Commit 5fa472ed authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Add documentation for the get_all_xrefs() method.

parent faf4fab3
......@@ -702,7 +702,8 @@ sub get_all_DBEntries {
present on the gene (i.e. they have not already been
added or loaded).
NB: This method is an alias for get_all_DBentries()
NB: This method is an alias for the
get_all_DBentries() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
......@@ -763,6 +764,40 @@ sub get_all_DBLinks {
return \@links;
}
=head2 get_all_xrefs
Arg [1] : String database name (optional)
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : @xrefs = @{ $gene->get_all_xrefs() };
@xrefs = @{ $gene->get_all_xrefs('Uniprot%') };
Description: Retrieves *all* related xrefs for this gene. This
includes all xrefs that are associated with the
transcripts and corresponding translations of this
gene.
If you want to retrieve the xrefs associated
with only the gene (and not the transcript
or translations) then you should use the
get_all_object_xrefs() method instead.
Note: Each entry may be listed more than once. No
uniqueness checks are done. Also if you put in an
incorrect external database name no checks are done
to see if this exists, you will just get an empty
list.
NB: This method is an alias for the
get_all_DBLinks() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable
=cut
sub get_all_xrefs {
my $self = shift;
return $self->get_all_DBLinks(@_);
......
......@@ -228,6 +228,39 @@ sub get_all_DBLinks {
return \@links;
}
=head2 get_all_xrefs
Arg [1] : String database name (optional)
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : @xrefs = @{ $transcript->get_all_xrefs() };
@xrefs = @{ $transcript->get_all_xrefs('Uniprot%') };
Description: Retrieves *all* related xrefs for this transcript.
This includes all xrefs that are associated with the
corresponding translation of this transcript.
If you want to retrieve the xrefs associated with
only the transcript (and not the translation) then
you should use the get_all_object_xrefs() method
instead.
Note: Each entry may be listed more than once. No
uniqueness checks are done. Also if you put in an
incorrect external database name no checks are done
to see if this exists, you will just get an empty
list.
NB: This method is an alias for the
get_all_DBLinks() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable
=cut
sub get_all_xrefs {
my $self = shift;
return $self->get_all_DBLinks(@_);
......@@ -301,7 +334,8 @@ sub get_all_DBEntries {
present on the transcript (i.e. they have not already
been added or loaded).
NB: This method is an alias for get_all_DBentries()
NB: This method is an alias for the
get_all_DBentries() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
......
......@@ -617,7 +617,8 @@ sub get_all_DBEntries {
are present on the translation (i.e. they have not
already been added or loaded).
NB: This method is an alias for get_all_DBentries()
NB: This method is an alias for the
get_all_DBentries() method.
Return type: Listref of Bio::EnsEMBL::DBEntry objects
......@@ -683,6 +684,26 @@ sub get_all_DBLinks {
return $self->get_all_DBEntries(@_);
}
=head2 get_all_xrefs
Arg [1] : String database name (optional)
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : @xrefs = @{ $translation->get_all_xrefs() };
@xrefs = @{ $translation->get_all_xrefs('Uniprot%') };
Description: This method is here for consistancy with the Gene
and Transcript classes. It is an alias for the
get_all_DBLinks() method, which in turn directly
calls get_all_DBEntries().
Return type: Listref of Bio::EnsEMBL::DBEntry objects
Status : Stable
=cut
sub get_all_xrefs {
my $self = shift;
return $self->get_all_DBLinks(@_);
......
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