/lucegene/report/NCBI_GNO_'.$1;
    }
  }

[pasaval]
feature = cDNA_match:pasaval_acyr
key     = cDNA/EST parts
category= EST

[pasagene]
feature = processed_transcript:pasagene_acyr
key     = cDNA genes: PASA
category= EST
link    = sub { my($f)=@_; my($d)= $f->name;
  if ($d =~ /(asmbl_\w+)/){
    return 'http://server2.eugenes.org/cgi-bin/PASA/cgi-bin/cdnaasmbl_report.cgi'
        .'?db=pasa_acyr&compare_id=1&cdna_acc='.$1;
    }
  }

[aug4]
feature = processed_transcript:AUGUSTUS.4
key     = Augustus+cDNA
category= Gene model

[processed_transcript:DETAILS]
protein = sub { my($d,$t,$f)= @_; my $n=$f->name; return "<font face='courier'>&gt;$n<br>\n$d</font>"; }
  #protein = <font face='courier'>$value</font>
Type = sub { my ($val,$tag,$f) = @_;
  my $surl= "../gbrowse/aphid/";  ## fixme, get from selfurl : CGI::url() ??
  my $fid= $f->display_name(); ##not id();
  my $furl= $surl."\?name=$fid;pid=1;plugin=ProteinDumper;plugin_do=1";
  return $val .  " &nbsp; &nbsp; ( <a href=\"$furl\">Get Protein</a> )";
  }


[aug5]
#feature = processed_transcript:AUGUSTUS.5
feature = processed_transcript:AUGUSTUS.DGIL5 
key     = Augustus+Prot+cDNA+Gnomon
category= Gene model

[gnomon]
#feature = processed_transcript:Gnomon processed_transcript:Chainer
feature = processed_transcript:Gnomon processed_transcript:RefSeq
bgcolor = sub { my $f=shift; return ($f->source() =~ /Ref/i) ? "yellow" : "turquoise"; } 
key     = Gnomon: NCBI
category= Gene model

[evm]
feature = processed_transcript:EVM.5
key	= EVidenceModeler
category= Gene model

# test 08jul23
[evg]
feature = processed_transcript:evigan
key     = Evigan
category= Gene model

[dgbest]
feature = processed_transcript:DGILbest
key     = DGIL Best Evd
category= Gene model

[snap]
feature = processed_transcript:SNAP
key     = SNAP
category= Gene model

[exrnasv]
feature = processed_transcript:exonr_nasv5
key     = Nasonia genes
category= Protein map

[exrtcas]
feature = processed_transcript:exonr_tcas3
key     = Tribolium genes
category= Protein map

[exrdaph]
feature = processed_transcript:exonr_daph5
key     = Daphnia genes
category= Protein map
link   = sub { my ($f)=@_; my($d)= $f->name();
  if ($d =~ /daphnia_g(\w+)/){
    return 'http://wfleabase.org/lucegene/report/NCBI_GNO_'.$1;
    }
  }


[dna]
glyph        = dna
global feature = 1
height       = 40
do_gc        = 1
fgcolor      = red
axis_color   = blue
nodump       = 1
category = Genome features
key = DNA/GC Content
balloon hover =