Inheritance diagram for Bio::EnsEMBL::DBSQL::BaseAdaptor:

Public Member Functions
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

Synopsis

# base adaptor provides
 
# SQL prepare function
$adaptor->prepare("sql statement");
 
# get of root DBAdaptor object
$adaptor->db();
 
# constructor, ok for inheritence
$adaptor = Bio::EnsEMBL::DBSQL::SubClassOfBaseAdaptor->new($dbobj);

Description

This is a true base class for Adaptors in the Ensembl DBSQL
system.

Adaptors are expected to have the following functions

  $obj = $adaptor->fetch_by_dbID($internal_id);

which builds the object from the primary key of the object. This
function is crucial because it allows adaptors to collaborate relatively
independently of each other - in other words, we can change the schema
under one adaptor without too many knock on changes through the other
adaptors.

Most adaptors will also have

  $dbid = $adaptor->store($obj);

which stores the object. Currently the storing of an object also causes
the objects to set

  $obj->dbID();

correctly and attach the adaptor.

Other fetch functions go by the convention of

  \@object_array = \@{ $adaptor->fetch_all_by_XXXX($arguments_for_XXXX) };

sometimes it returns an array ref denoted by the 'all' in the name of
the method, sometimes an individual object. For example

  $gene = $gene_adaptor->fetch_by_stable_id($stable_id);

or

  \@fp = \@{ $simple_feature_adaptor->fetch_all_by_Slice($slice) };

Occassionally adaptors need to provide access to lists of ids. In this
case the convention is to go list_XXXX, such as

  \@gene_ids = \@{ $gene_adaptor->list_geneIds() };

(note: this method is poorly named)

Definition at line 71 of file BaseAdaptor.pm.

Member Function Documentation

◆ _bind_param_generic_fetch()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_bind_param_generic_fetch ( )

Undocumented method

Code:

click to view

◆ _build_id_cache()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_build_id_cache ( )

Undocumented method

Code:

click to view

◆ _can_straight_join()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_can_straight_join ( )

Undocumented method

Code:

click to view

◆ _columns()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_columns ( )

Undocumented method

Code:

click to view

◆ _default_where_clause()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( )

Undocumented method

Code:

click to view

◆ _final_clause()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( )

Undocumented method

Code:

click to view

◆ _generate_sql()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_generate_sql ( )

Undocumented method

Code:

click to view

sub _generate_sql {
  my ($self, $constraint, @input_columns) = @_;
  
  my @tabs = $self->_tables();
 
  my $extra_default_where;
 
  # Hack for feature types that needs to be restricted to species_id (in
  # coord_system).
  if (    $self->is_multispecies()
       && $self->isa('Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor')
       && !$self->isa('Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor')
       && !$self->isa('Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor') )
  {
    # We do a check to see if there is already seq_region
    # and coord_system defined to ensure we get the right
    # alias.  We then do the extra query irrespectively of
    # what has already been specified by the user.
    my %thash = map { $_->[0] => $_->[1] } @tabs;
 
    my $sr_alias =
      ( exists( $thash{seq_region} ) ? $thash{seq_region} : 'sr' );
    my $cs_alias =
      ( exists( $thash{coord_system} ) ? $thash{coord_system} : 'cs' );
 
    if ( !exists( $thash{seq_region} ) ) {
      push( @tabs, [ 'seq_region', $sr_alias ] );
    }
    if ( !exists( $thash{coord_system} ) ) {
      push( @tabs, [ 'coord_system', $cs_alias ] );
    }
 
    $extra_default_where = sprintf(
                      '%s.seq_region_id = %s.seq_region_id '
                        . 'AND %s.coord_system_id = %s.coord_system_id '
                        . 'AND %s.species_id = ?',
                      $tabs[0]->[1], $sr_alias, $sr_alias,
                      $cs_alias,     $cs_alias );
 
    $self->bind_param_generic_fetch( $self->species_id(), SQL_INTEGER );
  } ## end if ( $self->is_multispecies...)
 
