Bio::EnsEMBL::DataFile Class Reference

Inheritance diagram for Bio::EnsEMBL::DataFile:

Public Member Functions
public Bio::EnsEMBL::DataFile	new ()
public Adaptor	get_ExternalAdaptor ()
public Scalar	path ()
public	get_all_paths ()
public Bio::EnsEMBL::CoordSystem	coord_system ()
public Bio::EnsEMBL::Analysis	analysis ()
public String	name ()
public Boolean	version_lock ()
public Boolean	absolute ()
public String	url ()
public String	file_type ()
Public Member Functions inherited from Bio::EnsEMBL::Storable
public Bio::EnsEMBL::Storable	new ()
public Instance	new_fast ()
public Int	dbID ()
public Bio::EnsEMBL::DBSQL::BaseAdaptor	adaptor ()
public Boolean	is_stored ()
public	get_all_DAS_Features ()

Detailed Description

Definition at line 9 of file DataFile.pm.

Member Function Documentation

absolute()

public Boolean Bio::EnsEMBL::DataFile::absolute

(

)

  Arg[1]      : Boolean Optional setter  
  Description : Indicates if the URL of this file is an absolute one i.e. 
                should be used verbatim or not.
  Returntype  : Boolean

Code:

analysis()

public Bio::EnsEMBL::Analysis Bio::EnsEMBL::DataFile::analysis

(

)

  Arg[1]      : Bio::EnsEMBL::Analysis Optional setter  
  Description : Mutator for the analysis field. All files are linked to one
  Returntype  : Bio::EnsEMBL::Analysis
  Exceptions  : Thrown if not of the expected type

Code:

coord_system()

public Bio::EnsEMBL::CoordSystem Bio::EnsEMBL::DataFile::coord_system

(

)

  Arg[1]      : Bio::EnsEMBL::CoordSystem Optional setter  
  Description : Mutator for the coord system field. All files are linked to one
  Returntype  : Bio::EnsEMBL::CoordSystem
  Exceptions  : Thrown if not of the expected type

Code:

file_type()

public String Bio::EnsEMBL::DataFile::file_type

(

)

  Arg[1]      : String Optional setter  
  Description : The type of file we are working with. Can be used to generate
                a file name.
  Returntype  : String

Code:

get_all_paths()

public Bio::EnsEMBL::DataFile::get_all_paths

(

)

Undocumented method

Code:

get_ExternalAdaptor()

public Adaptor Bio::EnsEMBL::DataFile::get_ExternalAdaptor

(

)

  Arg[1]        : Scalar; (optional) base path. Uses defaults if not given 
  Arg[2]        : Scalar; (optional) file type
  Example       :

my $ea = $df->get_ExternalAdaptor('/base/path');

  Description : Delegates to the parent adaptor to retrieve the external 
                  adaptor for this data type
  Returntype    : Adaptor; will be an adaptor that can read the given data file
  Exceptions    : Thrown if there is no attached adaptor.

Code:

name()

public String Bio::EnsEMBL::DataFile::name

(

)

  Arg[1]      : String Optional setter  
  Description : Mutator for the name of the file. Can be used in file location
                generation
  Returntype  : String

Code:

new()

public Bio::EnsEMBL::DataFile Bio::EnsEMBL::DataFile::new

(

)

  Arg [-ADAPTOR]      : Bio::EnsEMBL::DBSQL::DataFileAdaptor
  Arg [-DBID]         : Integer $dbID
  Arg [-COORD_SYSTEM] : Bio::EnsEMBL::CoordSystem $coord_system
  Arg [-ANALYSIS]     : Bio::EnsEMBL::Analysis $analysis
  Arg [-NAME]         : String $name
  Arg [-VERSION_LOCK] : Boolean $version_lock
  Arg [-ABSOLUTE]     : Boolean $absolute
  Arg [-URL]          : String $url
  Arg [-FILE_TYPE]    : String $file_type
  Example                 :

Bio::EnsEMBL::DataFile->new();

  Description       : Returns a new instance of this object
  Returntype          : Bio::EnsEMBL::DataFile
  Exceptions          : Thrown if data is not as expected

Code:

path()

public Scalar Bio::EnsEMBL::DataFile::path

(

)

  Arg[1]      : Scalar base of the path to use. Can be ignored if the instance
                already represents a canonical path 
  Example     :

my $f = $df->path();

  Description : Used to generate the path to the file resource. Can return a
                path to the file or a URL but it is up to the using code to
                know how to interprate the different returned forms.

                If the data file url is canonical then this is just returned. 
                If not then a path is generated of the form 
                /base/path/production_name/coord_system_version/[software_version]/db_group/name.ext

  Returntype  : Scalar the absolute path/url to the given resource
  Exceptions  : Thrown if the linked Coordinate System lacks a version and the
                current database also lacks a default version
  Caller      : public

Code:

url()

public String Bio::EnsEMBL::DataFile::url

(

)

  Arg[1]      : String Optional setter  
  Description : Location of the file. Can be optional and if set means once
                we are in an automatic location use this value to locate
                the file.
  Returntype  : String

Code:

version_lock()

public Boolean Bio::EnsEMBL::DataFile::version_lock

(

)

  Arg[1]      : Boolean Optional setter  
  Description : Boolean indicating if the file is linked to the version of the
                database it was found in.
  Returntype  : Boolean

Code:

---

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

• ensembl/modules/Bio/EnsEMBL/DataFile.pm