Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor:

Public Member Functions
public Listref	fetch_all_by_Slice_and_hcoverage ()
public Listref	fetch_all_by_Slice_and_external_db ()
public Listref	fetch_all_by_Slice_and_pid ()
public Listref	fetch_all_by_hit_name ()
public Listref	fetch_all_by_hit_name_unversioned ()
Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor
public Bio::EnsEMBL::BaseFeatureAdaptor	new ()
public Boolean	start_equals_end ()
public void	clear_cache ()
protected	_clear_slice_feature_cache ()
protected Bio::EnsEMBL::Utils::Cache	_slice_feature_cache ()
public Listref	fetch_all_by_Slice ()
public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice_method ()
public Bio::EnsEMBL::Utils::Iterator	fetch_Iterator_by_Slice ()
public Listref	fetch_all_by_Slice_and_score ()
public Listref	fetch_all_by_Slice_constraint ()
public Listref	fetch_all_by_logic_name ()
public Listref	fetch_all_by_stable_id_list ()
protected	_create_feature ()
protected	_create_feature_fast ()
public Int	count_by_Slice_constraint ()
protected ArrayRef	_get_and_filter_Slice_projections ()
protected ArrayRef	_generate_feature_bounds ()
protected Listref	_get_by_Slice ()
protected	_slice_fetch ()
public	get_seq_region_id_external ()
public	get_seq_region_id_internal ()
protected	_pre_store ()
protected	_pre_store_userdata ()
protected	_check_start_end_strand ()
protected	_remap ()
protected	_seq_region_boundary_from_db ()
public void	store ()
public void	remove ()
public void	remove_by_Slice ()
protected	_max_feature_length ()
protected	_list_seq_region_ids ()
public	remove_by_analysis_id ()
public	remove_by_feature_id ()
public Bio::EnsEMBL::Feature	fetch_nearest_by_Feature ()
public Listref	fetch_all_by_outward_search ()
public Listref	fetch_all_nearest_by_Feature ()
public Listref	select_nearest ()
protected Int	_compute_nearest_end ()
protected Int	_compute_prime_distance ()
protected Int	_compute_midpoint ()
protected	_discard_excess_features_from_matrix ()
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

Abstract class, should not be instantiated.  Implementation of abstract
methods must be performed by subclasses.

Description

This is a base adaptor for the align feature adaptors
DnaAlignFeatureAdaptor and ProteinAlignFeatureAdaptor.

Definition at line 18 of file BaseAlignFeatureAdaptor.pm.

Member Function Documentation

fetch_all_by_hit_name()

public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_hit_name

(

)

  Arg [1]    : string $hit_name
               The hit_name of the features to obtain
  Arg [2]    : (optional) string $logic_name
               The analysis logic name of the type of features to
               obtain.
  Example    :

@feats =
                @{ $adaptor->fetch_all_by_hit_name( 'AK078491.1',
                  'vertrna' ); }

  Description: Returns a listref of features created from the
               database which correspond to the given hit_name.  If
               logic name is defined, only features with an analysis
               of type $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : thrown if hit_name is not defined
  Caller     : general
  Status     : Stable

Code:

fetch_all_by_hit_name_unversioned()

public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_hit_name_unversioned

(

)

  Arg [1]    : string $hit_name
               The beginning of the hit_name of the features to
               obtain, e.g. AA768786 would retrieve AA768786.1,
               AA768786.2 etc.
  Arg [2]    : (optional) string $logic_name
               The analysis logic name of the type of features to
               obtain.
  Example    :

@feats =
                 @{ $adaptor->fetch_all_by_hit_name( $name,
                   $logic_name ) };

  Description: Returns a listref of features created from the
               database which start with the given hit_name.  If
               logic name is defined, only features with an analysis
               of type $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
  Exceptions : thrown if hit_name is not defined
  Caller     : general
  Status     : At risk

Code:

fetch_all_by_Slice_and_external_db()

public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_Slice_and_external_db

(

)

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice from which to obtain align features.
  Arg [2]    : String $external_db_name
               Name of the external DB to which the align features
               should be restricted.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    :

@feats = @{
                 $adaptor->fetch_all_by_Slice_and_external_db( $slice,
                   'EMBL' ) };

  Description: Returns a listref of features created from the
               database which are on the Slice $slice and associated
               with external DB $external_db_name.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : thrown if $external_db_name is not defined or if
               the subclass does not return a table alias for the
               external_db table from _tables()
  Caller     : general
  Status     : At Risk

Code:

fetch_all_by_Slice_and_hcoverage()

public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_Slice_and_hcoverage

(

)

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice from which to obtain align features.
  Arg [2]    : (optional) float $hcoverage 
               A lower bound for the hcoverage of feats to obtain.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    :

@feats = @{
               $adaptor->fetch_all_by_Slice_and_hcoverage( $slice,
                 50.0 ) };

  Description: Returns a listref of features created from the
               database which are on the Slice $slice and with a
               hcoverage greater than $hcoverage.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : none
  Caller     : general
  Status     : At Risk

Code:

fetch_all_by_Slice_and_pid()

public Listref Bio::EnsEMBL::DBSQL::BaseAlignFeatureAdaptor::fetch_all_by_Slice_and_pid

(

)

  Arg [1]    : Bio::EnsEMBL::Slice $slice
               The slice from which to obtain align features.
  Arg [2]    : (optional) float $pid 
               A lower bound for the percentage identity of features
               to obtain.
  Arg [3]    : (optional) string $logic_name
               The logic name of the type of features to obtain.
  Example    :

@feats =
                @{ $adaptor->fetch_all_by_Slice_and_pid( $slice, 50.0 ) };

  Description: Returns a listref of features created from the
               database which are on the Slice $slice and with a
               percentage identity greater than $pid.  If logic name
               is defined, only features with an analysis of type
               $logic_name will be returned.
  Returntype : listref of Bio::EnsEMBL::BaseAlignFeatures
               in Slice coordinates
  Exceptions : none
  Caller     : general
  Status     : Stable

Code:

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

• ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAlignFeatureAdaptor.pm