LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

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

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. 

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 
              B</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

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

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

name

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

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

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

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

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