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Bio::EnsEMBL::DataFile Class Reference
Inheritance diagram for Bio::EnsEMBL::DataFile:

List of all members.


Class Summary

Definition at line 10 of file DataFile.pm.

Available Methods

public Boolean absolute ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Bio::EnsEMBL::Analysis analysis ()
public Bio::EnsEMBL::CoordSystem coord_system ()
public Int dbID ()
public String file_type ()
public get_all_DAS_Features ()
public Any get_ExternalAdaptor ()
public Boolean is_stored ()
public String name ()
public Bio::EnsEMBL::DataFile new ()
public Bio::EnsEMBL::Feature new_fast ()
public Scalar path ()
public String url ()
public Boolean version_lock ()

Method Documentation

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
 
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public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
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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
 
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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
 
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public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
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Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

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
 
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public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

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Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Any Bio::EnsEMBL::DataFile::get_ExternalAdaptor ( )
  Arg[1]     	: Scalar; optional base path. Uses defaults if not given 
  Example			: my $ea = $df->get_ExternalAdaptor('/base/path');
  Description	: Delegates to the parent adaptor to retrieve the external 
                adaptor for this data type
  Returntype 	: Any; will be an adaptor that can read the given data file
  Exceptions 	: Thrown if there is no attached adaptor. Otherwise
 
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public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
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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
 
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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:
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Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::Feature Bio::EnsEMBL::DataFile::new_fast ( )
  Arg [1]    : hashref to be blessed
  Description: Construct a new Bio::EnsEMBL::Feature using the hashref.
  Exceptions : none
  Returntype : Bio::EnsEMBL::Feature
  Caller     : general, subclass constructors
  Status     : Stable
 
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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
 
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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
 
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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:
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The documentation for this class was generated from the following file: