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|
use CGI 'escape','img';
# here's the root of all our stuff
$ROOT = '/perl/ace/elegans';
$WB = '/wormbase'; # The root is at the top level
# ========= $NAME =========
# symbolic name of the database (defaults to name of file, lowercase)
$NAME = 'elegans';
# ========= $HOST =========
# name of the host to connect to
#$HOST = 'brie2.cshl.org';
#$HOST = 'stein.cshl.org';
$HOST = 'localhost';
#$HOST = 'brie.cshl.org';
# ========= $PORT =========
# Port number to connect to
$PORT = 2005;
# ========= $STYLESHEET =========
# stylesheet to use
$STYLESHEET = "$WB/stylesheets/wormdb.css";
# ========= $PICTURES ==========
# Where to write temporary picture files to:
# The URL and the physical location, which must be writable
# by the web server.
@PICTURES = ('/ace_images' => '/var/tmp/ace_images');
# This controls at what point the "pic" script should stop making individually-clickable
# elements.
$MAX_IN_COLUMN = 100;
# location of random pictures to display on certain pages
$RANDOM_PICTS = "$WB/random_pic";
$PIC_SCRIPT = "$ROOT/misc/random_pic";
#========================= WORMBASE-SPECIFIC CONFIGURATION ==================
# ========== An icon to use for "home" ==========
# leaving this undefined suppresses the generation of a "home" link
# $HOME_ICON = "$ICONS/arrows/uarrw.gif";
# ========= An icon to use for searching =======
# leaving this undefined suppresses the generation of a "search" link
# $SEARCH_ICON = "$ICONS/unknown.gif";
# position of the big banner
$BANNERS = "$WB/banners";
$BANNERS = "$WB/banners";
@BANNER_SIZE = (640,56);
# fixed width for the page
$PAGEWIDTH = 660;
# position of the "cross"
$CROSS_ICON = "$WB/images/cross1.gif";
$ARROWR_ICON = "$WB/images/arrow_right.gif";
$ARROWL_ICON = "$WB/images/arrow_left.gif";
# position of neuron diagrams
$NEURON_DIAGRAMS = "$WB/cell/diagrams";
# ======== BLAST DATABASES ===========
# location of BLAST databases
$BLAST_ROOT = '/usr/local/wublast';;
$BLAST_BIN = "$BLAST_ROOT/bin/";
$BLAST_MATRIX = "$BLAST_ROOT/matrix";
$BLAST_FILTER = "$BLAST_ROOT/filter";
$BLAST_DB = "/usr/local/acedb/elegans/blast";
$BLAST_CUTOFF = 0.001;
$BLAST_MAXHITS = 20;
@BLAST_default = ('blastp' => 'WormPep');
%BLAST_labels = ('EST_Elegans' => 'elegans ESTs',
'Elegans' => 'elegans genomic',
'WormPep' => 'WormPep');
%BLAST_ok = ('blastn' => [qw/Elegans EST_Elegans/],
'tblastn' => [qw/Elegans EST_Elegans/],
'blastp' => [qw/WormPep/],
'blastx' => [qw/WormPep/]
);
