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Bio::EnsEMBL::DBSQL::DBEntryAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::DBSQL::DBEntryAdaptor:

List of all members.


Class Summary

Synopsis

  $db_entry_adaptor =
    $registry-\>get_adaptor( 'Human', 'Core', 'DBEntry' );

  $db_entry = $db_entry_adaptor-\>fetch_by_dbID($id);

  my $gene_adaptor = $registry-\>get_adaptor( 'Human', 'Core', 'Gene' );

  my $gene = $gene_adaptor-\>fetch_by_stable_id('ENSG00000101367');

  @db_entries = @{ $db_entry_adaptor-\>fetch_all_by_Gene($gene) };
  @gene_ids   = $db_entry_adaptor-\>list_gene_ids_by_extids('BAB15482');

Definition at line 25 of file DBEntryAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected Arrayref _fetch_by_object_type ()
protected _final_clause ()
protected _get_all_dm ()
protected _get_all_dm_loc_sth ()
protected _get_all_dm_sth ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _straight_join ()
protected _tables ()
protected List _type_by_external_db_id ()
protected List _type_by_external_id ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public Int exists ()
public fetch_all ()
public Listref fetch_all_by_dbID_list ()
public Ref fetch_all_by_description ()
public Listref fetch_all_by_Gene ()
public fetch_all_by_name ()
public fetch_all_by_Operon ()
public Ref fetch_all_by_source ()
public Listref fetch_all_by_Transcript ()
public Listref fetch_all_by_Translation ()
public Listref fetch_all_synonyms ()
public Bio::EnsEMBL::DBSQL::DBEntry fetch_by_db_accession ()
public Bio::EnsEMBL::DBEntry fetch_by_dbID ()
public geneids_by_extids ()
public Listref generic_fetch ()
public Listref get_all_dependents ()
public Listref get_all_masters ()
public Scalar get_db_name_from_external_db_id ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public List list_gene_ids_by_external_db_id ()
public List list_gene_ids_by_extids ()
public List list_transcript_ids_by_extids ()
public List list_translation_ids_by_extids ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
new ()
public DBI::StatementHandle prepare ()
public void remove_from_object ()
public Int species_id ()
public Int store ()
public transcriptids_by_extids ()
public translationids_by_extids ()

Method Documentation

protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_default_where_clause ( ) [inherited]
protected Arrayref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::_fetch_by_object_type ( )
  Arg [1]    : string $ensID
  Arg [2]    : string $ensType (object type to be returned)
  Arg [3]    : optional $exdbname (external database name)
               (may be an SQL pattern containing '%' which matches any
               number of characters)
  Arg [4]    : optional $exdb_type (external database type)
               (may be an SQL pattern containing '%' which matches any
               number of characters)
  Example    : $self->_fetch_by_object_type( $translation_id, 'Translation' )
  Description: Fetches DBEntry by Object type
               NOTE:  In a multi-species database, this method will
               return all the entries matching the search criteria, not
               just the ones associated with the current species.
  Returntype : arrayref of DBEntry objects; may be of type IdentityXref if
               there is mapping data, or OntologyXref if there is linkage data.
  Exceptions : none
  Caller     : fetch_all_by_Gene
               fetch_all_by_Translation
               fetch_all_by_Transcript
  Status     : Stable
 
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protected Bio::EnsEMBL::DBSQL::BaseAdaptor::_final_clause ( ) [inherited]

Undocumented method

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

protected Bio::EnsEMBL::DBSQL::DBEntryAdaptor::_get_all_dm ( )

Undocumented method

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protected Bio::EnsEMBL::DBSQL::DBEntryAdaptor::_get_all_dm_loc_sth ( )

Undocumented method

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protected Bio::EnsEMBL::DBSQL::DBEntryAdaptor::_get_all_dm_sth ( )

