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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

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NAME

Bio::EnsEMBL::StableIdEvent- object representing a stable ID mapping event

SYNOPSIS

my $old_id = Bio::EnsEMBL::ArchiveStableId->new(
  -stable_id => 'ENSG001',
  -version   => 1,
  -type      => 'Gene',
);

my $new_id = Bio::EnsEMBL::ArchiveStableId->new(
  -stable_id => 'ENSG001',
  -version   => 2,
  -type      => 'Gene',
);

my $event = Bio::EnsEMBL::StableIdEvent->new(
  -old_id => $old_id,
  -new_id => $new_id,
  -score  => 0.997
);

# directly access attributes in old and new ArchiveStableId
my $old_stable_id = $event->get_attribute( 'old', 'stable_id' );

DESCRIPTION

This object represents a stable ID mapping event. Such an event links two ArchiveStableIds with a mapping score.

METHODS

new
old_ArchiveStableId
new_ArchiveStableId
score
get_attribute
ident_string

RELATED MODULES

Bio::EnsEMBL::ArchiveStableId
Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
Bio::EnsEMBL::StableIdHistoryTree

new

Arg[1]      : Bio::EnsEMBL::ArchiveStableId $old_id
              The old ArchiveStableId in the mapping event
Arg[2]      : Bio::EnsEMBL::ArchiveStableId $new_id
              The new ArchiveStableId in the mapping event
Arg[3]      : (optional) float $score - score of this mapping event
Example     : my $event = Bio::EnsEMBL::StableIdEvent->new(
                $arch_id1, $arch_id2, 0.977);
Description : object constructor
Return type : Bio::EnsEMBL::StableIdEvent
Exceptions  : thrown on wrong argument types
Caller      : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor::fetch_history_tree_by_stable_id, general
Status      : At Risk
            : under development

old_ArchiveStableId

Arg[1]      : (optional) Bio::EnsEMBL::ArchiveStableId $archive_id, or undef
              The old ArchiveStableId to set for this mapping event
Example     : # getter
              my $archive_id = $event->old_ArchiveStableId;
              
              # setter
              $event->old_ArchiveStableId($archive_id);
Description : Getter/setter for old ArchiveStableId in this mapping event.
Return type : Bio::EnsEMBL::ArchiveStableId
Exceptions  : thrown on wrong argument type
Caller      : general
Status      : At Risk
            : under development

new_ArchiveStableId

Arg[1]      : (optional) Bio::EnsEMBL::ArchiveStableId $archive_id, or undef
              The new ArchiveStableId to set for this mapping event
Example     : # getter
              my $archive_id = $event->new_ArchiveStableId;
              
              # setter
              $event->new_ArchiveStableId($archive_id);
Description : Getter/setter for new ArchiveStableId in this mapping event.
Return type : Bio::EnsEMBL::ArchiveStableId
Exceptions  : thrown on wrong argument type
Caller      : general
Status      : At Risk
            : under development

score

Arg[1]      : (optional) float $score - the score to set
Example     : my $score = $event->score;
Description : Getter/setter for mapping event score.
Return type : float or undef
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

get_attribute

Arg[1]      : String $type - determines whether to get attribute from 'old'
              or 'new' ArchiveStableId
Arg[2]      : String $attr - ArchiveStableId attribute to fetch
Example     : my $old_stable_id = $event->get_attribute('old', 'stable_id');
Description : Accessor to attributes of the ArchiveStableIds attached to this
              event. Convenience method that does the check for undef old
              and/or new ArchiveStableId for you.
Return type : same as respective method in Bio::EnsEMBL::ArchiveStableId, or
              undef
Exceptions  : thrown on wrong arguments
Caller      : general
Status      : At Risk
            : under development

ident_string

Example     : print $event->ident_string, "\n";
Description : Returns a string that can be used to identify your StableIdEvent.
              Useful in debug warnings.
Return type : String
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development