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

               Name of the external DB to which the align features
               should be restricted.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    : @feats = @{
                  $adaptor->fetch_all_by_Slice_and_external_db( $slice,
                    'EMBL' ) };
  Description: Returns a listref of features created from the
               database which are on the Slice $slice and associated
               with external DB $external_db_name.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : thrown if $external_db_name is not defined or if
               the subclass does not return a table alias for the
               external_db table from _tables()
  Caller     : general
  Status     : At Risk

=cut

sub fetch_all_by_Slice_and_external_db {
  my ( $self, $slice, $external_db_name, $logic_name ) = @_;

  if ( !defined($external_db_name) ) {
    throw("Need name of external DB to restrict to");
  }

  my @join_tables = $self->_tables();

  my $edb_alias;
  foreach my $join_table (@join_tables) {
    my ( $table, $table_alias ) = @{$join_table};
    if ( $table eq 'external_db' ) {
      $edb_alias = $table_alias;
      last;
    }
  }

  if ( !defined($edb_alias) ) {
    throw("Can not find alias for external_db table");
  }

  my $constraint = sprintf( "%s.db_name = %s",
                            $edb_alias,
                            $self->dbc()->db_handle()
                              ->quote( $external_db_name, SQL_VARCHAR )
  );

  return
    $self->fetch_all_by_Slice_constraint( $slice, $constraint,
                                          $logic_name );
} ## end sub fetch_all_by_Slice_and_external_db

=head2 fetch_all_by_Slice_and_pid

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice from which to obtain align features.
  Arg [2]    : (optional) float $pid 
               A lower bound for the percentage identity of features
               to obtain.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    : @feats =
                 @{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };
  Description: Returns a listref of features created from the
               database which are on the Slice $slice and with a
               percentage identity greater than $pid.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : none
  Caller     : general
  Status     : Stable

=cut

sub fetch_all_by_Slice_and_pid {
  my ( $self, $slice, $pid, $logic_name ) = @_;

  #  #get the primary table alias
  #  my @tabs = $self->_tables;
  #  my $alias = $tabs[0]->[1];

  #  if(defined $pid) {
  #    $constraint = "${alias}.perc_ident > $pid";
  #  }

  my $constraint;
  if ( defined($pid) ) {
    $constraint = sprintf( "perc_ident > %s",
                           $self->dbc()->db_handle()
                             ->quote( $pid, SQL_FLOAT ) );
  }

  return
    $self->fetch_all_by_Slice_constraint( $slice, $constraint,
                                          $logic_name );
}


=head2 fetch_all_by_hit_name

  Arg [1]    : string $hit_name
               The hit_name of the features to obtain
  Arg [2]    : (optional) string $logic_name
               The analysis logic name of the type of features to
               obtain.
  Example    : @feats =
                 @{ $adaptor->fetch_all_by_hit_name( 'AK078491.1',
                   'vertrna' ); }
  Description: Returns a listref of features created from the
               database which correspond to the given hit_name.  If
               logic name is defined, only features with an analysis
               of type $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : thrown if hit_name is not defined
  Caller     : general
  Status     : Stable

=cut

sub fetch_all_by_hit_name {
  my ( $self, $hit_name, $logic_name ) = @_;

  if ( !defined($hit_name) ) {
    throw("hit_name argument is required");