lib/CXGN/Cview/MapFactory/Cacao.pm

   1
   2 =head1 NAME
   3
   4 CXGN::Cview::MapFactory - a factory object for CXGN::Cview::Map objects
   5
   6 =head1 SYNOPSYS
   7
   8 my $map_factory  = CXGN::Cview::MapFactory->new($dbh);
   9 $map = $map_factory->create({map_version_id=>"u1"});
  10
  11 =head1 DESCRIPTION
  12
  13 see L<CXGN::Cview::MapFactory>.
  14
  15 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.
  16
  17 The function get_all_maps returns all maps as list of appropriate CXGN::Cview::Map::* objects.
  18
  19
  20 =head1 AUTHOR(S)
  21
  22 Lukas Mueller (lam87@cornell.edu)
  23
  24 =head1 VERSION
  25
  26 1.0, March 2007
  27
  28 =head1 LICENSE
  29
  30 Refer to the L<CXGN::LICENSE> file.
  31
  32 =head1 FUNCTIONS
  33
  34 This class implements the following functions:
  35
  36 =cut
  37
  38 use strict;
  39
  40 package CXGN::Cview::MapFactory::Cacao;
  41
  42 use base qw| CXGN::DB::Object |;
  43
  44 use Scalar::Util qw/blessed/;
  45
  46 use CXGN::Cview::Map::SGN::Genetic;
  47 #use CXGN::Cview::Map::SGN::User;
  48 use CXGN::Cview::Map::SGN::Fish;
  49 use CXGN::Cview::Map::SGN::Sequence;
  50 use CXGN::Cview::Map::SGN::IL;
  51 use CXGN::Cview::Map::SGN::Physical;
  52 use CXGN::Cview::Map::SGN::ProjectStats;
  53 use CXGN::Cview::Map::SGN::AGP;
  54 #use CXGN::Cview::Map::SGN::ITAG;
  55 use CXGN::Cview::Map::SGN::Contig;
  56 use CXGN::Cview::Map::SGN::Scaffold;
  57 use CXGN::Cview::Map::SGN::Image;
  58 use CXGN::Cview::Map::SGN::QTL;
  59
  60 =head2 function new()
  61
  62   Synopsis:     constructor
  63   Arguments:    a database handle
  64   Returns:      a CXGN::Cview::MapFactory::SGN object
  65   Side effects: none
  66   Description:  none
  67
  68 =cut
  69
  70 sub new {
  71     my $class = shift;
  72     my $dbh = shift;
  73     my $context = shift;
  74
  75     unless( blessed($context) && $context->isa('SGN::Context') ) {
  76         require SGN::Context;
  77         $context = SGN::Context->new();
  78     }
  79     my $self = $class->SUPER::new($dbh);
  80
  81     $self->{context}=$context;
  82
  83
  84     return $self;
  85 }
  86
  87 =head2 function create()
  88
  89   Description:  creates a map based on the hashref given, which
  90                 should either contain the key map_id or map_version_id
  91                 and an appropriate identifier. The function returns undef
  92                 if a map of the given id cannot be found/created.
  93   Example:
  94
  95 =cut
  96
  97 sub create {
  98     my $self = shift;
  99     my $hashref = shift;
 100     #print STDERR "Hashref = map_id => $hashref->{map_id}, map_version_id => $hashref->{map_version_id}\n";
 101
 102     my $c = $self->{context};
 103     my $temp_dir = $c->path_to( $c->config->{tempfiles_subdir} );
 104
 105     if (!exists($hashref->{map_id}) && !exists($hashref->{map_version_id})) {
 106         die "[CXGN::Cview::MapFactory] Need either a map_id or map_version_id.\n";
 107     }
 108     if ($hashref->{map_id} && $hashref->{map_version_id}) {
 109         die "[CXGN::Cview::MapFactory] Need either a map_id or map_version_id - not both.\n";
 110     }
 111     if ($hashref->{map_id}) {
 112         $hashref->{map_version_id}=CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), $hashref->{map_id});
 113     }
 114
 115     # now, we only deal with map_versions...