Undocumented method

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

Undocumented method

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

Undocumented method

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protected List Bio::EnsEMBL::DBSQL::DBEntryAdaptor::_type_by_external_db_id ( )
  Arg [1]    : integer $type - external_db_id
  Arg [2]    : string $ensType - ensembl_object_type
  Arg [3]    : (optional) string $extraType
  	       other object type to be returned
  Example    : $self->_type_by_external_db_id(1030, 'Translation');
  Description: Gets
               NOTE:  In a multi-species database, this method will
               return all the entries matching the search criteria, not
               just the ones associated with the current species.
  Returntype : list of dbIDs (gene_id, transcript_id, etc.)
  Exceptions : none
  Caller     : list_translation_ids_by_extids
               translationids_by_extids
  	       geneids_by_extids
  Status     : Stable
 
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protected List Bio::EnsEMBL::DBSQL::DBEntryAdaptor::_type_by_external_id ( )
  Arg [1]    : string $name - dbprimary_acc
  Arg [2]    : string $ensType - ensembl_object_type
  Arg [3]    : (optional) string $extraType
  Arg [4]    : (optional) string $external_db_name
  	       other object type to be returned
  Example    : $self->_type_by_external_id($name, 'Translation');
               NOTE:  In a multi-species database, this method will
               return all the entries matching the search criteria, not
               just the ones associated with the current species.
               SQL wildcards can be used in the external id, 
               but overly generic queries (two characters) will be prevented.
  Description: Gets
  Returntype : list of dbIDs (gene_id, transcript_id, etc.)
  Exceptions : none
  Caller     : list_translation_ids_by_extids
               translationids_by_extids
  	       geneids_by_extids
  Status     : Stable
 
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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
 
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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
 
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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
 
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public Bio::EnsEMBL::DBSQL::BaseAdaptor::dump_data ( ) [inherited]

Undocumented method

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public Int Bio::EnsEMBL::DBSQL::DBEntryAdaptor::exists ( )
  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe
  Example    : if($dbID = $db_entry_adaptor->exists($dbe)) { do stuff; }
  Description: Returns the db id of this DBEntry if it exists in this database
               otherwise returns undef.  Exists is defined as an entry with
               the same external_db and display_id
  Returntype : int
  Exceptions : thrown on incorrect args
  Caller     : GeneAdaptor::store, TranscriptAdaptor::store
  Status     : Stable
 
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public Listref Bio::EnsEMBL::DBSQL::BaseAdaptor::fetch_all_by_dbID_list ( ) [inherited]
  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
 
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Reimplemented in Bio::EnsEMBL::DBSQL::OntologyTermAdaptor.

public Ref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_by_description ( )
  Arg [1]    : string description to search for. Include % etc in this string
  Arg [2]    : <optional> string $dbname. Name of the database to search
  Example    : @canc_refs = @{$db_entry_adaptor->fetch_all_by_description("\%cancer\%")};
               @db_entries = @{$db_entry_adaptor->fetch_all_by_description("\%cancer\%","MIM_MORBID")};
  Description: Retrieves DBEntries that match the description.
               Optionally you can search on external databases type.
               NOTE:  In a multi-species database, this method will
               return all the entries matching the search criteria, not
               just the ones associated with the current species.
  Returntype : ref to array of Bio::EnsEMBL::DBSQL::DBEntry
  Exceptions : None.
  Caller     : General
  Status     : At Risk
 
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public Listref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_by_Gene ( )
  Arg [1]    : Bio::EnsEMBL::Gene $gene
               (The gene to retrieve DBEntries for)
  Arg [2]    : optional external database name
  Arg [3]    : optional external_db type
  Example    : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($gene)};
  Description: This returns a list of DBEntries associated with this gene.
               Note that this method was changed in release 15.  Previously
               it set the DBLinks attribute of the gene passed in to contain
               all of the gene, transcript, and translation xrefs associated
               with this gene.
  Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
               there is mapping data, or OntologyXref if there is linkage data.
  Exceptions : thows if gene object not passed
  Caller     : Bio::EnsEMBL::Gene
  Status     : Stable
 
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public Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_by_name ( )

Undocumented method

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public Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_by_Operon ( )

