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.

CONTACT

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NAME

Bio::EnsEMBL::IdMapping::MappingList - object holding a list of Entries

SYNOPSIS

  # create a new MappingList
  my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
    -DUMP_PATH  => $dump_path,
    -CACHE_FILE => 'gene_mappings.ser',
  );

  # add entries
  my $mappings->add_Entry($entry1);
  my $mappings->add_all( $entry2, $entry3 );

  # serialise to file
  $mappings->write_to_file;

  # later, read these mappings from file
  my $mappings1 = Bio::EnsEMBL::IdMapping::MappingList->new(
    -DUMP_PATH  => $dump_path,
    -CACHE_FILE => 'gene_mappings.ser',
  );
  $mappings1->read_from_file;

DESCRIPTION

This object represents a list of Bio::EnsEMBL::IdMapping::Entry objects. It's essentially an OO wrapper for an array with some type checking and convenience methods.

METHODS

  new
  add_Entry
  get_all_Entries
  add_all
  get_entry_count
  log
  to_string

new

  Arg[1-N]    : see superclass
  Example     : my $gene_mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
                  -DUMP_PATH   => $dump_path,
                  -CACHE_FILE  => 'gene_mappings.ser',
                );
  Description : Constructor.
  Return type : Bio::EnsEMBL::IdMapping::MappingList
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

add_Entry

  Arg[1]      : Bio::EnsEMBL::IdMapping::Entry - Entry to add
  Example     : $mappings->add_Entry($entry);
  Description : Adds an Entry to the MappingList.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

get_all_Entries

  Example     : foreach my $entry (@{ $mappings->get_all_Entries }) {
                  # do something with the entry
                }
  Description : Gets all Entries in the MappingList.
  Return type : Arrayref of Bio::EnsEMBL::IdMapping::Entry
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

add_all

  Arg[1]      : List of Bio::EnsEMBL::IdMapping::Entry objects
  Example     : my @entries = ($entry1, $entry2);
                $mappings->add_all(@entries);
  Description : Adds a list of Entries to the MappingList.
  Return type : none
  Exceptions  : thrown on wrong argument
  Caller      : general
  Status      : At Risk
              : under development

get_entry_count

  Example     : my $num_entries = $mappings->get_entry_count;
  Description : Returns the number of Entries in the MappingList.
  Return type : Int
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development

log

  Arg[1]      : String $type - object type (e.g. 'gene')
  Arg[2]      : String $dump_path - path for writing output
  Example     : $mappings->log('gene', $conf->param('basedir'));
  Description : Logs all Entries in the MappingList to a file. Used for
                debugging.
  Return type : none
  Exceptions  : thrown on I/0 error
  Caller      : general
  Status      : At Risk
              : under development

to_string

  Example     : print LOG $mappings->to_string, "\n";
  Description : Returns a string representation of the MappingList. This is
                simply a multi-line string, where each line is a stringified
                Entry.
                Useful for debugging and logging.
  Return type : String
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development