# gbrowse config file for flybase overview gene maps
# d.gilbert, aug02
# set for use in flybase portable server (all paths and urls are relative) 
## WARNING - gbrowse plumbing is now doing lc(key) on all config keys !


[GENERAL]
description = D. melanogaster Overview (R3.2.2)
#datapath    = /data2/fban/gnomap
datapath = /genomes/Drosophila_melanogaster/dmel_r3.2.2_10212004/gnomap
#datapath    = /data2/fban/current/gnomap
organism = D. melanogaster

# synteny tests; 04oct
synteny_idmap = dpse-synt-idmap.tsv
synteny_org = D. pseudoobscura
synteny_src = dpse_overview

#header = <h3>FlyBase Genome Browser</h3>
header = 
  <!--#include virtual="/templates/header.html" -->
  <h1>FlyBase Genome Overview: <i>D. melanogaster</i> 
  <br><small>Release 3.2.2; Oct 2004</small>
  </h1>
  
footer = <hr>
 Adapted from GBrowse of <a href="http://www.gmod.org"> 
 Generic Model Organism Database Project.</a>  
  <!--#include virtual="/templates/footer.html" -->


## expects adaptor to be subclass of Bio/DB/GFF/Adaptor/
adaptor     = flybase::gmod::FFFdb

default_name = X:
default_range = 1-30000000

# examples to show in the introduction
chromosomes = 
   X:  2L:  2R:  3L:  3R:  4: 

default features =  cytosegment syntenic_region scaffold BAC 
primary_feature = scaffold
scale_feature = cytoband
# scaffold was segment .. so term change


plugins =  
# plugins = BatchDumper TextMapDumper FastaDumper GFFDumper 
uploads = 0
dumpviews = 
# FastA GenBank GFF FFF
dataviews = 
# "Default" "Collapse All" "Expand All" "Gene Labelling On"

# Web site configuration info
# stylesheet  = /templates/gbrowse.css
# help        = /maps/gbrowse
help        = /common/perl/gbrowse_fb/htdocs
stylesheet  = /common/perl/gbrowse_fb/gbrowse.css
buttons     = /common/perl/gbrowse_fb/images/buttons
tmpimages   = /tmp/gbrowse_fb

#bac_insitu_pic = /images/lk/bac_insitu_pic
# max num bac image display (set to 0 to disable)
#max bac pic = 0

# max and default segment sizes for detailed view
max segment     = 100000000
default segment = 20000000

## base range to expand around gene given ID lookup
# expand_by = 60000
expand_by = 20000

zoom levels = 500000 1000000 5000000 10000000 20000000 30000000

searchhelp = 
# Search using Chromosome:base_start..end or FlyBase Gene ID.
  
#panel property
pad_left    = 20
pad_right   = 30
pad_top   = 10
pad_bottom   = 10
key_style = between
key bgcolor = whitesmoke
overview bgcolor = whitesmoke
grid = 0
# put reversed features on same track or below ?
mix_strand = 1


## where to link to when user clicks in detaild view -- go to detailed gbrowse 
## NOTE need proper config source name here
link = sub { my $f=shift; my $u=$ENV{REQUEST_URI}; 
	my $r= $f->ref.":".$f->to_FTstring.";doexpand=1";
	$u =~ s/\?.*$//; $u .= '?source=dmel&name='.$r;
	return $u;
	}

# title = sub { my $f=shift; return ($f->name())? $f->name(): "" ; }
# make_title in Browser should be doing this, but get only "Gene" == class?
## the perl syntax ->method||'' was causing failure !
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      = 8
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 of detailed view (pixels)
default width = 800
width				= 800

#---------- end [GENERAL] ------------------------
##? these sections seem to work only per GMOD->track not per feature ??
# bperl equates [label] with feature type

# [rev_ruler]
# glyph = ruler_arrow
# label = 0
# no_53_label = 1
# label_align = center
# tick = 1
# #both = 1
# no_tick_label = 0
# units = M
# key  = Base ruler
# keygroup = "  Genomic features"
# #height = 0
# #linewidth = 0

