Bio::EnsEMBL::DBSQL::DataFileAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::DataFileAdaptor:

Public Member Functions
public String	global_base_path ()
public String	get_base_path ()
public ArrayRef	DataFile_to_extensions ()
public Scalar	DataFile_to_adaptor ()
public ArrayRef	fetch_all_by_logic_name ()
public ArrayRef	fetch_all_by_Analysis ()
public ArrayRef	fetch_all_by_CoordSystem ()
public	fetch_by_name_and_type ()
public	generic_fetch ()
public	store ()
public	update ()
public	delete ()
protected	_tables ()
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 $dfa = $dba->get_DataFileAdaptor();
my $file = $dfa->fetch_by_dbID(1);
my $files = $dfa->fetch_all();
 
my $logic_name_files = $dfa->fetch_all_by_logic_name('bam_alignments');

Description

Provides a database wrapper to store the locations of files and to pull these
records back out. DataFile objects can only provide basic information but they
can return an intended external database adaptor which can be used to 
parse the information. This system assumes nothing about the file just that
your parser can access it.

Files are supported over any protocol your parser supports and locations can be
made absolute, built on the fly or versioned.

Definition at line 30 of file DataFileAdaptor.pm.

Member Function Documentation

_tables()

protected Bio::EnsEMBL::DBSQL::DataFileAdaptor::_tables

(

)

Undocumented method

Code:

DataFile_to_adaptor()

public Scalar Bio::EnsEMBL::DBSQL::DataFileAdaptor::DataFile_to_adaptor

(

)

  Arg[1]        : Bio::EnsEMBL::DataFile
  Arg[2]        : (optional) base path
  Arg[3]        : (optional) file type
  Example       :

my $bam = $dfa->DataFile_to_adaptor($bam_df);

  Description   : Returns an adaptor instance which will access the given DataFile.
                  Can explicitly request for an adaptor of a given file type (third
                  argument), useful with composite types, e.g. BAM coverage files
                  can be returned as BAM or BIGWIG
  Returntype    : Scalar actual return depends upon the given file type and the
                  requested type
  Exceptions    : Raised if the given file type is not understood or if the requested
                  file type is incompatible with the actual data file type.

Code:

DataFile_to_extensions()

public ArrayRef Bio::EnsEMBL::DBSQL::DataFileAdaptor::DataFile_to_extensions

(

)

  Arg[1]      : Bio::EnsEMBL::DataFile
  Example     :

my $exts = $dfa->DataFile_to_extensions($bam_df);

  Description : Returns all expected extensions for the given DataFile type. The
                first returned is the default extension
  Returntype  : ArrayRef
  Exceptions  : Raised if the given file type is not understood

Code:

delete()

public Bio::EnsEMBL::DBSQL::DataFileAdaptor::delete

(

)

Undocumented method

Code:

fetch_all_by_Analysis()

public ArrayRef Bio::EnsEMBL::DBSQL::DataFileAdaptor::fetch_all_by_Analysis

(

)

  Args [1]    : Bio::EnsEMBL::Analysis $analysis to look up by 
  Example     :

my $dfs = $dfa->fetch_all_by_Analysis($analysis);

  Description : Returns all DataFile entries linked to the given analysis
  Returntype  : ArrayRef contains Bio::EnsEMBL::DataFile instances
  Exceptions  : None

Code:

fetch_all_by_CoordSystem()

public ArrayRef Bio::EnsEMBL::DBSQL::DataFileAdaptor::fetch_all_by_CoordSystem

(

)

  Args [1]    : Bio::EnsEMBL::CoordSystem $coord_system to look up by 
  Example     :

my $dfs = $dfa->fetch_all_by_CoordSystem($cs);

  Description : Returns all DataFile entries linked to the given coordinate
                system. Does not support toplevel
  Returntype  : ArrayRef contains Bio::EnsEMBL::DataFile instances
  Exceptions  : None

Code:

fetch_all_by_logic_name()

public ArrayRef Bio::EnsEMBL::DBSQL::DataFileAdaptor::fetch_all_by_logic_name

(

)

  Args [1]      : String $logic_name for the linked analysis 
  Example       :

my $dfs = $dfa->fetch_all_by_logic_name('bam_alignments');

  Description : Returns all DataFile entries linked to the given analysis 
                logic name
  Returntype    : ArrayRef contains Bio::EnsEMBL::DataFile instances
  Exceptions    : Thrown if logic name does not exist

Code:

fetch_by_name_and_type()

public Bio::EnsEMBL::DBSQL::DataFileAdaptor::fetch_by_name_and_type

(

)

Undocumented method

Code:

generic_fetch()

public Bio::EnsEMBL::DBSQL::DataFileAdaptor::generic_fetch

(

)

Undocumented method

Code:

get_base_path()

public String Bio::EnsEMBL::DBSQL::DataFileAdaptor::get_base_path

(

)

  Arg[1]      : String; (optional) base path 
  Example     :

$dfa->get_base_path();

  Description : If given the path it will return that path; if not it consults
                $self->global_base_path() for a value. As a last resort
                it will look at the meta table for an entry keyed by
                data_file.base_path
  Returntype  : String
  Exceptions  : Thrown if nothing is found after consulting all three locations

Code:

global_base_path()

public String Bio::EnsEMBL::DBSQL::DataFileAdaptor::global_base_path

(

)

  Arg[1]        : String; base path 
  Example       :

Bio::EnsEMBL::DBSQL::DataFileAdaptor->global_base_path('/base/path');

  Description : Stores a global value to be used when building data file paths
  Returntype    : String
  Exceptions    : None

Code:

store()

public Bio::EnsEMBL::DBSQL::DataFileAdaptor::store

(

)

Undocumented method

Code:

update()

public Bio::EnsEMBL::DBSQL::DataFileAdaptor::update

(

)

Undocumented method

Code:

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

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