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