  @input_columns = $self->_columns() if ! @input_columns;
  my $columns = join(', ', @input_columns);
 
  #
  # Construct a left join statement if one was defined, and remove the
  # left-joined table from the table list
  #
  my @left_join_list = $self->_left_join();
  my $left_join_prefix = '';
  my $left_join = '';
  my @tables;
  if(@left_join_list) {
    my %left_join_hash = map { $_->[0] => $_->[1] } @left_join_list;
    while(my $t = shift @tabs) {
        my $t_alias = $t->[0] . " " . $t->[1];
      if( exists $left_join_hash{ $t->[0] } || exists $left_join_hash{$t_alias}) {
        my $condition = $left_join_hash{ $t->[0] };
        $condition ||= $left_join_hash{$t_alias};
        my $syn = $t->[1];
        $left_join .=
          "\n  LEFT JOIN " . $t->[0] . " $syn ON $condition ) ";
        $left_join_prefix .= '(';
      } else {
        push @tables, $t;
      }
    }
  } else {
    @tables = @tabs;
  }
 
  my $straight_join = '';
 
  if($self->_straight_join() and $self->_can_straight_join) {
    $straight_join = "STRAIGHT_JOIN";
  }
 
  #construct a nice table string like 'table1 t1, table2 t2'
  my $tablenames = join(', ', map({ join(' ', @$_) } @tables));
 
  my $sql =
      "SELECT $straight_join $columns \n"
    . "FROM $left_join_prefix ($tablenames) $left_join";
 
  my $default_where = $self->_default_where_clause();
  my $final_clause = $self->_final_clause;
 
  if ($extra_default_where) {
    if ($default_where) {
      $default_where .= "\n AND $extra_default_where";
    } else {
      $default_where = $extra_default_where;
    }
  }
 
  #append a where clause if it was defined
  if ($constraint) {
    $sql .= "\n WHERE $constraint ";
    if ($default_where) {
      $sql .= " AND\n       $default_where ";
    }
  } elsif ($default_where) {
    $sql .= "\n WHERE $default_where ";
  }
 
  #append additional clauses which may have been defined, don't append ORDER BY twice
  if (index($final_clause, "ORDER") == -1 || index($sql, "ORDER") == -1) {
    $sql .= "\n$final_clause";
  }
  
  # FOR DEBUG:
  #printf(STDERR "SQL:\n%s\n", $sql);
  
  return $sql;
}

◆ _id_cache()

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

  Description : Used to return an instance of a support BaseCache module
                which can be used to speed up object access. The method
                also respects the DBAdaptor's no_cache() flag and will
                return undef in those situations
  Example     :

my $cache = $self->_id_cache();

  Returntype  : Bio::EnsEMBL::DBSQL::Support::BaseCache

Code:

click to view

◆ _left_join()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_left_join ( )

Undocumented method

Code:

click to view

◆ _list_dbIDs()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( )

Undocumented method

Code:

click to view

◆ _logic_name_to_constraint()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_logic_name_to_constraint ( )

Undocumented method

Code:

click to view

◆ _no_id_cache()

protected Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::_no_id_cache ( )

  Description : Flags if the ID based caching is active or not. This could be
                due to the adaptor not wanting to cache or because of
                a global no_cache() flag on the DBAdaptor instance
  Returntype  : Boolean

Code:

click to view

◆ _objs_from_sth()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_objs_from_sth ( )

Undocumented method

Code:

click to view

◆ _straight_join()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( )

Undocumented method

Code:

click to view

◆ _tables()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_tables ( )

Undocumented method

Code:

click to view

◆ _uncached_fetch_all_by_dbID_list()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_uncached_fetch_all_by_dbID_list ( )

Undocumented method

Code:

click to view

◆ _uncached_fetch_all_by_id_list()

protected ArrayRef Bio::EnsEMBL::DBSQL::BaseAdaptor::_uncached_fetch_all_by_id_list ( )

  Arg [1]    : listref of IDs
  Arg [2]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Arg [3]    : String describing the ID type.
               Valid values include dbID and stable_id. dbID is an alias for
               the primary key, while other names map directly to table columns
               of the Feature this adaptor manages.
  Arg [4]    : Boolean $numeric
               Indicates if the incoming data is to be processed as a numeric
               or as a String. If arg [3] was set to dbID then we default this to
               be true. If arg [3] was set to stable_id then we default this to
               be false.
               When not using a standard arg[3] the IDs are assumed to be Strings.
  Arg [5]    : Integer $max_size
               Control the maximum number of IDs sent to a database in a single 
               query. Defaults to 2K for Strings and 16K for integers. Only
               provide if you know *exactly* why you need to edit it.
  Example    :

