Raw content of Bio::EnsEMBL::IdMapping::MappingList
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::IdMapping::MappingList - object holding a list of Entries
=head1 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;
=head1 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.
=head1 METHODS
new
add_Entry
get_all_Entries
add_all
get_entry_count
log
to_string
=cut
package Bio::EnsEMBL::IdMapping::MappingList;
use strict;
use warnings;
no warnings 'uninitialized';
use Bio::EnsEMBL::IdMapping::Serialisable;
our @ISA = qw(Bio::EnsEMBL::IdMapping::Serialisable);
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
=head2 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
=cut
sub new {
my $caller = shift;
my $class = ref($caller) || $caller;
my $self = $class->SUPER::new(@_);
# initialise internal datastructure unless we loaded a serialised object
unless ($self->loaded) {
$self->{'cache'}->{'entries'} = [];
}
return $self;
}
=head2 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
=cut
sub add_Entry {
my $self = shift;
my $entry = shift;
unless ($entry and $entry->isa('Bio::EnsEMBL::IdMapping::Entry')) {
throw("Need a Bio::EnsEMBL::IdMapping::Entry");
}
push @{ $self->{'cache'}->{'entries'} }, $entry;
}
=head2 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
=cut
sub get_all_Entries {
my $self = shift;
return $self->{'cache'}->{'entries'};
}
=head2 add_all
Arg[1] : List of Bio::EnsEMBL::IdMapping::Entry objects
Example : my @entries = ($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
=cut
sub add_all {
my $self = shift;
my @mappings = @_;
foreach my $mapping (@mappings) {
unless ($mapping->isa('Bio::EnsEMBL::IdMapping::MappingList')) {
throw("Need a Bio::EnsEMBL::IdMapping::MappingList");
}
push @{ $self->{'cache'}->{'entries'} }, @{ $mapping->get_all_Entries };
}
}
=head2 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
=cut
sub get_entry_count {
my $self = shift;
return scalar(@{ $self->{'cache'}->{'entries'} });
}
=head2 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
=cut
sub log {
my $self = shift;
my $type = shift;
my $dump_path = shift;
my $debug_path = path_append($dump_path, 'debug');
my $logfile = "$debug_path/${type}_final_scores.txt";
open(my $fh, '>', $logfile) or
throw("Unable to open $logfile for writing: $!");
foreach my $entry (@{ $self->get_all_Entries }) {
print $fh ($entry->to_string."\n");
}
close($fh);
}
=head2 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
=cut
sub to_string {
my $self = shift;
my $string = '';
foreach my $entry (@{ $self->get_all_Entries }) {
$string .= $entry->to_string."\n";
}
return $string;
}
1;
]]>