# ========= $BANNER =========
# Banner HTML
# This will appear at the top of each page.
$BANNER = 'WormBase';
# ========= $FOOTER =========
# Footer HTML
# This will appear at the bottom of each page
# $FOOTER = img({-src=>"$WORMBASE/images/foot_logo.gif"});
$MY_FOOTER = a({-href=>'http://stein.cshl.org/'},
img({-border=>0,-src=>"$WB/images/foot_logo2.gif"})
);
# ========= @SEARCHES =========
# search scripts available
# NOTE: the order is important
@SEARCHES = (
basic => { name => 'Simple Search',
url => "$ROOT/searches/basic",
onimage => "$WB/buttons/basic_on.gif",
offimage => "$WB/buttons/basic_off.gif",
#width, height
size => [109,20], },
expr_search => { name => 'Expr. Pattern Search',
url => "$ROOT/searches/expr_search",
onimage => "$WB/buttons/expr_on.gif",
offimage => "$WB/buttons/expr_off.gif",
size => [147,20], },
hunter => { name => 'Gene Hunter',
url => "$ROOT/hunter/hunter.cgi",
onimage => "$WB/buttons/hunter_on.gif",
offimage => "$WB/buttons/hunter_off.gif",
size => [100,20], },
# browser => { name => 'Class Browser',
# url => "$ROOT/searches/browser",
# onimage => "$WB/buttons/browser_on.gif",
# offimage => "$WB/buttons/browser_off.gif",
# size => [100,20], },
blast => { name => 'Blast Search',
url => "$ROOT/searches/blast",
onimage => "$WB/buttons/blast_on.gif",
offimage => "$WB/buttons/blast_off.gif",
size => [99,20], },
advanced => { name => 'Advanced Search',
url => "$ROOT/searches/query",
onimage => "$WB/buttons/advanced_on.gif",
offimage => "$WB/buttons/advanced_off.gif",
size => [129,20], },
atlas => { name => 'Worm Atlas',
url => "$WB/atlas/atlas.html",
onimage => "$WB/buttons/atlas_on.gif",
offimage => "$WB/buttons/atlas_off.gif",
size => [46,20], },
);
# ========= %HOME =========
# Home page URL
@HOME = (
'http://www.wormbase.org' => 'WormBase home'
);
@HOME_BUTTON = ("$WB/buttons/home_bottom.gif" => [20,56]);
# ========= %DISPLAYS =========
%DISPLAYS = (
gene => {'url' => "$ROOT/gene/locus",
'label' => 'Gene Report'},
cell => {'url' => "$ROOT/cell/cell.cgi",
'label' => 'Cell Summary'},
pedigree => {'url' => "$ROOT/cell/pedigree",
'label' => 'Pedigree Browser'},
mappingdata => {'url' => "$ROOT/gene/mapping_data",
'label' => 'Map Data'},
biblio => {'url' => "$ROOT/misc/biblio",
'label' => 'Bibliography'},
nearby_genes => {'url' =>"$ROOT/gene/genetable#pos",
'label' => 'Nearby Genes'},
geneapplet => {'url' =>"$ROOT/gene/geneapplet",
'label' => 'Interactive Map'},
hunter => {'url' =>"$ROOT/hunter/hunter.cgi",
'label' => 'Genome Hunter'},
sequence => { 'url' => "$ROOT/seq/sequence",
'label' => 'Sequence Report'},
author => { 'url' => "$ROOT/misc/author",
'label' => 'Author Info'},
biblio => {'url' => "$ROOT/misc/biblio",
'label' => 'Bibliography'},
clone => {'url' => "$ROOT/seq/clone",
'label' => 'Clone Report'},
paper => {'url' => "$ROOT/misc/paper",
'label' => 'Citation'},
laboratory => { 'url' => "$ROOT/misc/laboratory",
'label' => 'Lab Listing'},
expr_pattern => { 'url' => "$ROOT/gene/expression",
'label' => 'Expression Pattern'},
tree => { 'url' => "$ROOT/misc/etree",
'label' => 'Tree Display'},
xml => { 'url' => "$ROOT/misc/xml",
'label' => 'XML Dump'},
pic => { 'url' => "$ROOT/misc/epic",
'label' => 'Graphic Display'},
align => { 'url' => "$ROOT/seq/align",
'label' => 'alignment'},
);
# ========= %CLASSES =========
# displays to show
%CLASSES = (
# There are three representations of Locus, in addition to the basic ones
Locus => [ qw/gene mappingdata nearby_genes hunter biblio geneapplet/ ],
# there are two representations of sequence, in addition to the basic ones
Sequence => [ qw/sequence nearby_genes hunter/ ],
# two representations of Author
Author => [ qw/author biblio/ ],
# one representation of Clone, Paper, Laboratory, and Expr_pattern
Clone => [ 'clone' ],
Paper => [ 'paper' ],
Cell => [ 'cell','pedigree' ],
Map => [ 'pic', 'geneapplet' ],
Laboratory => [ 'laboratory' ],
Expr_pattern => [ 'expr_pattern' ],
# default has special meaning
Default => [ qw/tree xml pic/ ],
);