 $list_of_features = $adaptor->_uncached_fetch_all_by_id_list(
                   [qw(ENSG00000101321 ENSG00000101346 ENSG00000101367)],
                   undef,
                   "stable_id", 0); #using strings
               
@section autotoc_md2 Numeric set to true because we are using numerics
               $list_of_features = $adaptor->_uncached_fetch_all_by_id_list(
                   [1,2,3,4],
                   undef,
                   "dbID", 1);
 
@section autotoc_md3 Numeric defaults to true because we are querying using dbID
               $list_of_features = $adaptor->_uncached_fetch_all_by_id_list(
                   [1,2,3,4],
                   undef,
                   "dbID");

  Description: This is a generic method used to fetch lists of features by IDs.
               It avoids caches, meaning it is best suited for block fetching.
               See fetch_all_by_dbID_list() for more info.
  Returntype : ArrayRef of Bio::EnsEMBL::Feature
  Exceptions : Thrown if a list of IDs is not supplied.
  Caller     : BaseFeatureAdaptor, BaseAdaptor and derived classes.

Code:

click to view

sub _uncached_fetch_all_by_id_list {
    my ( $self, $id_list_ref, $slice, $id_type, $numeric, $max_size ) = @_;
 
  if ( !defined($id_list_ref) || ref($id_list_ref) ne 'ARRAY' ) {
    throw("id_list list reference argument is required");
  }
 
  if ( !@{$id_list_ref} ) { return [] }
 
  # Construct a constraint like 't1.table1_id = 123'
  my @tabs = $self->_tables();
  my ( $name, $syn ) = @{ $tabs[0] };
 
  # prepare column name for query. If the id_type was
  # set to dbID then we assume the column must be
  # tablename_id e.g. gene_id. Otherwise we assume the id_type
  # is the field/column name
  my $field_name;
  if($id_type eq 'dbID') {
    $field_name = $name.'_id';
    # If numeric was not set default it to 1 since this is an int
    $numeric = 1 if ! defined $numeric;
  }
  elsif($id_type eq 'stable_id') {
    # If numeric was not set default it to 0 since this is a string
    $numeric = 0 if ! defined $numeric; 
    $field_name = $id_type;
  }
  else {
    $field_name = $id_type;
  }
 
  my $sql_data_type;
 
  # Ensuring we do not exceed MySQL's max_allowed_packet (defaults to 1MB)
  # by splitting large queries into smaller queries of at most 256KB
  # (262,144 8-bit characters)
  # If we had a numeric then really we are talking about working with
  # integers. Normal max ensembl id size is 12 plus 2 characters for
  # commas in our IN statement comes to 14. Even bloating this to 16 gives
  # a max number of 16,384 IDs (262114/16).
  # 
  if($numeric) {
    my $first_id = $id_list_ref->[0];
    if(!looks_like_number($first_id)) {
      throw "You specified that we are looking for numerics but $first_id is not a numeric";
    }
    $max_size = 16384 if ! defined $max_size;
    $sql_data_type = SQL_INTEGER;
  }
  # However when dealing with Strings those can be very large (assuming
  # 128 is the max length of a stable ID). 128 is 8x smaller than our
  # previous max expected integer so we reduce the max ids by 8. This gives
  # 2048 IDs (16384/8)
  else {
    $max_size = 2048 if ! defined $max_size;
    $sql_data_type = SQL_VARCHAR;
  }
  
  # build up unique id list, also validate on the way by
  my %id_list;
  for (@{$id_list_ref}) {
    $id_list{$_}++;
  }
  my @id_list = keys %id_list;
 
  my @out;
  my $inline = 1;
  while (@id_list) {
    my @ids;
    my $id_str;
 
    if ( scalar(@id_list) > $max_size ) {
      @ids = splice( @id_list, 0, $max_size );
    } 
    else {
      @ids     = @id_list;
      @id_list = ();
    }
    # Push off to our IN statement constructor for this work
    my $constraint = $self->generate_in_constraint(\@ids, "${syn}.${field_name}", $sql_data_type, $inline);
    push @out, @{ $self->generic_fetch($constraint, undef, $slice) };
  }
 
  return \@out;
}

◆ _uncached_fetch_by_dbID()

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_uncached_fetch_by_dbID ( )

