[GENERAL]
description = RICE FPC (Chromosome)
db_adaptor    = Bio::DB::GFF
db_args       = -adaptor dbi::mysqlopt 
	        -dsn     dbi:mysql:database=rice_fpc_chromosome;host=localhost
user          = nobody
pass          = 

aggregators = transcript alignment orf
plugins = SequenceDumper FastaDumper RestrictionAnnotator

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

# Default glyph settings
glyph       = generic
height      = 8
bgcolor     = black
fgcolor     = black
label density = 500
bump density  = 5000

# where to link to when user clicks in detaild view
link      = sub {
                  my $feature = shift;
                  my $name = $feature->name;
                  my $type = $feature->primary_tag;
                  my $source_link;
                  my %source =( 
                     contig => "/cgi-bin/gbrowse/gbrowse?source=ricefpcctg&name=",
                     BAC => "/cgi-bin/fpc_gbrowse/clone.cgi?db=rice_fpc_chromosome&bac=", 
                     Clone => "/cgi-bin/fpc_gbrowse/clone.cgi?db=rice_fpc_chromosome&bac=",
                     marker => "/cgi-bin/fpc_gbrowse/marker.cgi?db=rice_fpc_chromosome&marker=",
                     frameworkmarker => "/cgi-bin/fpc_gbrowse/marker.cgi?db=rice_fpc_chromosome&marker=",
                     placementmarker => "/cgi-bin/fpc_gbrowse/marker.cgi?db=rice_fpc_chromosome&marker=",
                     electronicmarker => "/cgi-bin/fpc_gbrowse/marker.cgi?db=rice_fpc_chromosome&marker="
                  );
                  my $link = $source{$type}.$name;
                  return $link;
            }

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

# default width of detailed view (pixels)
default width = 800
default features = contig
                   BACs
                   Sequence_Clones
                   Markers 

# max and default segment sizes for detailed view
max segment     = 10000000
default segment = 100000

# zoom levels
zoom levels    = 100 500 1000 2000 5000 10000 20000 40000 100000 200000 500000 750000 1000000 5000000 10000000

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

# examples to show in the introduction
examples = Chr1 Chr2 Chr3 Chr4 Chr5 Chr6 Chr7 Chr8 Chr9 Chr10 Chr11 Chr12 Chr0
           ctg1
           R687 
           AP002969
           a0037O09
           AEST157

# "automatic" classes to try when an unqualified identifier is given
automatic classes = Sequence_Clones marker frameworkmarker

# 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.yeast.conf,v 1.11 2002/10/08 20:23:08 lstein 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

[contig:overview]
feature       = contig:FPC
glyph         = generic
fgcolor       = black
bgcolor       = yellow
fillcolor     = red
bump          = 1
label density = 10
height        = 4
key           = Contigs


[frameworkmarker:overview]
feature       = frameworkmarker:FPC
bgcolor       = red
glyph         = dot
fgcolor       = black
height        = 8
point         = 1
key           = Framework Marker

[contig]
feature       = contig:FPC
glyph         = generic
fgcolor       = black
bgcolor       = yellow
fillcolor     = red
bump          = 1
label density = 10
height        = 4
key           = Contigs

[Markers]
feature       = marker:FPC frameworkmarker:FPC electronicmarker:FPC placementmarker:FPC
bgcolor       = black
glyph         = dot
fgcolor       = sub { 
                      my $marker_type =  shift->primary_tag;
                      my $color;
                      $color = 'limegreen' if ( $marker_type eq 'marker' );
                      $color = 'red' if ( $marker_type eq 'frameworkmarker' ); 
                      $color = 'yellow' if ( $marker_type eq 'electronicmarker' );
                      $color = 'blue' if ( $marker_type eq 'placementmarker' );
                      return $color;
                    }
height        = 5
point         = 1
key           = Markers
citation      = Markers from FPC (Framework markers are in red, electronic markers are in yellow, placement markers are in blue and other markers are represented in green)

[Sequence_Clones]
feature       = sequenced:FPC
fgcolor       = black
bgcolor       = blue
glyph         = generic
height        = 5
link          = sub { my $name = shift->name;
                      my $link = "http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=2&form=1&term=".$name;
                      return $link;
                }
key           = Sequence
citation      = Sequence obtained from GenBank

[BACs]
feature       = BAC:FPC Clone:FPC
fgcolor       = black
bgcolor       = green
glyph         = anchored_arrow
height        = 3
label         = 1
key           = BACs
citation      = BACs from FPC