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Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor:

List of all members.


Class Summary

Definition at line 11 of file MemberAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _fetch_all_by_source_taxon_chr_name_start_end_strand ()
protected _fetch_all_by_source_taxon_chr_name_start_end_strand_limit ()
protected _fetch_sequence_by_id ()
protected _fetch_sequence_cds_by_member_id ()
protected _fetch_sequence_exon_bounded_by_member_id ()
protected _final_clause ()
protected Listref _generic_fetch ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public columns ()
public create_AlignedMember_from_member_attribute ()
public create_instance_from_rowhash ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public Listref fetch_all ()
public Listref fetch_all_by_dbID_list ()
public fetch_all_by_relation ()
public fetch_all_by_sequence_id ()
public Listref fetch_all_by_source ()
public Listref fetch_all_by_source_genome_db_id ()
public fetch_all_by_source_stable_ids ()
public Listref fetch_all_by_source_taxon ()
public List fetch_all_by_subset_id ()
public Array fetch_all_peptides_for_gene_member_id ()
public
Bio::EnsEMBL::Compara::Member 
fetch_by_dbID ()
public fetch_by_dbIDs ()
public
Bio::EnsEMBL::Compara::Member 
fetch_by_source_stable_id ()
public fetch_by_source_taxon ()
public
Bio::EnsEMBL::Compara::Member 
fetch_canonical_peptide_member_for_gene_member_id ()
public
Bio::EnsEMBL::Compara::Member 
fetch_canonical_transcript_member_for_gene_member_id ()
public
Bio::EnsEMBL::Compara::Member 
fetch_gene_for_peptide_member_id ()
public Listref generic_fetch ()
public get_dumped_data ()
public Int get_source_taxon_count ()
public init_instance_from_rowhash ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public member_cache ()
public new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public store ()
public store_gene_peptide_link ()
public store_reused ()
public tables ()
public update_sequence ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_default_where_clause ( )

Undocumented method

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

protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_fetch_all_by_source_taxon_chr_name_start_end_strand ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_fetch_all_by_source_taxon_chr_name_start_end_strand_limit ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_fetch_sequence_by_id ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_fetch_sequence_cds_by_member_id ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_fetch_sequence_exon_bounded_by_member_id ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_final_clause ( )

Undocumented method

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

protected Listref Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_generic_fetch ( )
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  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
 
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protected Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::_objs_from_sth ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::columns ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::create_AlignedMember_from_member_attribute ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::create_instance_from_rowhash ( )

Undocumented method

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public Listref Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all ( )
  Arg        : None
  Example    : my $members = $ma->fetch_all;
  Description: Fetch all the members in the db
  Returntype : listref of Bio::EnsEMBL::Compara::Member objects
  Exceptions : 
  Caller     :
 
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_by_relation ( )
  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :
 
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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_by_sequence_id ( )

Undocumented method

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public Listref Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_by_source ( )
  Arg [1]    : string $source_name
  Example    : my $members = $ma->fetch_all_by_source(
                   "Uniprot/SWISSPROT");
  Description: Fetches the member corresponding to a source_name.
  Returntype : listref of Bio::EnsEMBL::Compara::Member objects
  Exceptions : throws if $source_name is undef
  Caller     :
 
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public Listref Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_by_source_genome_db_id ( )
  Arg [1]    : string $source_name
  Arg [2]    : int $genome_db_id
  Example    : my $members = $ma->fetch_all_by_source_genome_db_id(
                   "Uniprot/SWISSPROT", 90);
  Description: Fetches the member corresponding to a source_name and a genome_db_id.
  Returntype : listref of Bio::EnsEMBL::Compara::Member objects
  Exceptions : throws if $source_name or $genome_db_id is undef
  Caller     :
 
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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_by_source_stable_ids ( )

Undocumented method

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public Listref Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_by_source_taxon ( )
  Arg [1]    : string $source_name
  Arg [2]    : int $taxon_id
  Example    : my $members = $ma->fetch_all_by_source_taxon(
                   "Uniprot/SWISSPROT", 9606);
  Description: Fetches the member corresponding to a source_name and a taxon_id.
  Returntype : listref of Bio::EnsEMBL::Compara::Member objects
  Exceptions : throws if $source_name or $taxon_id is undef
  Caller     :
 
