Inheritance diagram for Bio::EnsEMBL::DBSQL::TranscriptSupportingFeatureAdaptor:

Public Member Functions
public List	fetch_all_by_Transcript ()

public void	store ()

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

Synopsis

$supporting_feature_adaptor =
  $database_adaptor->get_TranscriptSupportingFeatureAdaptor;
 
@supporting_feats =
  @{ $supporting_feat_adaptor->fetch_all_by_Transcript($transcript) };

Definition at line 16 of file TranscriptSupportingFeatureAdaptor.pm.

Member Function Documentation

◆ fetch_all_by_Transcript()

public List Bio::EnsEMBL::DBSQL::TranscriptSupportingFeatureAdaptor::fetch_all_by_Transcript ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript 
               The transcript to fetch supporting features for
  Arg [2]    : String (optional)
               Feature type to filter upon (either 'dna_align_feature' or 'protein_align_feature')
  Example    :

@sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript)};

@sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript, $feature_type)};

  Description: Retrieves supporting features (evidence) for a given transcript. 
  Returntype : list of Bio::EnsEMBL::BaseAlignFeatures in the same coordinate
               system as the $transcript argument
  Exceptions : warning if $transcript is not in the database (i.e. dbID not defined)
               throw if a retrieved or requested supporting feature is of unknown type 
  Caller     : Bio::EnsEMBL::Transcript
  Status     : Stable

Code:

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◆ store()

public void Bio::EnsEMBL::DBSQL::TranscriptSupportingFeatureAdaptor::store ( )

  Arg [2]    : Int $transID
               The dbID of an EnsEMBL transcript to associate with supporting
               features
  Arg [1]    : Ref to array of Bio::EnsEMBL::BaseAlignFeature (the support)
  Example    :

$dbea->store($transcript_id, \@features);

  Description: Stores a set of alignment features and associates an EnsEMBL transcript
               with them
  Returntype : none
  Exceptions : thrown when invalid dbID is passed to this method
  Caller     : TranscriptAdaptor
  Status     : Stable