From 8766efdbe7a57445a66c812e17aa1bb559a1799a Mon Sep 17 00:00:00 2001
From: Alessandro Vullo <avullo@ebi.ac.uk>
Date: Tue, 5 Dec 2017 14:32:44 +0000
Subject: [PATCH] [ENSCORESW-2165]. Added extra parameter doc with example,
with revised description of first one.
---
modules/Bio/EnsEMBL/Gene.pm | 19 ++++++++++++++++---
modules/Bio/EnsEMBL/Transcript.pm | 19 ++++++++++++++++---
modules/Bio/EnsEMBL/Translation.pm | 21 +++++++++++++++++----
3 files changed, 49 insertions(+), 10 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Gene.pm b/modules/Bio/EnsEMBL/Gene.pm
index b1743bb3ee..adb808ee50 100755
--- a/modules/Bio/EnsEMBL/Gene.pm
+++ b/modules/Bio/EnsEMBL/Gene.pm
@@ -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
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index be65486ed7..8f9a87b583 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -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
diff --git a/modules/Bio/EnsEMBL/Translation.pm b/modules/Bio/EnsEMBL/Translation.pm
index 6d15dbbf85..372f1f01c4 100755
--- a/modules/Bio/EnsEMBL/Translation.pm
+++ b/modules/Bio/EnsEMBL/Translation.pm
@@ -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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