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public List Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_by_subset_id ( )
  Arg [1]    : int subset_id
  Example    : @members = @{$memberAdaptor->fetch_all_by_subset_id($subset_id)};
  Description: given a subset_id, does a join to the subset_member table
               to return a list of Member objects in this subset
  Returntype : list by reference of Compara::Member objects
  Exceptions :
  Caller     : general
 
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public Array Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_all_peptides_for_gene_member_id ( )
  Arg [1]    : int member_id of a gene member
  Example    : @pepMembers = @{$memberAdaptor->fetch_all_peptides_for_gene_member_id($gene_member_id)};
  Description: given a member_id of a gene member,
               fetches all peptide members for this gene
  Returntype : array ref of Bio::EnsEMBL::Compara::Member objects
  Exceptions :
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_by_dbID ( )
  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234);
  Description: Returns the Member created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Compara::Member
  Exceptions : thrown if $id is not defined
  Caller     : general
 
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_by_dbIDs ( )

Undocumented method

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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_by_source_stable_id ( )
  Arg [1]    : (optional) string $source_name
  Arg [2]    : string $stable_id
  Example    : my $member = $ma->fetch_by_source_stable_id(
                   "Uniprot/SWISSPROT", "O93279");
  Example    : my $member = $ma->fetch_by_source_stable_id(
                   undef, "O93279");
  Description: Fetches the member corresponding to this $stable_id.
               Although two members from different sources might
               have the same stable_id, this never happens in a normal
               compara DB. You can set the first argument to undef
               like in the second example.
  Returntype : Bio::EnsEMBL::Compara::Member object
  Exceptions : throws if $stable_id is undef
  Caller     :
 
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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_by_source_taxon ( )
Deprecated:
: use fetch_all_by_source_taxon instead
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_canonical_peptide_member_for_gene_member_id ( )
  Arg [1]    : int member_id of a gene member
  Example    : $pepMembers = $memberAdaptor->fetch_canonical_peptide_member_for_gene_member_id($gene_member_id);
  Description: given a member_id of a gene member,
               fetches all canonical peptide members for this gene
  Returntype : Bio::EnsEMBL::Compara::Member object
  Exceptions :
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_canonical_transcript_member_for_gene_member_id ( )
  Arg [1]    : int member_id of a gene member
  Example    : $transMembers = $memberAdaptor->fetch_canonical_transcript_member_for_gene_member_id($gene_member_id);
  Description: given a member_id of a gene member,
               fetches all canonical transcript members for this gene
  Returntype : Bio::EnsEMBL::Compara::Member object
  Exceptions :
  Caller     : general
 
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public Bio::EnsEMBL::Compara::Member Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::fetch_gene_for_peptide_member_id ( )
  Arg [1]    : int member_id of a peptide member
  Example    : $geneMember = $memberAdaptor->fetch_gene_for_peptide_member_id($peptide_member_id);
  Description: given a member_id of a peptide member,
               does a join to a copy of member table to extract a member for its gene
  Returntype : Bio::EnsEMBL::Compara::Member object
  Exceptions :
  Caller     : general
 
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public Int Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::get_source_taxon_count ( )
  Arg [1]    : string $source_name
  Arg [2]    : int $taxon_id
  Example    : my $sp_gene_count = $memberDBA->get_source_taxon_count('ENSEMBLGENE',$taxon_id);
  Description: 
  Returntype : int $sp_gene_count is the number of members for this source_name and taxon_id
  Exceptions : 
  Caller     :
 
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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::init_instance_from_rowhash ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::member_cache ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::new ( )

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::store ( )
  Arg [1]    : 
  Example    : 
  Description: 
  Returntype : 
  Exceptions : 
  Caller     :
 
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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::store_gene_peptide_link ( )

Undocumented method

public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::store_reused ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::tables ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::MemberAdaptor::update_sequence ( )

Undocumented method

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