Inheritance diagram for Bio::EnsEMBL::DBSQL::RNAProductAdaptor:

Public Member Functions
public Arrayref	fetch_all_by_Transcript ()

public Listref	fetch_all_by_external_name ()

public Arrayref	fetch_all_by_type ()

public Bio::EnsEMBL::RNAProduct	fetch_by_dbID ()

public Bio::EnsEMBL::RNAProduct	fetch_by_stable_id ()

public List	list_dbIDs ()

public void	remove ()

public Int	store ()

protected ArrayRef	_list_dbIDs ()

protected ArrayRef	_fetch_direct_query ()

protected ArrayRef	_obj_from_sth ()

protected List	_tables ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Description

This adaptor provides a means to retrieve and store
Bio::EnsEMBL::RNAProduct objects from/in a database.

RNAProduct objects only truly make sense in the context of their
transcripts so the recommended means to retrieve RNAProducts is
by retrieving the Transcript object first, and then fetching the
RNAProduct.

Synopsis

use Bio::EnsEMBL::Registry;
 
Bio::EnsEMBL::Registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);
 
$rnaproduct_adaptor =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core",
  "rnaproduct" );
 
...

Definition at line 37 of file RNAProductAdaptor.pm.

Member Function Documentation

◆ _fetch_direct_query()

protected ArrayRef Bio::EnsEMBL::DBSQL::RNAProductAdaptor::_fetch_direct_query ( )

  Arg [1]    : reference to an array consisting of:
the name of the column to use in the WHERE clause,
the value fields from that column are to be equal to,
the data type of that column (e.g. SQL_INTEGER)
  Description: PRIVATE internal method shared between public fetch methods
               in order to avoid duplication of SQL-query logic. NOT SAFE
               to be handed directly to users because in its current form
               it can be trivially exploited to inject arbitrary SQL.
  Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs
  Exceptions : throws if RNAProduct type is absent or unknown
  Caller     : internal
  Status     : At Risk (In Development)

Code:

click to view

◆ _list_dbIDs()

protected ArrayRef Bio::EnsEMBL::DBSQL::RNAProductAdaptor::_list_dbIDs ( )

  Arg[1]      : String $table
  Arg[2]      : String $column
  Example     :

$rnaproduct_adaptor->_list_dbIDs('rnaproduct', 'rnaproduct_id');

  Description : Local reimplementation to ensure multi-species RNAProducts
                are limited to their species alone
  Returntype  : ArrayRef of specified IDs
  Caller      : Internal
  Status      : Unstable

Code:

click to view

◆ _obj_from_sth()

protected ArrayRef Bio::EnsEMBL::DBSQL::RNAProductAdaptor::_obj_from_sth ( )

  Arg [1]    : DBI statement handle
  Description: PRIVATE internal method shared between public SQL-query
               methods in order to avoid duplication of object-creation
               logic.
  Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs
  Exceptions : throws if RNAProduct type is absent or unknown
  Caller     : internal
  Status     : At Risk (In Development)

Code:

click to view

◆ _tables()

protected List Bio::EnsEMBL::DBSQL::RNAProductAdaptor::_tables ( )

  Arg [1]    : none
  Description: PROTECTED implementation of superclass abstract method.
               Returns the names, aliases of the tables to use for queries.
  Returntype : list of listrefs of strings
  Exceptions : none
  Caller     : internal
  Status     : Stable

Code:

click to view

◆ fetch_all_by_external_name()

public Listref Bio::EnsEMBL::DBSQL::RNAProductAdaptor::fetch_all_by_external_name ( )

  Arg [1]    : String $external_name
               An external identifier of the RNAProduct to be obtained
  Arg [2]    : (optional) String $external_db_name
               The name of the external database from which the
               identifier originates.
  Arg [3]    : Boolean override. Force SQL regex matching for users
               who really do want to find all 'NM'
  Example    :

my @rnaproducts =
                 @{ $rp_a->fetch_all_by_external_name('MIMAT0000416') };
              my @more_rnaproducts =
                 @{ $rp_a->fetch_all_by_external_name('hsa-miR-1-__') };