Undocumented method

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public Ref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_by_source ( )
  Arg [1]    : string source to search for. Include % etc in this string
               if you want to use SQL patterns
  Example    : @unigene_refs = @{$db_entry_adaptor->fetch_all_by_source("\%unigene\%")};
  Description: Retrieves DBEntrys that match the source name.
  Returntype : ref to array of Bio::EnsEMBL::DBSQL::DBEntry
  Exceptions : None.
  Caller     : General
  Status     : At Risk
 
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public Listref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_by_Transcript ( )
  Arg [1]    : Bio::EnsEMBL::Transcript
  Arg [2]    : optional external database name
  Arg [3]    : optional external_db type
  Example    : @db_entries = @{$db_entry_adaptor->fetch_by_Gene($trans)};
  Description: This returns a list of DBEntries associated with this
               transcript. Note that this method was changed in release 15.
               Previously it set the DBLinks attribute of the gene passed in
               to contain all of the gene, transcript, and translation xrefs
               associated with this gene.
  Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
               there is mapping data, or OntologyXref if there is linkage data.
  Exceptions : throes if transcript argument not passed
  Caller     : Bio::EnsEMBL::Gene
  Status     : Stable
 
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public Listref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_by_Translation ( )
  Arg [1]    : Bio::EnsEMBL::Translation $trans
               (The translation to fetch database entries for)
  Arg [2]    : optional external database name
  Arg [3]    : optional externaldb type
  Example    : @db_entries = @{$db_entry_adptr->fetch_all_by_Translation($trans)};
  Description: Retrieves external database entries for an EnsEMBL translation
  Returntype : listref of Bio::EnsEMBL::DBEntries; may be of type IdentityXref if
               there is mapping data, or OntologyXref if there is linkage data.
  Exceptions : throws if translation object not passed
  Caller     : general
  Status     : Stable
 
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public Listref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_all_synonyms ( )
  Arg [1]    : dbID of DBEntry to fetch synonyms for. Used in lazy loading of synonyms.
  Example    : @canc_refs = @{$db_entry_adaptor->fetch_all_synonyms(1234)};
  Description: Fetches the synonyms for a particular DBEntry.
  Returntype : listref of synonyms. List referred to may be empty if there are no synonyms.
  Exceptions : None.
  Caller     : General
  Status     : At Risk
 
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public Bio::EnsEMBL::DBSQL::DBEntry Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_by_db_accession ( )
  Arg [1]    : string $dbname - The name of the database which the provided
               accession is for.
  Arg [2]    : string $accession - The accesion of the external reference to
               retrieve.
  Example    : my $xref = $dbea->fetch_by_db_accession('Interpro','IPR003439');
               print $xref->description(), "\\n" if($xref);
  Description: Retrieves a DBEntry (xref) via the name of the database
               it is from and its primary accession in that database.
               Undef is returned if the xref cannot be found in the
               database.
               NOTE:  In a multi-species database, this method will
               return all the entries matching the search criteria, not
               just the ones associated with the current species.
  Returntype : Bio::EnsEMBL::DBSQL::DBEntry
  Exceptions : thrown if arguments are incorrect
  Caller     : general, domainview
  Status     : Stable
 
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public Bio::EnsEMBL::DBEntry Bio::EnsEMBL::DBSQL::DBEntryAdaptor::fetch_by_dbID ( )
  Arg [1]    : int $dbID
               the unique database identifier for the DBEntry to retrieve
  Example    : my $db_entry = $db_entry_adaptor->fetch_by_dbID($dbID);
  Description: Retrieves a dbEntry from the database via its unique
               identifier.
  Returntype : Bio::EnsEMBL::DBEntry
  Exceptions : none
  Caller     : general
  Status     : Stable
 
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::DBSQL::DBEntryAdaptor::geneids_by_extids ( )
  Description:

Deprecated:
use list_gene_ids_by_extids instead
 
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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
 
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Reimplemented in Bio::EnsEMBL::DBSQL::DataFileAdaptor.

