Raw content of Bio::EnsEMBL::ArchiveStableId
<![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::ArchiveStableId
=head1 SYNOPSIS
=head1 DESCRIPTION
ArchiveStableId objects are the main workunit for retrieving stable id
archived information from EnsEMBL core database.
Attributes:
type: Gene, Transcript, Translation, Exon, other, undef
stable_id: eg. ENSG00000000001
version: e.g. 1
db_name: eg. homo_sapiens_core_12_31
release: e.g. 35
assembly: e.g. NCBI35
successors: listref of Bio::EnsEMBL::ArchiveStableIds
adaptor: Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Status: At Risk. This module is in development.
=head1 METHODS
new
new_fast
get_history_tree
get_all_predecessors
get_all_successors
get_peptide
get_all_associated_archived
get_all_gene_archive_ids
get_all_transcript_archive_ids
get_all_translation_archive_ids
current_version
is_current
get_latest_incarnation
is_latest
stable_id
version
db_name
release
assembly
type
adaptor
successors
=head1 RELATED MODULES
Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Bio::EnsEMBL::StableIdEvent
Bio::EnsEMBL::StableIdHistoryTree
=cut
package Bio::EnsEMBL::ArchiveStableId;
use strict;
use warnings;
no warnings qw(uninitialized);
use Bio::EnsEMBL::Root;
our @ISA = qw(Bio::EnsEMBL::Root);
use Bio::EnsEMBL::Utils::Argument qw(rearrange);
=head2 new
Arg [STABLE_ID] : String $stable_id
Arg [VERSION] : Int $version
Arg [CURRENT_VERSION] : Int $current_version
Arg [DB_NAME] : String $db_name
Arg [RELEASE] : String $release
Arg [ASSEMBLY_NAME] : String $assembly
Arg [TYPE] : String $type - "Gene", "Transcript", "Translation", "Exon"
Arg [ADAPTOR] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor
Example : none
Description : standard constructor with named arguments to create
ArchiveStableId
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general, Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Status : At Risk
: under development
=cut
sub new {
my $class = shift;
$class = ref( $class ) || $class;
my $self = bless {}, $class;
my ($stable_id, $version, $current_version, $db_name, $release, $assembly,
$type, $adaptor) = rearrange([qw( STABLE_ID VERSION CURRENT_VERSION DB_NAME
RELEASE ASSEMBLY TYPE ADAPTOR)], @_ );
$self->{'stable_id'} = $stable_id;
$self->{'version'} = $version;
$self->{'current_version'} = $current_version;
$self->{'db_name'} = $db_name;
$self->{'release'} = $release;
$self->{'assembly'} = $assembly;
$self->{'type'} = $type;
$self->{'adaptor'} = $adaptor;
return $self;
}
=head2 new_fast
Arg [1] : String $stable_id
Arg [2] : Int $version
Arg [3] : String $db_name
Arg [4] : String $release
Arg [5] : String $assembly
Arg [6] : String $type - "Gene", "Transcript", "Translation", "Exon"
Arg [7] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor
Arg [8] : Int $current_version
Example : none
Description : faster version of above constructor
Returntype : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general, Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Status : At Risk
: under development
=cut
sub new_fast {
my $class = shift;
$class = ref ($class) || $class;
my $self = bless {
'stable_id' => $_[0],
'version' => $_[1],
'db_name' => $_[2],
'release' => $_[3],
'assembly' => $_[4],
'type' => $_[5],
'adaptor' => $_[6],
'current_version' => $_[7],
}, $class;
return $self;
}
=head2 get_history_tree
Arg[1] : (optional) Int $num_high_scorers
number of mappings per stable ID allowed when filtering
Arg[2] : (optional) Int $max_rows
maximum number of stable IDs in history tree (used for
filtering)
Example : my $history_tree = $archive_id->get_history_tree;
Description : Returns the history tree of this ArchiveStableId
Return type : Bio::EnsEMBL::StableIdHistoryTree
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_history_tree {
my ($self, $num_high_scorers, $max_rows) = @_;
unless ($self->{'history'}) {
$self->{'history'} = $self->adaptor->fetch_history_tree_by_stable_id(
$self->stable_id, $num_high_scorers, $max_rows);
}
return $self->{'history'};
}
=head2 get_all_predecessors
Args : none
Example : none
Description : Retrieve a list of ArchiveStableIds that were mapped to this
one.
Returntype : listref of Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_predecessors {
my $self = shift;
my $predecessors = $self->adaptor->fetch_predecessors_by_archive_id($self);
foreach my $pre (@$predecessors) {
$pre->successors($self);
}
return $predecessors;
}
=head2 get_all_successors
Args : none
Example : none
Description : Retrieve a list of ArchiveStableIds that this one was mapped to.
Returntype : listref Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_successors {
my $self = shift;
if ($self->{'successors'}) {
return $self->{'successors'};
} else {
my $successors = $self->adaptor->fetch_successors_by_archive_id($self);
return $self->successors(@$successors);
}
}
=head2 get_peptide
Example : none
Description : Retrieves the peptide string for this ArchiveStableId.
Returntype : String, or undef if this is not a Translation or cant be found
in the database.