Undocumented method

Code:

click to view

◆ bind_param_generic_fetch()

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch ( )

 Arg [1]   : (optional)  scalar $param
              This is the parameter to bind
 Arg [2]   : (optional) int $sql_type
              Type of the parameter (from DBI (:sql_types))
 Example   :

$adaptor->bind_param_generic_fetch($stable_id,SQL_VARCHAR);

$adaptor->generic_fetch();

 Description:  When using parameters for the query, will call the bind_param to avoid
               some security issues. If there are no arguments, will return the bind_parameters
 ReturnType : listref
 Exceptions:  if called with one argument

Code:

click to view

◆ db()

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

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBAdaptor $obj 
               the database this adaptor is using.
  Example    :

$db = $adaptor->db();

  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBAdaptor
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

click to view

◆ dbc()

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

  Arg [1]    : (optional) Bio::EnsEMBL::DBSQL::DBConnection $obj 
               the database this adaptor is using.
  Example    :

$db = $adaptor->db();

  Description: Getter/Setter for the DatabaseConnection that this adaptor is 
               using.
  Returntype : Bio::EnsEMBL::DBSQL::DBConnection
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

click to view

◆ fetch_all()

public Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all ( )

Undocumented method

Code:

click to view

◆ fetch_all_by_dbID_list()

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list ( )

  Arg [1]    : listref of integers $id_list
               The unique database identifiers for the features to
               be obtained.
  Arg [2]    : optional - Bio::EnsEMBL::Slice to map features onto.
  Example    :

@feats = @{$adaptor->fetch_all_by_dbID_list([1234, 2131, 982]))};

  Description: Returns the features created from the database
               defined by the the IDs in contained in the provided
               ID list $id_list.  The features will be returned
               in their native coordinate system.  That is, the
               coordinate system in which they are stored in the
               database.  In order to convert the features to a
               particular coordinate system use the transfer() or
               transform() method.  If none of the features are
               found in the database a reference to an empty list is
               returned.
  Returntype : listref of Bio::EnsEMBL::Features
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

click to view

◆ fetch_by_dbID()

public Bio::EnsEMBL::Feature Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_by_dbID ( )

  Arg [1]    : int $id
               The unique database identifier for the feature to be obtained
  Example    :

$feat = $adaptor->fetch_by_dbID(1234));

$feat = $feat->transform('contig');

  Description: Returns the feature created from the database defined by the
               the id $id.  The feature will be returned in its native
               coordinate system.  That is, the coordinate system in which it
               is stored in the database.  In order to convert it to a
               particular coordinate system use the transfer() or transform()
               method.  If the feature is not found in the database then
               undef is returned instead
  Returntype : Bio::EnsEMBL::Feature or undef
  Exceptions : thrown if $id arg is not provided
               does not exist
  Caller     : general
  Status     : Stable

Code:

click to view

◆ generate_in_constraint()

public String Bio::EnsEMBL::DBSQL::BaseAdaptor::generate_in_constraint ( )

  
  Arg [1]     : ArrayRef or Scalar $list
                List or a single value of items to be pushed into an IN statement
  Arg [2]     : Scalar $column
                Column this IN statement is being applied to. Please fully resolve the
                column.
  Arg [3]     : Scalar $param_type
                Data type which should be used when binding. Please use DBI data type symbols
  Arg [4]     : Scalar boolean $inline_variables
                Boolean to control if variables are inlined in the constraint. If
                false values are bound via bind_param_generic_fetch() (the default behaviour).

  Description : Used internally to generate a SQL constraint to restrict a query by an IN statement.
                The code generates the complete IN statement.
  Returntype  : String
  Exceptions  : If no list is supplied, the list of values is empty or no data type was given
  Caller      : general

Code:

click to view

◆ generic_count()

public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_count ( )

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Example    :

$number_feats = $a->generic_count('contig_id in (1234, 1235)');

  Description: Performs a database fetch and returns a count of those features
               found. This is analagous to generic_fetch()
  Returntype : Integer count of the elements.
  Exceptions : Thrown if there is an issue with querying the data

Code:

click to view

◆ generic_fetch()

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch ( )

  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) Bio::EnsEMBL::AssemblyMapper $mapper
               A mapper object used to remap features
               as they are retrieved from the database
  Arg [3]    : (optional) Bio::EnsEMBL::Slice $slice
               A slice that features should be remapped to
  Example    :

