Commit 8766efdb authored by Alessandro Vullo's avatar Alessandro Vullo
Browse files

[ENSCORESW-2165]. Added extra parameter doc with example, with revised description of first one.

parent d315e0bd
......@@ -567,11 +567,18 @@ sub add_DBEntry {
=head2 get_all_DBEntries
Arg [1] : (optional) String, external database name
Arg [1] : (optional) String, external database name,
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external_db type
Arg [2] : (optional) String, external_db type, can be one of
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : @dbentries = @{ $gene->get_all_DBEntries() };
Example : my @dbentries = @{ $gene->get_all_DBEntries() };
@dbentries = @{ $gene->get_all_DBEntries('Uniprot%') };
@dbentries = @{ $gene->get_all_DBEntries('%', 'ENSEMBL') };}
Description: Retrieves DBEntries (xrefs) for this gene. This does
*not* include DBEntries that are associated with the
......@@ -654,8 +661,14 @@ sub get_all_object_xrefs {
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external database type, can be one of
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : @dblinks = @{ $gene->get_all_DBLinks() };
@dblinks = @{ $gene->get_all_DBLinks('Uniprot%') };
@dblinks = @{ $gene->get_all_DBLinks('%', 'ENSEMBL') };}
Description: Retrieves *all* related DBEntries for this gene. This
includes all DBEntries that are associated with the
......
......@@ -200,8 +200,14 @@ sub new {
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external database type, can be one of
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : my @dblinks = @{ $transcript->get_all_DBLinks() };
my @dblinks = @{ $transcript->get_all_DBLinks('Uniprot%') };
@dblinks = @{ $transcript->get_all_DBLinks('Uniprot%') };}
@dblinks = @{ $transcript->get_all_DBLinks('%', 'ENSEMBL') };
Description: Retrieves *all* related DBEntries for this
transcript. This includes all DBEntries that are
......@@ -283,11 +289,18 @@ sub get_all_xrefs {
=head2 get_all_DBEntries
Arg [1] : (optional) String, external database name
Arg [1] : (optional) String, external database name,
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external database type
Arg [2] : (optional) String, external database type, can be one of
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : my @dbentries = @{ $transcript->get_all_DBEntries() };
@dbentries = @{ $transcript->get_all_DBEntries('Uniprot%') };}
@dbentries = @{ $transcript->get_all_DBEntries('%', 'ENSEMBL') };}
Description: Retrieves DBEntries (xrefs) for this transcript.
This does *not* include the corresponding
......
......@@ -582,11 +582,18 @@ sub transform {
=head2 get_all_DBEntries
Arg [1] : (optional) String, external database name
Arg [1] : (optional) String, external database name,
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external_db type
Arg [2] : (optional) String, external_db type,
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : @dbentries = @{ $translation->get_all_DBEntries() };
Example : my @dbentries = @{ $translation->get_all_DBEntries() };
@dbentries = @{ $translation->get_all_DBEntries('Uniprot%') };
@dbentries = @{ $translation->get_all_DBEntries('%', 'ENSEMBL') };
Description: Retrieves DBEntries (xrefs) for this translation.
......@@ -691,8 +698,14 @@ sub add_DBEntry {
SQL wildcard characters (_ and %) can be used to
specify patterns.
Arg [2] : (optional) String, external database type, can be one of
('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL'),
SQL wildcard characters (_ and %) can be used to
specify patterns.
Example : my @dblinks = @{ $translation->get_all_DBLinks() };
my @dblinks = @{ $translation->get_all_DBLinks('Uniprot%') };
@dblinks = @{ $translation->get_all_DBLinks('Uniprot%') };
@dblinks = @{ $translation->get_all_DBLinks('%', 'ENSEMBL') };
Description: This is here for consistancy with the Transcript
and Gene classes. It is a synonym for the
......
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