public Listref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::get_all_dependents ( )
  Args[1]    : dbID of the DBentry to get the dependents of.
  Args[2]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
  Example    : my @dependents = @{ $dbe_adaptor->get_all_dependents(1234) };
  Description: Get a list of DBEntrys that are depenednet on the DBEntry.
               if an ensembl gene transcript or translation is given then only
               the ones on that object will be given
  Returntype : listref of DBEntrys. May be empty.
  Exceptions : none
  Caller     : DBEntry->get_all_dependnets
  Status     : UnStable
 
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public Listref Bio::EnsEMBL::DBSQL::DBEntryAdaptor::get_all_masters ( )
  Args[1]    : dbID of the DBentry to get the masters of.
  Args[2]    : (optional) Bio::EnsEMBL::Gene, Transcript or Translation object
  Example    : my @masters = @{ $dbe_adaptor->get_all_masters(1234) };
  Description: Get a list of DBEntrys that are the masters of the DBEntry.
               if an ensembl gene transcript or translation is given then only
               the ones on that object will be given.
  Returntype : listref of DBEntrys. May be empty.
  Exceptions : none
  Caller     : DBEntry->get_all_masters
  Status     : UnStable
 
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public Scalar Bio::EnsEMBL::DBSQL::DBEntryAdaptor::get_db_name_from_external_db_id ( )
  Arg [1]    : external_dbid of database to get the database_name
  Example    : my $db_name = $db_entry_adaptor->get_db_name_from_external_db_id(1100);
  Description: Gets the database name for a certain external_db_id
  Returntype : scalar
  Exceptions : None.
  Caller     : General
  Status     : At Risk
 
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public Bio::EnsEMBL::DBSQL::BaseAdaptor::get_dumped_data ( ) [inherited]

Undocumented method

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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
 
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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
 
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public List Bio::EnsEMBL::DBSQL::DBEntryAdaptor::list_gene_ids_by_external_db_id ( )
  Arg [1]    : string $external_id
  Example    : @gene_ids = $dbea->list_gene_ids_by_external_db_id(1020);
  Description: Retrieve a list of geneid by an external identifier that
               is linked to any of the genes transcripts, translations
               or the gene itself.
               NOTE:  If more than one external identifier has the
               same primary accession then genes for each of these is
               returned.
               NOTE:  In a multi-species database, this method will
               return all the entries matching the search criteria, not
               just the ones associated with the current species.
  Returntype : list of ints
  Exceptions : none
  Caller     : unknown
  Status     : Stable
 
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public List Bio::EnsEMBL::DBSQL::DBEntryAdaptor::list_gene_ids_by_extids ( )
  Arg [1]    : string $external_name
  Arg [2]    : (optional) string $external_db_name
  Example    : @gene_ids = $dbea->list_gene_ids_by_extids('CDPX');
  Description: Retrieve a list of geneid by an external identifier that is
               linked to  any of the genes transcripts, translations or the
               gene itself
  Returntype : list of ints
  Exceptions : none
  Caller     : unknown
  Status     : Stable
 
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public List Bio::EnsEMBL::DBSQL::DBEntryAdaptor::list_transcript_ids_by_extids ( )
  Arg [1]    : string $external_name
  Arg [2]    : (optional) string $external_db_name
  Example    : @tr_ids = $dbea->list_transcript_ids_by_extids('BCRA2');
  Description: Retrieve a list transcript ids by an external identifier that
               is linked to any of the genes transcripts, translations or the
               gene itself
  Returntype : list of ints
  Exceptions : none
  Caller     : unknown
  Status     : Stable
 
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public List Bio::EnsEMBL::DBSQL::DBEntryAdaptor::list_translation_ids_by_extids ( )
  Arg [1]    : string $external_name
  Arg [2]    : (optional) string $external_db_name
  Example    : @tr_ids = $dbea->list_translation_ids_by_extids('GO:0004835');
  Description: Gets a list of translation IDs by external display IDs
  Returntype : list of Ints
  Exceptions : none
  Caller     : unknown
  Status     : Stable
 
