Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::StableIdEvent Class Reference

List of all members.


Class Summary

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.

Available Methods

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

Method Documentation

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:
click to view
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:
click to view
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:
click to view
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;
                # 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:
click to view
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;
                # 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:
click to view
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:
click to view

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