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_peptide {
my $self = shift;
if( $self->type() eq "Translation" ) {
return $self->adaptor->get_peptide( $self );
} else {
return undef;
}
}
=head2 get_all_associated_archived
Example : my ($arch_gene, $arch_tr, $arch_tl, $pep_seq) =
@{ $arch_id->get_all_associated_archived };
Description : Fetches associated archived stable IDs from the db for this
ArchiveStableId (version is taken into account).
Return type : Listref of
ArchiveStableId archived gene
ArchiveStableId archived transcript
(optional) ArchiveStableId archived translation
(optional) peptide sequence
Caller : webcode, general
Status : At Risk
: under development
=cut
sub get_all_associated_archived {
my $self = shift;
return $self->adaptor->fetch_associated_archived($self);
}
=head2 get_all_gene_archive_ids
Example : my @archived_genes = @{ $arch_id->get_all_gene_archive_ids };
Description : Returns gene ArchiveStableIds associated with this
ArchiveStableId. If this is a gene, it returns itself.
Returntype : listref of Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_gene_archive_ids {
my $self = shift;
if ($self->type eq "Gene") {
return [$self];
} else {
return $self->adaptor->fetch_all_by_archive_id($self, 'Gene');
}
}
=head2 get_all_transcript_archive_ids
Example : none
Example : my @archived_transcripts =
@{ $arch_id->get_all_transcript_archive_ids };
Description : Returns transcript ArchiveStableIds associated with this
ArchiveStableId. If this is a transcript, it returns itself.
Returntype : listref of Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_transcript_archive_ids {
my $self = shift;
if ($self->type eq "Transcript") {
return [$self];
} else {
return $self->adaptor->fetch_all_by_archive_id($self, 'Transcript');
}
}
=head2 get_all_translation_archive_ids
Example : my @archived_peptides =
@{ $arch_id->get_all_translation_archive_ids };
Description : Returns translation ArchiveStableIds associated with this
ArchiveStableId. If this is a translation, it returns itself.
Returntype : listref of Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_all_translation_archive_ids {
my $self = shift;
if ($self->type eq "Translation") {
return [$self];
} else {
return $self->adaptor->fetch_all_by_archive_id($self, 'Translation');
}
}
=head2 current_version
Example : if (my $v = $arch_id->current_version) {
print "Current version of this stable ID: ", $v, "\n";
} else {
print "This stable ID is not in the current db.\n";
}
Description : Lazy-loads the current version of stable ID
Return type : Boolean (TRUE is current version found, else FALSE)
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub current_version {
my $self = shift;
if (@_) {
$self->{'current_version'} = shift;
} elsif (! defined $self->{'current_version'}) {
if (defined $self->{'adaptor'}) {
# lazy load
$self->{'adaptor'}->lookup_current($self);
}
}
return $self->{'current_version'};
}
=head2 is_current
Example : if ($arch_id->is_current) {
print $arch_id->version, " is the current version of this
stable ID.\n";
}
Description : Determines if the version of this object is the current version
of this stable ID. Note that this method doesn't lazy-load the
current version of an ArchiveStableId; if you want to be sure,
use current_version() instead.
Return type : Boolean (TRUE if it is current, else FALSE)
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub is_current {
my $self = shift;
return ($self->{'version'} == $self->{'current_version'});
}
=head2 get_latest_incarnation
Example : my $latest = $arch_id->get_latest_incarnation;
print "Latest version of ".$arch_id->stable_id." is ".
$latest->version."\n";
Description : Returns the ArchiveStableId representing the latest version
of this stable ID. Returns itself if this already is the latest
version, otherwise fetches it from the db.
Return type : Bio::EnsEMBL::ArchiveStableId
Exceptions : none
Caller : general
Status : At Risk
: under development
=cut
sub get_latest_incarnation {
my $self = shift;
return $self if ($self->is_latest);
my $latest = $self->adaptor->fetch_by_stable_id($self->stable_id);
return $latest;
}
=head2 is_latest
Arg[1] : (optional) Boolean $is_latest
Example : if ($arch_id->is_latest) {
print "Version ".$arch_id->version." is the latest version
of ".$arch_id->stable_id."\n";
}
Description : Indicates whether this is the latest version of this stable ID.
Can also be used as a setter if we know this is the latest
version.
Return type : Boolean (TRUE if yes, FALSE if no)
Exceptions : none
Caller : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor->fetch_by_stable_id, general
Status : At Risk
: under development
=cut
sub is_latest {
my $self = shift;
$self->{'is_latest'} = shift if (@_);
return ($self->{'is_latest'} || $self->is_current);
}
#
# getter/setters for attributes
#
sub stable_id {
my $self = shift;
$self->{'stable_id'} = shift if (@_);
return $self->{'stable_id'};
}
sub version {
my $self = shift;
$self->{'version'} = shift if (@_);
return $self->{'version'};
}
sub db_name {
my $self = shift;
$self->{'db_name'} = shift if (@_);
return $self->{'db_name'};
}
sub release {
my $self = shift;
$self->{'release'} = shift if (@_);
return $self->{'release'};
}
sub assembly {
my $self = shift;
$self->{'assembly'} = shift if (@_);
return $self->{'assembly'};
}
sub type {
my $self = shift;
$self->{'type'} = shift if (@_);
return $self->{'type'};
}
sub adaptor {
my $self = shift;
$self->{'adaptor'} = shift if (@_);
return $self->{'adaptor'};
}
sub successors {
my $self = shift;
$self->{'successors'} = \@_;
return $self->{'successors'};
}
1;
]]>