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acebrowser/conf/elegans.pm  view on Meta::CPAN

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";

acebrowser/conf/elegans.pm  view on Meta::CPAN

	     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' ],