view release on metacpan or  search on metacpan

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

    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";