$fts = $a->generic_fetch('contig_id in (1234, 1235)');

  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : Thrown if there is an issue with querying the data
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
  Status     : Stable

Code:

click to view

◆ ignore_cache_override()

public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::ignore_cache_override ( )

    Description : Method to interfere with no_cache directive from Registry on
                  a per adaptor basis. This method should be called after new()
                  in order to trigger the _build_id_cache at first query.                  
    Example     :

$adaptor->ignore_cache_override(1);

<br>

    Returntype  : Boolean

Code:

click to view

◆ insert_ignore_clause()

public Bio::EnsEMBL::DBSQL::BaseAdaptor::insert_ignore_clause ( )

Code:

click to view

◆ is_multispecies()

public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies ( )

  Arg [1]    : (optional) boolean $arg
  Example    :

if ($adaptor->is_multispecies()) { }

  Description: Getter/Setter for the is_multispecies boolean of
               to use for this adaptor.
  Returntype : boolean
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

click to view

◆ last_insert_id()

public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id ( )

  Arg [1]     : (optional) $field the name of the field the inserted ID was pushed 
                into
  Arg [2]     : (optional) HashRef used to pass extra attributes through to the 
                DBD driver
  Arg [3]     : (optional) $table the name of the table to use if the adaptor
                does not implement _tables()
  Description : Delegating method which uses DBI to extract the last inserted 
                identifier. If using MySQL we just call the DBI method 
                DBI::last_insert_id() since MySQL ignores any extra
                arguments. See DBI for more information about this 
                delegated method. 
  Example     :

my $id = $self->last_insert_id('my_id'); my $other_id = $self->last_insert_id();

  Returntype  : Scalar or undef

Code:

click to view

◆ new()

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::new ( )

  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection $dbobj
  Example    :

$adaptor = new AdaptorInheritedFromBaseAdaptor($dbobj);

  Description: Creates a new BaseAdaptor object.  The intent is that this
               constructor would be called by an inherited superclass either
               automatically or through $self->SUPER::new in an overridden 
               new method.
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
  Status     : Stable

Code:

click to view

◆ prepare()

public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( )

  Arg [1]    : string $string
               a SQL query to be prepared by this adaptors database
  Example    :

$sth = $adaptor->prepare("select yadda from blabla")

  Description: provides a DBI statement handle from the adaptor. A convenience
               function so you dont have to write $adaptor->db->prepare all the
               time
  Returntype : DBI::StatementHandle
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

click to view

◆ schema_version()

public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::schema_version ( )

    Description : Returns the schema version of the currently connected
                  DBAdaptor. The subroutine also caches this value so
                  repeated calls continue to be speedy.                  
    Example     :

$adaptor->schema_version();

<br>

    Returntype  : Integer

Code:

click to view

◆ species_id()

public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( )

  Arg [1]    : (optional) int $species_id
               The internal ID of the species in a multi-species database.
  Example    :

$db = $adaptor->db();

  Description: Getter/Setter for the internal ID of the species in a
               multi-species database.  The default species ID is 1.
  Returntype : Integer
  Exceptions : none
  Caller     : Adaptors inherited from BaseAdaptor
  Status     : Stable

Code:

click to view

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

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

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _bind_param_generic_fetch()

◆ _build_id_cache()

◆ _can_straight_join()

◆ _columns()

◆ _default_where_clause()

◆ _final_clause()

◆ _generate_sql()

◆ _id_cache()

◆ _left_join()

◆ _list_dbIDs()

◆ _logic_name_to_constraint()

◆ _no_id_cache()

◆ _objs_from_sth()

◆ _straight_join()

◆ _tables()

◆ _uncached_fetch_all_by_dbID_list()

◆ _uncached_fetch_all_by_id_list()

◆ _uncached_fetch_by_dbID()

◆ bind_param_generic_fetch()

◆ db()

◆ dbc()

◆ fetch_all()

◆ fetch_all_by_dbID_list()

◆ fetch_by_dbID()

◆ generate_in_constraint()

◆ generic_count()

◆ generic_fetch()

◆ ignore_cache_override()

◆ insert_ignore_clause()

◆ is_multispecies()

◆ last_insert_id()

◆ new()

◆ prepare()

◆ schema_version()

◆ species_id()