ensembl-hive
2.6
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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 () |
Definition at line 9 of file DataFile.pm.
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
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
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
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
public Bio::EnsEMBL::DataFile::get_all_paths | ( | ) |
Undocumented method
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 :
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.
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
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 :
Description : Returns a new instance of this object Returntype : Bio::EnsEMBL::DataFile Exceptions : Thrown if data is not as expected
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 :
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
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
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