Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor:

Public Member Functions
public Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor	new ()
public Listref	fetch_by_version ()
public Listref	fetch_by_name ()
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

my $slice =
  $slice_adaptor->fetch_by_region( 'chromosome', 14, 900000, 950000 );
 
my $msc = Bio::EnsEMBL::MappedSliceContainer->new( -SLICE => $slice );
 
my $asa = Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;
 
my ($mapped_slice) = @{ $asa->fetch_by_version( $msc, 'NCBIM36' ) };

Description

NOTE: this code is under development and not fully functional nor tested
yet.  Use only for development.

This adaptor is a factory for creating MappedSlices representing
alternative assemblies and attaching them to a MappedSliceContainer. A
mapper will be created to map between the reference slice and the common
container slice coordinate system.

Definition at line 33 of file AssemblySliceAdaptor.pm.

Member Function Documentation

fetch_by_name()

public Listref Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor::fetch_by_name

(

)

  Arg[1]      : Bio::EnsEMBL::MappedSliceContainer $container - the container
                  to attach MappedSlices to
  Arg[2]      : String $name - the assembly name to fetch
  Arg[3]      : (optional) String $version -- the version for the new assembly
  Example     :

my ($mapped_slice) = @{ $msc->fetch_by_name('LRG1','1') };

  Description : Creates a MappedSlice representing an alternative assembly
                version of the container's reference slice.
  Return type : listref of Bio::EnsEMBL::MappedSlice
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general, Bio::EnsEMBL::MappedSliceContainer
  Status      : At Risk
              : under development

Code:

fetch_by_version()

public Listref Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor::fetch_by_version

(

)

  Arg[1]      : Bio::EnsEMBL::MappedSliceContainer $container - the container
                  to attach MappedSlices to
  Arg[2]      : String $version - the assembly version to fetch
  Example     :

my ($mapped_slice) = @{ $msc->fetch_by_version('NCBIM36') };

  Description : Creates a MappedSlice representing an alternative assembly
                version of the container's reference slice.
  Return type : listref of Bio::EnsEMBL::MappedSlice
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general, Bio::EnsEMBL::MappedSliceContainer
  Status      : At Risk
              : under development

Code:

new()

public Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor::new

(

)

  Example     :

my $assembly_slice_adaptor =
                 Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor->new;

  Description : Constructor.
  Return type : Bio::EnsEMBL::DBSQL::AssemblySliceAdaptor
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

Code:

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

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