lib/CXGN/MapFactory/Cmap.pm

   1
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::MapFactory::Custom - a class to provide custom behaviour for the comparative viewer
   6
   7 =head1 DESCRIPTION
   8
   9 For the interface to be implemented, see L<CXGN::Cview::MapFactory>, and for an example, see L<CXGN::Cview::MapFactory::SGN>.
  10
  11 =head1 AUTHOR
  12
  13 Lukas Mueller <lam87@cornell.edu>
  14
  15 =cut
  16
  17 use strict;
  18
  19 package CXGN::Cview::MapFactory::Cmap;
  20
  21 use base qw| CXGN::DB::Object |;
  22
  23 use CXGN::Cview::Map::SGN::Genetic;
  24 use CXGN::Cview::Map::SGN::User;
  25 use CXGN::Cview::Map::SGN::Fish;
  26 use CXGN::Cview::Map::SGN::Sequence;
  27 use CXGN::Cview::Map::SGN::IL;
  28 use CXGN::Cview::Map::SGN::Physical;
  29 use CXGN::Cview::Map::SGN::ProjectStats;
  30 use CXGN::Cview::Map::SGN::AGP;
  31 use CXGN::Cview::Map::SGN::Contig;
  32 use CXGN::Cview::Map::GMOD::Cmap;
  33
  34 =head2 function new()
  35
  36   Synopsis:     constructor
  37   Arguments:    none
  38   Returns:      a CXGN::Cview::MapFactory object
  39   Side effects: none
  40   Description:  none
  41
  42 =cut
  43
  44 sub new {
  45     my $class = shift;
  46     my $dbh = shift;
  47
  48     my $self = $class->SUPER::new($dbh);
  49     # at this point throw away the database handle which will be to a SGN postgresql database.
  50
  51     my $mysql = DBI->connect("DBI:mysql:database=CMAP;host=localhost", "web_usr", "tomato");
  52     $self->set_dbh($mysql);
  53
  54     return $self;
  55 }
  56
  57 =head2 function create()
  58
  59   Description:  creates a map based on the hashref given, which
  60                 should either contain the key map_id or map_version_id
  61                 and an appropriate identifier. The function returns undef
  62                 if a map of the given id cannot be found/created.
  63   Example:
  64
  65 =cut
  66
  67 sub create {
  68     my $self = shift;
  69     my $args = shift;
  70
  71     my $id = 0;
  72     if (exists($args->{map_version_id})) {
  73         $id=$args->{map_version_id};
  74
  75     }
  76     elsif (exists($args->{map_id})) {
  77         $id=$args->{map_id};
  78     }
  79     else {
  80         die "Need a map_id or map_version_id key in hashref\n";
  81     }
  82
  83     print STDERR "Create: Using id = $id\n";
  84
  85     my $map = CXGN::Cview::Map::GMOD::Cmap->new($self->get_dbh(), $id);
  86
  87     return $map;
  88
  89
  90
  91 }
  92
  93 =head2 function get_all_maps()
  94
  95   Synopsis:     my @maps = $map_factory->get_all_maps();
  96   Arguments:    none
  97   Returns:      a list of all maps currently defined, as
  98                 CXGN::Cview::Map objects (and subclasses)
  99   Side effects: Queries the database for certain maps
 100   Description:
 101
 102 =cut
 103
 104 sub get_all_maps {
 105     my $self = shift;
 106     my $query = "SELECT map_set_id FROM cmap_map_set";
 107     my $sth = $self->get_dbh()->prepare($query);
 108     $sth->execute();
 109     my @maps = ();
 110     while (my ($map_id) = $sth->fetchrow_array()) {
 111         push @maps, $self->create({ map_version_id=>"cmap".$map_id} );
 112     }
 113     return @maps;
 114 }
 115
 116 sub get_system_maps {
 117     my $self = shift;
 118     return $self->get_all_maps();
 119 }
 120
 121 sub get_user_maps {
 122 }
 123
 124 return 1;