lib/CXGN/Cview/MapFactory.pm

   1
   2
   3
   4 =head1 NAME
   5
   6 CXGN::Cview::MapFactory - a factory object for CXGN::Cview::Map objects
   7
   8 =head1 SYNOPSYS
   9
  10  my $map_factory  = CXGN::Cview::MapFactory->new($dbh);
  11  $map = $map_factory->create({map_version_id=>"u1"});
  12
  13 =head1 DESCRIPTION
  14
  15 The MapFactory object is part of a compatibility layer that defines the data sources of the comparative mapviewer. If there are different types of maps that can be distinguished by their ids, the MapFactory should be implemented to return the right map object for the given id. Of course, the corresponding map object also needs to be implemented, using the interface defined in CXGN::Cview::Map .
  16
  17 The MapFactory constructor takes a database handle (preferably constructed using CXGN::DB::Connection object). The map objects can then be constructed using the create function, which takes a hashref as a parameter, containing either map_id or map_version_id as a key (but not both). map_ids will be converted to map_version_ids immediately. Map_version_ids are then analyzed and depending on its format, CXGN::Cview::Map object of the proper type is returned.
  18
  19 The function get_all_maps returns all maps as list of appropriate CXGN::Cview::Map::* objects.
  20
  21 For the current SGN implementation, the following identifier formats are defined and yield following corresponding map objects
  22
  23  \d+       refers to a map id in the database and yields either a
  24            CXGN::Cview::Map::SGN::Genetic (type genetic)
  25            CXGN::Cview::Map::SGN::FISH (type fish)
  26            CXGN::Cview::Map::SGN::Sequence (type sequence)
  27  u\d+      refers to a user defined map and returns:
  28            CXGN::Cview::Map::SGN::User object
  29  filepath  refers to a map defined in a file and returns a
  30            CXGN::Cview::Map::SGN::File object
  31  il\d+      refers to a population id in the phenome.population table
  32            (which must be of type IL) and returns a
  33            CXGN::Cview::Map::SGN::IL object
  34  p\d+      CXGN::Cview::Map::SGN::Physical
  35  c\d+      CXGN::Cview::Map::SGN::Contig
  36  o         CXGN::Cview::Map::SGN::ProjectStats map object
  37
  38 The actual map objects returned are defined in the CXGN::Cview::Maps namespace. Because this is really a compatibility layer, an additional namespace of the resource is appended, such that a genetic map at SGN could be defined as CXGN::Cview::Maps::SGN::Genetic . If no corresponding map is found, undef is returned.
  39
  40 =head1 AUTHOR(S)
  41
  42 Lukas Mueller (lam87@cornell.edu)
  43
  44 =head1 LICENSE
  45
  46 Refer to the L<CXGN::LICENSE> file.
  47
  48 =head1 FUNCTIONS
  49
  50 This class implements the following functions:
  51
  52 (See the superclass, CXGN::Cview::Maps, for a definition of the class interface)
  53
  54 =cut
  55
  56 package CXGN::Cview::MapFactory;
  57 use strict;
  58 use warnings;
  59 use Carp;
  60
  61 use base qw| CXGN::DB::Object |;
  62
  63
  64 our $VERSION = '2.00';
  65 $VERSION = eval $VERSION;
  66
  67 =head2 function new()
  68
  69   Synopsis:     constructor
  70   Arguments:    database handle, configuration variable hashref
  71                 the configuration hashref supports the following
  72                 hash keys:
  73                 o cview_db_backend
  74
  75                 with the following values:
  76                 o cxgn_and_cmap
  77                 o cmap
  78                 o cxgn [DEFAULT]
  79
  80   Returns:      a CXGN::Cview::MapFactory object
  81   Side effects: none
  82   Description:  none
  83
  84 =cut
  85
  86 sub new {
  87     my $class  = shift;
  88     my ($dbh, $conf_hash_ref) = @_;
  89
  90     my $db_backend = $conf_hash_ref->{cview_db_backend};
  91
  92     # figure out what map factory class we need.  if cview_db_backend
  93     # conf var is set, use that, otherwise try to use the project_name
  94     # conf var, and if that's not set then fall back to SGN
  95
  96      my $mf_name = $db_backend ?     $db_backend eq 'cxgn_and_cmap' ? 'CviewAndCmap'
  97                                       : $db_backend eq 'cmap'          ? 'Cmap'
  98                                       : $db_backend eq 'cxgn'          ? 'SGN'
  99                                       : $db_backend eq 'Cassava'       ? 'Cassava'
 100                                       : $db_backend eq 'Cacao'         ? 'Cacao'
 101                                       : $db_backend eq 'Ricebase'         ? 'Ricebase'
 102                                       : croak "invalid cview backend $db_backend"
 103                                       : 'SGN';
 104
 105 #    print STDERR "Using cview backend $mf_name (conf has is $conf_hash_ref->{cview_db_backend}\n";
 106
 107     # try to load the mapfactory class
 108     my $mf_class = __PACKAGE__."::$mf_name";
 109     eval "require $mf_class";
 110     $@ and die "error loading $mf_class:\n$@";
 111
 112     # now instantiate it, passing along the same dbh and config we got
 113     return $mf_class->new( @_ );
 114 }
 115
 116
 117
 118
 119
 120 return 1;