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

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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