# gbrowse config file for sample chado gene maps
# d.gilbert, oct03
## update 04oct;

## need these to make flybase chado compliant w/ gbrowse chado expects
#  psql -h bugbane -p 7302 -U gilbertd -d dmel_chado -f $gs/./genetic/genetic.sql
#  psql -h bugbane -p 7302 -U gilbertd -d dmel_chado -f $gf/sequence-gff-views.sql
#  psql -h bugbane -p 7302 -U gilbertd -d dmel_chado -f $gf/sequence-gff-funcs.pgsql
## also dang relation ontols missing 
## Bio::DB::Das::Chado::Segment::Feature::sub_SeqFeature
## MSG: part_of cvterm wasn't found.  is DB sane?
#  ## dang; flybase chado has the OLD cvs, with 'partof' instead of 'part_of' !!

## need to call as 'gene:toy' or other class prefix..


[GENERAL]

description = D. melanogaster (dmelr41; Chado-Pg)
header =  <h2><i>D. melanogaster</i> Genome,
  <small>Annotation Release 4.1; Feb 2005 ,
  using Chado-Pg data adaptor
  </small> </h2>


db_adaptor    = Bio::DB::Das::Chado
database      = dbi:Pg:dbname=dmel_chado;host=localhost;port=7302
# public chado dbs: dmel_chado  dmelhet_chado  dpse_chado
## also sgdlite_20040519 ; fb versions
user          = flybase
pass  =

# need long time for chado db ?? secs
request timeout = 300

## need this for flybase Chado segment lookup in Browser.pm _feature_get ...
reference class = chromosome_arm

default name = 4:100000-200000

# examples to show in the introduction
examples = 
    X  2L  2R 3L 3R 4
    chromosome_arm:4
    2L:80,000..120,000
    4:200000..500000
    plex*  Ank
    Gadfly:CG11186  FlyBase:FBan0011186

# plugins = SequenceDumper FastaDumper RestrictionAnnotator

cache_overview = 360
cachedir = 360

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


# Default glyph settings
glyph       = generic
height      = 8
bgcolor     = cyan
fgcolor     = cyan
label density = 25
bump density  = 10000

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

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

# default width of detailed view (pixels)
default width = 800
default features =  Genes 

# max and default segment sizes for detailed view
max segment     = 500000
default segment = 50000

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

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

           

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

language = en

# a footer
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>  For other questions, send
	mail to <a href="mailto:lstein@cshl.org">lstein@cshl.org</a>.
	</TD>
	</TR>
	</table>
	<hr>
	<pre>$Id: 01.dmel_chado_ch.conf,v 1.0   gilbertd Exp $</pre>

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

### TRACK CONFIGURATION ####
# the remainder of the sections configure individual tracks

[Genes]
feature      = gene
# glyph        = transcript2
glyph        = segments
stranded     = 1
base         = 1
fgcolor      = red
height       = 5
linewidth    = 2
key          = gene
# description  = sub{my $self = shift;
#                    my @syns = $self->synonyms;
#                    my $list = join(", ",@syns);
#                    return $list; }

[transcript]
feature      = mRNA
#glyph        = transcript
glyph         = transcript2
stranded     = 1
height       = 6
key          = Transcript
citation     = This track shows spliced transcripts
# description  = sub{my $self = shift;
#                    my @syns = $self->synonyms;
#                    my $list = join(", ",@syns);
#                    return $list; }

[Alignment]
feature      = match
glyph        = segments
bgcolor      = limegreen
fgcolor      = black
height       = 4
stranded     = 1
connector    = solid
key          = Generic alignment
citation     = This feature show similarity alignments and HSPs

[tRNA]
feature      = tRNA
bgcolor      = white
fgcolor      = black
curatedexon  = slateblue
fontcolor    = slateblue
height       = 3
key          = tRNAs

[noncodingRNA]
feature      = ncRNA snoRNA snRNA
glyph        = generic
bgcolor      = peachpuff
height       = 4
stranded     = 1
key          = Various non coding RNAs

[golden]
feature      = golden_path_region
glyph        = generic
bgcolor      = lightblue
height       = 3
key          = Golden path tiles

[transposable]
feature      = transposable_element
glyph        = generic
bgcolor      = blue
height       = 4
key          = Transposable element

.
