Bio::EnsEMBL::StableIdEvent Class Reference

Public Member Functions
public Bio::EnsEMBL::StableIdEvent	new ()
public Bio::EnsEMBL::ArchiveStableId	old_ArchiveStableId ()
public Bio::EnsEMBL::ArchiveStableId	new_ArchiveStableId ()
public Float	score ()
public Same	get_attribute ()
public String	ident_string ()

Detailed Description

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.

Definition at line 36 of file StableIdEvent.pm.

Member Function Documentation

get_attribute()

public Same Bio::EnsEMBL::StableIdEvent::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

Code:

ident_string()

public String Bio::EnsEMBL::StableIdEvent::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

Code:

new()

public Bio::EnsEMBL::StableIdEvent Bio::EnsEMBL::StableIdEvent::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

Code:

new_ArchiveStableId()

public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::StableIdEvent::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;
                
@section autotoc_md22 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

Code:

old_ArchiveStableId()

public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::StableIdEvent::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;
                
@section autotoc_md21 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

Code:

score()

public Float Bio::EnsEMBL::StableIdEvent::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

Code:

---

The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/StableIdEvent.pm