[cytosegment]
feature = cytoband_major
glyph = generic
# glyph = anchored_arrow
fgcolor = black
bgcolor = lightgreen
# height = 5
linewidth = 1
label = 1
label density = 10000
bump = 0
bump density = 0
label_align = center
key  = Cytology segment 
keygroup = "  Genomic features"
# link = sub { my $f=shift; my $u=$ENV{REQUEST_URI}; 
# 	my $r= $f->ref.":".$f->to_FTstring.";doexpand=1";
# 	$u =~ s/\?.*$//; $u .= '?name='.$r;
# 	# $u =~ s/\;doexpand=\d+//g; $u =~ s/(\W)(id|name)[^\;\,\+\&]*/${1}name=$r/i;
# 	return $u;
# 	}
# feature = cytoband_major cytoband
# secondary     = cytoband
# secondary_bgcolor = green
# secondary_fgcolor = green



	
[gene]
feature       = gene
glyph         = transcript2
bgcolor       = mediumblue
fgcolor       = blue
# secondary     = mRNA
# secondary_bgcolor = mediumblue
# secondary_fgcolor = mediumblue
# highlight_color = red
# higlighted = 1
label = 1
label density = 50
# height        = 6
key           = Gene  
link = sub { 
 my $f= shift; my $u='/.bin/'; 
 my $d= $f->primary_id() if $f->can('primary_id');
 $d= $f->source() unless($d);
 if ($d =~ /(FB\w\w\d+)/){ $u .= 'fbidq.html?'.$1; }
 else { $u.='fbgenq.html?symbol='.$f->name(); }
 return $u ; }
keygroup = "  Genomic features"

# [pseudogene]
# feature  = pseudogene
# glyph = segments
# #glyph         = anchored_arrow
# fgcolor       = orange
# # height        = 6
# label = 1
# key           = Pseudogene

[RNA]
feature      = tRNA ncRNA snoRNA snRNA miscRNA
glyph        = generic
bgcolor      = peachpuff
height       = 4
stranded     = 1
key          = Non-coding RNAs
keygroup = "  Genomic features"

[syntenic_region]
feature  = syntenic_region
glyph = segments
bgcolor = pink
fgcolor = darkred
label = 1
bump          = 1
bump density  = 1000
key  = Syntenic region
citation     = Syntenic_region
keygroup = "  Genomic features"
# link = sub { my $f= shift; if ($f->name()) { return '?syn='.$f->name(); } }


# [transposable_element]
# feature  = transposable_element
# # fgcolor       = violet
# bgcolor       = magenta
# fgcolor       = magenta
# label = 1
# glyph         = anchored_arrow
# # height        = 5
# key           = Transposon


# [EST]
# feature       = cDNA_clone EST
# glyph         = segments
# bgcolor       = lightgreen
# fgcolor       = green
# secondary     = cDNA_clone
# secondary_bgcolor = mediumseagreen
# secondary_fgcolor = mediumseagreen
# # bump          = 1
# key           = cDNA and EST 
# link          = http://www.fruitfly.org/cgi-bin/EST/community_query/ctgReport.pl?db=estlabtrack&id_type=0&id_value=$info
# #max_score     = 100


# [repeat_region]
# feature   = repeat_region
# glyph         = segments
# bgcolor       = darkorchid
# fgcolor       = darkorchid
# height        = 4
# connector     = solid
# bump          = 1
# label         = 0
# key           = Repeat region
# keygroup = "  Genomic features"


[BAC]
feature  = BAC
glyph         = generic
#glyph         =  extending_arrow
no_arrows     = 1
base          = 0
bgcolor       = #DD66DD
fgcolor       = black
linewidth     = 1
bump          = 1
bump density  = 1000
label         = 1
key           = Tiling BAC
keygroup = "  Genomic features"
# link = sub { my $f= shift;
#  return ($f->name())?'/cgi-bin/fbannq.html?DBX='.$f->name() : ''; }

[scaffold]
feature  = golden_path scaffold  
glyph         = generic
# glyph         = anchored_arrow
# anchored_arrow
no_arrows     = 1
#northeast     = 1
base          = 0
fgcolor       = black
bgcolor       = yellow
linewidth     = 1
bump          = 1
bump density  = 1000
label         = 1
key           = GenBank Scaffold
keygroup = "  Genomic features"
# relative_coords  = 1
# link = sub { my $f= shift;
#  return ($f->name())?'/cgi-bin/fbannq.html?ARM='.$f->name() : ''; }


### cytos

[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"

[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"

[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"

[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"

[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"

[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"

[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"