  Description: Retrieves all RNAProducts which are associated with
               an external identifier such as a GO term, miRBase
               identifer, etc. Usually there will only be a single
               RNAProduct returned in the list reference, but not
               always. If no RNAProducts with the external identifier
               are found, a reference to an empty list is returned.
               SQL wildcards % and _ are supported in the $external_name
               but their use is somewhat restricted for performance reasons.
               Users that really do want % and _ in the first three characters
               should use argument 3 to prevent optimisations
  Returntype : listref of Bio::EnsEMBL::RNAProduct
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

click to view

◆ fetch_all_by_Transcript()

public Arrayref Bio::EnsEMBL::DBSQL::RNAProductAdaptor::fetch_all_by_Transcript ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
  Example    :

$rps = $rnaproduct_adaptor->fetch_by_Transcript($transcript);

  Description: Retrieves RNAProducts via their associated transcript.
               If no RNAProducts are found, an empty list is returned.
  Returntype : arrayref of Bio::EnsEMBL::RNAProducts
  Exceptions : throw on incorrect argument
  Caller     : Transcript
  Status     : Stable

Code:

click to view

◆ fetch_all_by_type()

public Arrayref Bio::EnsEMBL::DBSQL::RNAProductAdaptor::fetch_all_by_type ( )

  Arg [1]    : string $type_code
  Example    :

$rps = $rp_a->fetch_all_by_type('miRNA');

  Description: Retrieves RNAProducts via their type (e.g. miRNA, circRNA).
               If no matching RNAProducts are found, an empty list is
               returned.
  Returntype : arrayref of Bio::EnsEMBL::RNAProducts
  Exceptions : throws if type code is undefined
  Caller     : ?
  Status     : In Development

Code:

click to view

◆ fetch_by_dbID()

public Bio::EnsEMBL::RNAProduct Bio::EnsEMBL::DBSQL::RNAProductAdaptor::fetch_by_dbID ( )

  Arg [1]    : int $dbID
               The internal identifier of the RNAProduct to obtain
  Example    :

$rnaproduct = $rnaproduct_adaptor->fetch_by_dbID(1234);

  Description: This fetches a RNAProduct object via its internal id.
               This is only debatably useful since RNAProducts do
               not make much sense outside of the context of their
               Transcript.  Consider using fetch_by_Transcript instead.
  Returntype : Bio::EnsEMBL::RNAProduct, or undef if the RNAProduct is not
               found.
  Caller     : ?
  Status     : Stable

Code:

click to view

◆ fetch_by_stable_id()

public Bio::EnsEMBL::RNAProduct Bio::EnsEMBL::DBSQL::RNAProductAdaptor::fetch_by_stable_id ( )

  Arg [1]    : string $stable_id
               The stable identifier of the RNAProduct to obtain
  Example    :

$rnaproduct = $rnaproduct_adaptor->fetch_by_stable_id("ENSS00001");

  Description: This fetches a RNAProduct object via its stable id.
  Returntype : Bio::EnsEMBL::RNAProduct, or undef if the RNAProduct is not
               found.
  Caller     : ?
  Status     : Stable

Code:

click to view

◆ list_dbIDs()

public List Bio::EnsEMBL::DBSQL::RNAProductAdaptor::list_dbIDs ( )

  Arg [1]    : none
  Example    :

@rnaproduct_ids = @{$rnaproduct_adaptor->list_dbIDs()};

  Description: Gets an array of internal ids for all RNAProducts in the current db
  Returntype : list of ints
  Exceptions : none
  Caller     : ?
  Status     : Stable

Code:

click to view

◆ remove()

public void Bio::EnsEMBL::DBSQL::RNAProductAdaptor::remove ( )

  Arg [1]    : Bio::EnsEMBL::RNAProduct $rnaproduct
               The RNAProduct to be removed from the database
  Example    :

$rpID = $rp_adaptor->remove($rnaproduct, $transcript->dbID());

  Description: Removes a RNAProduct, along with all associated information
               from the database.
  Returntype : none
  Exceptions : throw on incorrect arguments
  Caller     : ?
  Status     : Stable

Code:

click to view

◆ store()

public Int Bio::EnsEMBL::DBSQL::RNAProductAdaptor::store ( )

  Arg [1]    : Bio::EnsEMBL::RNAProduct $rnaproduct
               The RNAProduct to be written to the database
  Arg [2]    : Int $transcript_dbID
               The identifier of the transcript that this RNAProduct is
               associated with
  Example    :

$rpID = $rp_adaptor->store($rnaproduct, $transcript->dbID());