# ========= &URL_MAPPER =========
# mapping from object type to URL. Return empty list to fall through
# to default.
sub URL_MAPPER {
my ($display,$name,$class) = @_;
# Small Ace inconsistency: Models named "#name" should be
# transduced to Models named "?name"
$name = "?$1" if $class eq 'Model' && $name=~/^\#(.*)/;
my $n = escape($name);
my $c = escape($class);
my $qs = "name=$n";
my $qsc = "name=$n&class=$c";
return (laboratory => $qs) if $class eq 'Laboratory';
return (paper => $qs) if $class eq 'Paper';
return (biblio => "$qs&class=Keyword") if $class eq 'Keyword';
return (clone => $qs ) if $class eq 'Clone';
return (gene => $qs ) if $class eq 'Locus';
return (sequence => $qs ) if $class eq 'Sequence';
return (expr_pattern => $qs) if $class eq 'Expr_pattern';
return (author => $qs ) if $class eq 'Author';
return (tree => $qsc) if $class eq 'Metabolite';
return (cell => $qs) if $class eq 'Cell';
if ($class eq 'Pathway') {
return (pic => $qsc ) if $name =~ /^\*/;
return (tree => $qsc) if $name !~ /^\*/;
}
# maps are always displayed graphically by default
return (pic => $qsc ) if $class =~ /map/i;
# pictures remain pictures
return (pic => $qsc ) if $display eq 'pic';
return (tree => $qsc );
}
# ========= Configuration information for the simple search script
@SIMPLE = ('Any' => '<i>Anything</i>',
'Accession_number' => 'Genbank Accession Number',
'Author' => 'Author',
'Cell' => 'Cell',
'Clone' => 'Clone',
'Locus' => 'Confirmed Gene',
'Genetic_map' => 'Genetic Map',
'Predicted_gene' => 'Predicted Gene',
'Sequence' => 'Sequence (any)',
'Genome_sequence', => 'Sequence (genomic)',
'Sequence_map' => 'Sequence Map',
'Strain' => 'Worm Strain',
);
# Jalview configuration information
$JALVIEW = '/applets/jalview.jar';
$JALVIEW_MAIL = 'beta.crbm.cnrs-mop.fr';
$JALVIEW_HELP = 'http://circinus.ebi.ac.uk:6543/jalview/help.html';
# Meow configuration
$MEOW_CONFIRMED = 'http://iubio.bio.indiana.edu/meow/.bin/moquery?dbid=ACEDB:';
$MEOW_PREDICTED = 'http://iubio.bio.indiana.edu/meow/.bin/moquery?dbid=ACEPRED:';
# ========= Configuration information for the feedback script
@FEEDBACK_RECIPIENTS = (
[ ' Paul Sternberg <pws@its.caltech.edu>' => 'general complaints and suggestions'=>1 ],
[ ' Lincoln Stein <lstein@cshl.org>' => 'user interface' ],
[ ' Norma Foltz <norma@caltech.edu>' => 'cells and expression patterns' ],
[ ' Jonathan Hodgkin & Sylvia Martinelli <cgc@mrc-lmb.cam.ac.uk>' => 'genetic data; gene names'],
[ ' wormbase@caltech.edu ' => 'gene regulation and interactions' ],
[ ' Sylvia Martinelli <cgc@mrc-lmb.cam.ac.uk>' => 'addresses' ],
[ ' Theresa Stiernagle <stier@biosci.cbs.umn.edu>' => 'strains, bibliographic references' ],
[ ' Richard Durbin <rd@sanger.ac.uk>' =>'systematic genome sequence analysis, acedb problems' ],
[ ' Danielle & Jean Thierry-Mieg <mieg@ncbi.nlm.nih.gov>' => 'gene structures, ESTs and new largescale datasets' ],
[ ' John Spieth <jspieth@watson.wustl.edu>' => 'St. Louis sequence annotations; gene structures' ],
[ ' worm@sanger.ac.uk' => 'Cambridge sequence annotations; gene structures' ],
[ ' Alan Coulson <alan@sanger.ac.uk> ' => 'physical map' ],
);
@FEEDBACK_CHECKED = (0); # number zero is paul
# position of the chromosome tables, in URL space
$CHROMOSOME_TABLES = "$WB/chromosomes";
$CHROMOSOME_TABLE_LENGTH = 2_000_000;
# all-important copyright statement
$COPYRIGHT = "$WB/copyright.html";
# ========= transcript script ===========
# dimensions of the transcript picture shown in the sequence screen
@TRANSCRIPT_DIMENSIONS = ($PAGEWIDTH,150);
$TRANSCRIPT_HEIGHT = 10;
# ======== geneapplet script ==========
$JADEX_PORT = 2005;
$JADEX_PATH = '/applets/jadex.jar';
$JADEX_IMAGE = "$WB/images/geneticMapApplet.gif";
# ======== promoter motif search script ==========
$PROMOTER_DB = "$WB/chromosomes/promoters.db";
|
