Bio::EnsEMBL::DBSQL::MetaCoordContainer Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::MetaCoordContainer:

Public Member Functions
public	new ()
public Listref	fetch_all_CoordSystems_by_feature_type ()
public Int	fetch_max_length_by_CoordSystem_feature_type ()
public void	add_feature_type ()
public void	remove_feature_type ()
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

Definition at line 6 of file MetaCoordContainer.pm.

Member Function Documentation

add_feature_type()

public void Bio::EnsEMBL::DBSQL::MetaCoordContainer::add_feature_type

(

)

  Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
               The coordinate system to associate with a feature table
  Arg [2]    : string $table - the name of the table in which features of
               a given coordinate system will be stored in
  Arg [3]    : int $length
               This length is used to update the max_length in the database
               and the internal cache. 
  Example    :

$csa->add_feature_table($chr_coord_system, 'gene');

  Description: This function tells the coordinate system adaptor that
               features from a specified table will be stored in a certain
               coordinate system.  If this information is not already stored
               in the database it will be added.
  Returntype : none
  Exceptions : none
  Caller     : BaseFeatureAdaptor
  Status     : Stable

Code:

fetch_all_CoordSystems_by_feature_type()

public Listref Bio::EnsEMBL::DBSQL::MetaCoordContainer::fetch_all_CoordSystems_by_feature_type

(

)

  Arg [1]    : string $table - the name of the table to retrieve coord systems
               for.  E.g. 'gene', 'exon', 'dna_align_feature'
  Example    :

@css = @{$mcc->fetch_all_CoordSystems_by_feature_type('gene')};

  Description: This retrieves the list of coordinate systems that features
               in a particular table are stored.  It is used internally by
               the API to perform queries to these tables and to ensure that
               features are only stored in appropriate coordinate systems.
  Returntype : listref of Bio::EnsEMBL::CoordSystem objects
  Exceptions : throw if name argument not provided
  Caller     : BaseFeatureAdaptor
  Status     : Stable

Code:

fetch_max_length_by_CoordSystem_feature_type()

public Int Bio::EnsEMBL::DBSQL::MetaCoordContainer::fetch_max_length_by_CoordSystem_feature_type

(

)

  Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
  Arg [2]    : string $table
  Example    :

$max_len = $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');

  Description: Returns the maximum length of features of a given type in
               a given coordinate system.
  Returntype : int or undef
  Exceptions : throw on incorrect argument
  Caller     : BaseFeatureAdaptor
  Status     : Stable

Code:

new()

public Bio::EnsEMBL::DBSQL::MetaCoordContainer::new

(

)

Undocumented method

Code:

remove_feature_type()

public void Bio::EnsEMBL::DBSQL::MetaCoordContainer::remove_feature_type

(

)

  Arg [1]    : Bio::EnsEMBL::CoordSystem $cs
               The coordinate system to associate with a feature table
  Arg [2]    : string $table - the name of the table in which features of
               a given coordinate system are being removed
  Example    :

$csa->remove_feature_table($chr_coord_system, 'gene');

  Description: This function tells the coordinate system adaptor that
               features have been fully removed from a certain coordinate system.
               Use with caution as it will cause issues if there are still features
               left.
  Returntype : none
  Exceptions : none
  Caller     : BaseFeatureAdaptor
  Status     : Stable

Code:

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

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