  Description: Stores a RNAProduct in the database and returns the new
               internal identifier for the stored RNAProduct.
  Returntype : Int
  Exceptions : throw on incorrect arguments
  Caller     : general
  Status     : Stable

Code:

click to view

sub store {
  my ($self, $rnaproduct, $transcript_dbID) = @_;
 
  if (!ref($rnaproduct) || !$rnaproduct->isa('Bio::EnsEMBL::RNAProduct')) {
    throw("$rnaproduct is not a EnsEMBL rnaproduct - not storing");
  }
 
  my $db = $self->db();
 
  # Avoid creating duplicate entries
  if ($rnaproduct->is_stored($db)) {
    return $rnaproduct->dbID();
  }
 
  my ( $start_exon_dbID, $end_exon_dbID );
  if ( $rnaproduct->start_Exon() ) {
    $start_exon_dbID = $rnaproduct->start_Exon()->dbID();
  }
  if ( $rnaproduct->end_Exon() ) {
    $end_exon_dbID = $rnaproduct->end_Exon()->dbID();
  }
 
  # Store rnaproduct
 
  my @columns = qw{ transcript_id seq_start start_exon_id seq_end end_exon_id };
 
  my @canned_columns = ( 'rnaproduct_type_id' );
  my @canned_values
    = ( '(SELECT rnaproduct_type_id FROM rnaproduct_type WHERE code=?)' );
 
  if (defined($rnaproduct->stable_id())) {
    push @columns, 'stable_id', 'version';
 
    my $created = $db->dbc->from_seconds_to_date($rnaproduct->created_date());
    if ($created) {
      push @canned_columns, 'created_date';
      push @canned_values,  $created;
    }
 
    my $modified = $db->dbc->from_seconds_to_date($rnaproduct->modified_date());
    if ($modified) {
      push @canned_columns, 'modified_date';
      push @canned_values,  $modified;
    }
  }
 
  my $column_string = join(', ', @columns, @canned_columns);
  my $value_string  = join(', ', (q{?}) x @columns, @canned_values);
  my $store_rnaproduct_sql
    = "INSERT INTO rnaproduct ( $column_string ) VALUES ( $value_string )";
  my $rp_st = $self->prepare($store_rnaproduct_sql);
 
  $rp_st->bind_param(  1, $transcript_dbID,         SQL_INTEGER);
  $rp_st->bind_param(  2, $rnaproduct->start(),     SQL_INTEGER);
  $rp_st->bind_param(  3, $start_exon_dbID,         SQL_INTEGER);
  $rp_st->bind_param(  4, $rnaproduct->end(),       SQL_INTEGER);
  $rp_st->bind_param(  5, $end_exon_dbID,           SQL_INTEGER);
  if (defined($rnaproduct->stable_id())) {
    $rp_st->bind_param(6, $rnaproduct->stable_id(), SQL_VARCHAR);
    $rp_st->bind_param(7, $rnaproduct->version(),   SQL_INTEGER);
  }
  $rp_st->bind_param(  8, $rnaproduct->type_code(), SQL_VARCHAR);
  $rp_st->execute();
  $rp_st->finish();
 
  # Retrieve the newly assigned dbID
  my $rp_dbID = $self->last_insert_id('rnaproduct_id', undef, 'rnaproduct');
 
  # Store attributes
  $rnaproduct->synchronise_attributes();
  my $attr_adaptor = $db->get_AttributeAdaptor();
  $attr_adaptor->store_on_RNAProduct($rp_dbID,
                                     $rnaproduct->get_all_Attributes());
 
  # Store xrefs
  my $dbe_adaptor = $db->get_DBEntryAdaptor();
  for my $dbe (@{ $rnaproduct->get_all_DBEntries() }) {
    $dbe_adaptor->store($dbe, $rp_dbID, 'RNAProduct', 1);
  }
 
  # Link the rnaproduct object to its data row
  $rnaproduct->dbID($rp_dbID);
  $rnaproduct->adaptor($self);
 
  return $rp_dbID;
}

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm

Public Member Functions

Detailed Description

Description

Synopsis

Member Function Documentation

◆ _fetch_direct_query()

◆ _list_dbIDs()

◆ _obj_from_sth()

◆ _tables()

◆ fetch_all_by_external_name()

◆ fetch_all_by_Transcript()

◆ fetch_all_by_type()

◆ fetch_by_dbID()

◆ fetch_by_stable_id()

◆ list_dbIDs()

◆ remove()

◆ store()