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public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::DBSQL::BaseAdaptor::new ( ) [inherited]
  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
 
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Reimplemented in Bio::EnsEMBL::DBSQL::AnalysisAdaptor, Bio::EnsEMBL::DBSQL::AssemblyExceptionFeatureAdaptor, Bio::EnsEMBL::DBSQL::AssemblyMapperAdaptor, Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor, Bio::EnsEMBL::DBSQL::AttributeAdaptor, Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor, Bio::EnsEMBL::DBSQL::CoordSystemAdaptor, Bio::EnsEMBL::DBSQL::DensityFeatureAdaptor, Bio::EnsEMBL::DBSQL::DensityTypeAdaptor, Bio::EnsEMBL::DBSQL::GOTermAdaptor, Bio::EnsEMBL::DBSQL::MetaCoordContainer, Bio::EnsEMBL::DBSQL::MiscSetAdaptor, Bio::EnsEMBL::DBSQL::SequenceAdaptor, Bio::EnsEMBL::DBSQL::SliceAdaptor, Bio::EnsEMBL::DBSQL::SOTermAdaptor, Bio::EnsEMBL::DBSQL::StrainSliceAdaptor, Bio::EnsEMBL::DBSQL::UnmappedObjectAdaptor, and Bio::EnsEMBL::External::BlastAdaptor.

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

public void Bio::EnsEMBL::DBSQL::DBEntryAdaptor::remove_from_object ( )
  Arg [1]    : Bio::EnsEMBL::DBEntry $dbe - The external reference which
               is to be disassociated from an ensembl object.
  Arg [2]    : Bio::EnsEMBL::Storable $object - The ensembl object the
               external reference is to be disassociated from
  Arg [3]    : string $object_type - The type of the ensembl object.
               E.g. 'Gene', 'Transcript', 'Translation'
  Example    :
               # remove all dbentries from this translation
               foreach my $dbe (@{$translation->get_all_DBEntries()}) {
                 $dbe_adaptor->remove($dbe, $translation, 'Translation');
               }
  Description: Removes an association between an ensembl object and a
               DBEntry (xref).  This does not remove the actual xref from
               the database, only its linkage to the ensembl object.
  Returntype : none
  Exceptions : Throw on incorrect arguments.
               Warning if object or dbentry is not stored in this database.
  Caller     : TranscriptAdaptor::remove, GeneAdaptor::remove,
               TranslationAdaptor::remove
  Status     : Stable
 
Code:
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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:
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public Int Bio::EnsEMBL::DBSQL::DBEntryAdaptor::store ( )
  Arg [1]    : Bio::EnsEMBL::DBEntry $exObj
               The DBEntry (xref) to be stored
  Arg [2]    : Int $ensID
               The dbID of an EnsEMBL object to associate with this external
               database entry
  Arg [3]    : string $ensType ('Transcript', 'Translation', 'Gene')
               The type of EnsEMBL object that this external database entry is
               being associated with.
  Arg [4]    : boolean $ignore_release
               If unset or zero, will require that the release string
               of the DBEntry object is identical to the release of the
               external database.  If set and non-zero, will ignore the
               release information.
  Example    : $dbea->store($db_entry, $transcript_id, 'Transcript');
  Description: Stores a reference to an external database (if it is not stored
               already) and associates an EnsEMBL object of a specified type
               with the external identifier.
  Returntype : int - the dbID of the newly created external refernce
  Exceptions : thrown when invalid dbID is passed to this method
  Caller     : scripts which load Xrefs and ObjectXrefs, etc. into Ensembl
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::DBSQL::DBEntryAdaptor::transcriptids_by_extids ( )
  Description:

Deprecated:
use transcriptids_by_extids instead
 
Code:
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public Bio::EnsEMBL::DBSQL::DBEntryAdaptor::translationids_by_extids ( )
  Description:

Deprecated:
use list_translation_ids_by_extids instead
 
Code:
click to view

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