 116     #
 117     my $id = $hashref->{map_version_id};
 118
 119     #print STDERR "MapFactory: dealing with id = $id\n";
 120
 121     # if the map_version_id is purely numeric,
 122     # check if the map is in the maps table and generate the
 123     # appropriate map
 124
 125     if ($id=~/^\d+$/) {
 126         my $query = "SELECT map_version_id, map_type, map_id, short_name FROM sgn.map join sgn.map_version using(map_id) WHERE map_version_id=?";
 127         my $sth = $self->get_dbh()->prepare($query);
 128         $sth->execute($id);
 129         my ($id, $map_type) = $sth->fetchrow_array();
 130         $map_type ||= '';
 131         if ($map_type =~ /genetic/i) {
 132             return CXGN::Cview::Map::SGN::Genetic->new($self->get_dbh(), $id);
 133
 134         }
 135
 136         elsif ($map_type =~ /seq/) {
 137             print STDERR "Creating a seq map...($map_type, $id)\n";
 138             my $map = CXGN::Cview::Map::SGN::Sequence->new($self->get_dbh(), $id);
 139             $map->set_marker_link("http://gbrowse-cacao.sgn.cornell.edu/gb2/gbrowse/cacao1/?q=");
 140             $map->set_link_by_name(1);
 141             return $map;
 142         }
 143     }
 144
 145     return;
 146
 147 }
 148
 149 =head2 function get_all_maps()
 150
 151   Synopsis:
 152   Arguments:    none
 153   Returns:      a list of all maps currently defined, as
 154                 CXGN::Cview::Map objects (and subclasses)
 155   Side effects: Queries the database for certain maps
 156   Description:
 157
 158 =cut
 159
 160 sub get_all_maps {
 161     my $self = shift;
 162
 163     my @system_maps = $self->get_system_maps();
 164     my @user_maps = $self->get_user_maps();
 165     my @maps = (@system_maps, @user_maps);
 166     return @maps;
 167
 168 }
 169
 170
 171 =head2 get_system_maps
 172
 173   Usage:        my @system_maps = $map_factory->get_system_maps();
 174   Desc:         retrieves a list of system maps (from the sgn
 175                 database) as a list of CXGN::Cview::Map objects
 176   Ret:
 177   Args:
 178   Side Effects:
 179   Example:
 180
 181 =cut
 182
 183 sub get_system_maps {
 184     my $self = shift;
 185
 186     my @maps = ();
 187
 188     my $query = "SELECT map.map_id FROM sgn.map LEFT JOIN sgn.map_version USING(map_id) LEFT JOIN sgn.accession on(parent_1=accession.accession_id) LEFT JOIN sgn.organism USING(organism_id) LEFT JOIN common_name USING(common_name_id) WHERE current_version='t' ORDER by common_name.common_name";
 189     my $sth = $self->get_dbh()->prepare($query);
 190     $sth->execute();
 191
 192     while (my ($map_id) = $sth->fetchrow_array()) {
 193         my $map = $self->create({ map_id => $map_id });
 194         if ($map) { push @maps, $map; }
 195     }
 196
 197     # push il, physical, contig, and agp map
 198     #
 199     # foreach my $id ("il6.5", "il6.9", "p9", "c9", "agp", "pachy") {
 200     #   my $map = $self->create( {map_id=>$id} );
 201     #   if ($map) { push @maps, $map; }
 202     # }
 203
 204     return @maps;
 205 }
 206
 207
 208
 209 =head2 get_user_maps
 210
 211  Status:       DEPRECATED. Does nothing now, as user maps have been disabled.
 212  Usage:
 213  Desc:         retrieves the current user maps of the logged in user.
 214  Ret:          a list of CXGN::Cview::Map objects
 215  Args:         none
 216  Side Effects: none
 217  Example:
 218
 219 =cut
 220
 221 sub get_user_maps {
 222     my $self = shift;
 223     # push the maps that are specific to that user and not public, if somebody is logged in...
 224     #
 225     my @maps = ();
 226 #     my $login = CXGN::Login->new($self->get_dbh());
 227 #     my $user_id = $login->has_session();
 228 #     if ($user_id) {
 229 #       my $q3 = "SELECT user_map_id FROM sgn_people.user_map WHERE obsolete='f' AND sp_person_id=?";
 230 #       my $h3 = $self->get_dbh()->prepare($q3);
 231 #       $h3->execute($user_id);
 232 #       while (my ($user_map_id) = $h3->fetchrow_array()) {
 233 #           my $map = $self->create( {map_id=>"u".$user_map_id} );
 234
 235 #           if ($map) { push @maps, $map; }
 236 #       }
 237 #     }
 238     return @maps;
 239 }
 240
 241
 242 sub get_db_ids {
 243     my $self = shift;
 244     my $id = shift;
 245
 246     my $population_id = 6;
 247     my $reference_map_id=5;
 248
 249     if ($id=~/il(\d+)\.?(\d*)?/) {
 250         $population_id=$1;
 251         $reference_map_id=$2;
 252     }
 253     if (!$reference_map_id) { $reference_map_id=5; }
 254     if (!$population_id) { $population_id=6; }
 255     #print STDERR "Population ID: $population_id, reference_map_id = $reference_map_id\n";
 256
 257     return ($population_id, $reference_map_id);
 258 }
 259
 260 return 1;