Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::DBSQL::GOTermAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::DBSQL::GOTermAdaptor:

List of all members.


Class Summary

Description

A specialization of Bio::EnsEMBL::DBSQL::OntologyTermAdaptor,
specifically for Gene Ontology (GO) terms.  See the documentation of
Bio::EnsEMBL::DBSQL::OntologyTermAdaptor for further information.
 

Definition at line 11 of file GOTermAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected A _fetch_ancestor_chart ()
protected _fetch_synonyms_by_dbID ()
protected _final_clause ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_ancestor_term ()
public Listref fetch_all_by_child_term ()
public fetch_all_by_dbID_list ()
public Listref fetch_all_by_descendant_term ()
public Listref fetch_all_by_name ()
public Listref fetch_all_by_parent_term ()
public Bio::EnsEMBL::OntologyTerm fetch_by_accession ()
public fetch_by_dbID ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::DBSQL::GOTermAdaptor 
new ()
public DBI::StatementHandle prepare ()
public Int species_id ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]
protected A Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::_fetch_ancestor_chart ( ) [inherited]
  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.
  Description   : Given a child ontology term, returns a hash
                  structure containing its ancestor terms, up to and
                  including any root term.  Relations of the type
                  'is_a' and 'part_of' are included.
  Example       :
    my %chart = %{ $ot_adaptor->_fetch_ancestor_chart($term) };
  Return type   : A reference to a hash structure like this:
    {
      'GO:XXXXXXX' => {
        'term' =>           # ref to Bio::EnsEMBL::OntologyTerm object
        'is_a'    => [...], # listref of Bio::EnsEMBL::OntologyTerm
        'part_of' => [...], # listref of Bio::EnsEMBL::OntologyTerm
      },
      'GO:YYYYYYY' => {
        # Similarly for all ancestors,
        # and including the query term itself.
      }
    }
 
Code:
click to view
protected Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::_fetch_synonyms_by_dbID ( ) [inherited]

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::ExonAdaptor, Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor, and Bio::EnsEMBL::DBSQL::PredictionExonAdaptor.

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_list_dbIDs ( ) [inherited]

Undocumented method

Code:
click to view
protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_straight_join ( ) [inherited]

Undocumented method

Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::bind_param_generic_fetch ( ) [inherited]
 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
public Bio::EnsEMBL::DBSQL::DBAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::db ( ) [inherited]
  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
public Bio::EnsEMBL::DBSQL::DBConnection Bio::EnsEMBL::DBSQL::BaseAdaptor::dbc ( ) [inherited]
  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
public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

Code:
click to view
public Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_ancestor_term ( ) [inherited]
  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose descendant terms should be fetched.
  Description   : Given a parent ontology term, returns a list of
                  all its descendant terms, down to and including
                  any leaf terms.  Relations of the type 'is_a' and
                  'part_of' are followed.
  Example       :
    my @descendants =
      @{ $ot_adaptor->fetch_all_by_ancestor_term($term) };
  Return type   : listref of Bio::EnsEMBL::OntologyTerm
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_child_term ( ) [inherited]
  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose parent terms should be fetched.
  Description   : Given a child ontology term, returns a list of
                  its immediate parent terms.
  Example       :
    my @parents = @{ $ot_adaptor->fetch_all_by_child_term($term) };
  Return type   : listref of Bio::EnsEMBL::OntologyTerm
 
Code:
click to view
public Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_dbID_list ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_descendant_term ( ) [inherited]
  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose ancestor terms should be fetched.
  Arg [2]       : (optional) String
                  The subset within the ontolgy to which the query
                  should be restricted.  The subset may be specified as
                  a SQL pattern, e.g., "\%goslim\%" (but "goslim\%" might
                  not do what you expect), or as a specific subset name,
                  e.g., "goslim_generic".
  Arg [3]       : (optional) Boolean
                  If true (non-zero), only return the closest
                  term(s).  If this argument is true, and the
                  previous argument is left undefined, this method
                  will return the parent(s) of the given term.
  Description   : Given a child ontology term, returns a list of
                  all its ancestor terms, up to and including any
                  root term.  Relations of the type 'is_a' and
                  'part_of' are followed.  Optionally, only terms in
                  a given subset of the ontology may be returned,
                  and additionally one may ask to only get the
                  closest term(s) to the given child term.
  Example       :
    my @ancestors =
      @{ $ot_adaptor->fetch_all_by_descendant_term($term) };
  Return type   : listref of Bio::EnsEMBL::OntologyTerm
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_name ( ) [inherited]
  Arg [1]       : String, name of term, or SQL pattern
  Arg [2]       : (optional) String, name of ontology
  Description   : Fetches ontology term(s) given a name, a synonym, or a
                  SQL pattern like "\%splice_site\%"
  Example       :
    my ($term) =
      @{ $ot_adaptor->fetch_by_name( 'DNA_binding_site', 'SO' ) };
    # Will find terms in both SO and GO:
    my @terms = @{ $ot_adaptor->fetch_by_name('%splice_site%') };
  Return type   : listref of Bio::EnsEMBL::OntologyTerm
 
Code:
click to view
public Listref Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_all_by_parent_term ( ) [inherited]
  Arg [1]       : Bio::EnsEMBL::OntologyTerm
                  The term whose children terms should be fetched.
  Description   : Given a parent ontology term, returns a list of
                  its immediate children terms.
  Example       :
    my @children =
      @{ $ot_adaptor->fetch_all_by_parent_term($term) };
  Return type   : listref of Bio::EnsEMBL::OntologyTerm
 
Code:
click to view
public Bio::EnsEMBL::OntologyTerm Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_by_accession ( ) [inherited]
  Arg [1]       : String
  Description   : Fetches an ontology term given an accession.
  Example       :
    my $term = $ot_adaptor->fetch_by_accession('GO:0030326');
  Return type   : Bio::EnsEMBL::OntologyTerm
 
Code:
click to view
public Bio::EnsEMBL::DBSQL::OntologyTermAdaptor::fetch_by_dbID ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch ( ) [inherited]
  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)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::SeqFeature in contig coordinates
  Exceptions : none
  Caller     : BaseFeatureAdaptor, ProxyDnaAlignFeatureAdaptor::generic_fetch
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

Code:
click to view
public Boolean Bio::EnsEMBL::DBSQL::BaseAdaptor::is_multispecies ( ) [inherited]
  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
public Scalar Bio::EnsEMBL::DBSQL::BaseAdaptor::last_insert_id ( ) [inherited]
  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
  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
public Bio::EnsEMBL::DBSQL::GOTermAdaptor Bio::EnsEMBL::DBSQL::GOTermAdaptor::new ( )
  Arg [1]       : Bio::EnsEMBL::DBSQL::DBAdaptor
                  Argument required for parent class
                  Bio::EnsEMBL::DBSQL::BaseAdaptor.
  Description   : Creates an ontology term adaptor for GO terms.
  Example       :
    my $go_adaptor = Bio::EnsEMBL::DBSQL::GOTermAdaptor->new( $dba );
  Return type   : Bio::EnsEMBL::DBSQL::GOTermAdaptor
 
Code:
click to view

Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public DBI::StatementHandle Bio::EnsEMBL::DBSQL::BaseAdaptor::prepare ( ) [inherited]
  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

Reimplemented in Bio::EnsEMBL::DBSQL::SliceAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

public Int Bio::EnsEMBL::DBSQL::BaseAdaptor::species_id ( ) [inherited]
  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: