Bio::EnsEMBL GoXref
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Summary
Bio::EnsEMBL::GoXref
Package variables
No package variables defined.
Inherit
Bio::EnsEMBL::DBEntry
Synopsis
  my $goxref = Bio::EnsEMBL::GoXref->new();
  $goxref->add_linkage_type('IEA');

  foreach my $evtag ( @{ $goxref->get_all_linkage_types() } ) {
    print "$evtag\n";
  }
Description
This class extends the DBEntry in order to associate Evidence Tags
to the relationship between EnsEMBL objects and GO identifiers. The
relationship to GO that is stored in the database is actually derived
through the relationship of EnsEMBL peptides to SwissProt peptides, i.e.
the relationship is derived like this:
  ENSP -> SWISSPROT -> GO
And the evidence tag describes the relationship between the SwissProt
Peptide and the GO entry.
In reality, however, we store this in the database like this:
  ENSP -> SWISSPROT
  ENSP -> GO
and the evidence tag hangs off of the relationship between the ENSP and
the GO identifier. Some ENSPs are associated with multiple closely
related Swissprot entries which may both be associated with the same GO
identifier but with different evidence tags. For this reason a single
'GoXref' can have multiple evidence tags.
Methods
add_linkage_typeDescriptionCode
flush_linkage_typesDescriptionCode
get_all_linkage_infoDescriptionCode
get_all_linkage_typesDescriptionCode
Methods description
add_linkage_typecode    nextTop
  Arg [1]    : string $value
               allowed values:
               'IC', 'IDA', 'IEA', 'IEP', 'IGI', 'IMP', 'IPI',
               'ISS', NAS', 'ND', 'TAS', 'NR', 'RCA'
  Arg [2]    : (optional) Bio::EnsEMBL::DBEntry $source
  Example    : $go_xref->add_linkage_type('IGI');
  Description: Associates a linkage type and source DBEntry with this go_xref
  Returntype : integer; number of linkages
  Exceptions : thrown if $linkage_type argument not supplied or
               the optional DBEntry is not a DBEntry object.
  Caller     : DBEntryAdaptor
  Status     : Experimantal
flush_linkage_typescodeprevnextTop
  Arg [1]    : none
  Example    : $goxr->flush_linkage_types
  Description: Removes any associated evidence tags
  Returntype : none
  Exceptions : none
  Caller     : general 
  Status     : Stable
get_all_linkage_infocodeprevnextTop
  Arg [1]    : none
  Example    : foreach (@{$gox->get_all_linkage_info})
                { print "evidence: $_->[0] via $_->[1]->display_id" }
  Description: Retrieves a list of evidence-tag/source-DBEntry pairs
               associated with this go_xref
  Returntype : listref of listrefs
  Exceptions : none
  Caller     : geneview? general.
  Status     : Experimental
get_all_linkage_typescodeprevnextTop
  Arg [1]    : none
  Example    : print( join( ' ',
                            @{ $goxr->get_all_linkage_types() } ),
                      "\n" );
  Description: Retrieves a unique list of evidence tags associated with 
               this go_xref
  Returntype : none
  Exceptions : none
  Caller     : geneview? general
  Status     : Stable
Methods code
add_linkage_typedescriptionprevnextTop
sub add_linkage_type {
  my ( $self, $lt, $source_dbentry ) = @_;

  if ( !defined($lt) ) {
    $self->throw("linkage type argument required");
  }

  if ( defined($source_dbentry)
       && !$source_dbentry->isa('Bio::EnsEMBL::DBEntry') )
  {
    $self->throw("source_dbentry must be a Bio::EnsEMBL::DBEntry");
  }

  $self->{'linkage_types'} ||= [];

  push @{ $self->{'linkage_types'} },
    [ $lt, ( $source_dbentry || () ) ];
}
flush_linkage_typesdescriptionprevnextTop
sub flush_linkage_types {
  my ($self) = @_;

  $self->{'linkage_types'} = [];
}

1;
}
get_all_linkage_infodescriptionprevnextTop
sub get_all_linkage_info {
  my ($self) = @_;

  return $self->{'linkage_types'} || [];
}
get_all_linkage_typesdescriptionprevnextTop
sub get_all_linkage_types {
  my ($self) = @_;

  my %seen;
  return [ grep  { !$seen{$_}++ }
             map { $_->[0] } @{ $self->{'linkage_types'} } ];

  #return [ map{ $_->[0]} @{ $self->{'linkage_types'} || [] } ];
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.