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lib/Bio/EnsEMBL/Map/DBSQL/DitagAdaptor.pm  view on Meta::CPAN

  my @ditags       = @{ $ditagadaptor->fetch_by_type("ZZ11") };

=head1 DESCRIPTION

Provides database interaction for the Bio::EnsEMBL::Map::Ditag object

=head1 METHODS

=cut

package Bio::EnsEMBL::Map::DBSQL::DitagAdaptor;
$Bio::EnsEMBL::Map::DBSQL::DitagAdaptor::VERSION = '114.0.0';
use strict;
use vars ('@ISA');

use Bio::EnsEMBL::Map::Ditag;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );

@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);


=head2 fetch_all_by_name

  Arg [1]    : ditag name
  Example    : $tag = $ditag_adaptor->fetch_by_name("U3");
  Description: Retrieves ditags from the database using the name
  Returntype : listref of Bio::EnsEMBL::Map::Ditag
  Caller     : general

=cut

sub fetch_all_by_name {
  my ($self, $tagname) = @_;

  if(!$tagname){
    throw "must be called with a name of a ditag.";
  }
  my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
                            FROM   ditag d
                            WHERE  d.name = ?");
  $sth->execute($tagname);
  my $result = $self->_fetch($sth);

  return $result;

}


=head2 fetch_by_dbID

  Arg [1]    : ditag type
  Example    : @all_tags = @{$ditag_adaptor->fetch_by_dbID(1003)};
  Description: Retrieve ditags with a certain id from the database
  Returntype : Bio::EnsEMBL::Map::Ditag
  Caller     : general

=cut

sub fetch_by_dbID {
  my ($self, $tagid) = @_;

  if(!$tagid){
    throw "must be called with the type of a ditag.";
  }
  my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
                            FROM   ditag d
                            WHERE  d.ditag_id = ?");
  $sth->execute($tagid);
  my $result = $self->_fetch($sth);

  return $result->[0];
}


=head2 fetch_all_by_type

  Arg [1]    : ditag type
  Example    : @all_tags = @{$ditag_adaptor->fetch_by_type("SME005")};
  Description: Retrieves all ditags of a certain type from the database
  Returntype : listref of Bio::EnsEMBL::Map::Ditag
  Caller     : general

=cut

sub fetch_all_by_type {
  my ($self, $tagtype) = @_;

  if(!$tagtype){
    throw "must be called with the type of a ditag.";
  }
  my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
                            FROM   ditag d
                            WHERE  d.type = ?");
  $sth->execute($tagtype);
  my $result = $self->_fetch($sth);

  return $result;
}


=head2 fetch_by_name_and_type

  Arg [1]    : ditag name
  Arg [2]    : ditag type
  Example    : $tag = $ditag_adaptor->fetch_by_name_and_type("U3", "SME005");
  Description: Retrieves ditags from the database using name/type combination
               which should be non-ambiguous
  Returntype : Bio::EnsEMBL::Map::Ditag
  Caller     : general

=cut

sub fetch_by_name_and_type {
  my ($self, $tagname, $tagtype) = @_;

  if(!$tagname or !$tagtype){
    throw "must be called with a name and type of a ditag.";
  }
  my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
                            FROM   ditag d
                            WHERE  d.name = ? and d.type = ?");
  $sth->execute($tagname, $tagtype);
  my $result = $self->_fetch($sth);

  return $result->[0];
}