From 26a31e8762bc9a80dddfa5c20c1e2986103b3e56 Mon Sep 17 00:00:00 2001
From: Dan Bolser <dbolser@ebi.ac.uk>
Date: Fri, 13 Sep 2013 16:16:58 +0000
Subject: [PATCH] Documentation changes worked out with Andy
---
modules/Bio/EnsEMBL/DBEntry.pm | 27 +++++++++++++++++++++------
1 file changed, 21 insertions(+), 6 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBEntry.pm b/modules/Bio/EnsEMBL/DBEntry.pm
index c828d46a6c..f5331ba1ab 100644
--- a/modules/Bio/EnsEMBL/DBEntry.pm
+++ b/modules/Bio/EnsEMBL/DBEntry.pm
@@ -337,8 +337,8 @@ sub comment {
Arg [1] : int $priority
Example : none
- Priority : Getter/setter for attribute 'priority'. Note this
- is the priority from the external_db table.
+ Priority : Getter/setter for attribute 'priority'.
+ The external database priority.
Returntype : String
Exceptions : none
Caller : general
@@ -391,6 +391,11 @@ sub db_display_name {
Arg [1] : String $info_type
Example : none
Description: Getter/setter for attribute 'info_type'.
+ Defines the method by which the linked object was
+ connected to this xref. Available types are:
+ 'CHECKSUM', 'COORDINATE_OVERLAP', 'DEPENDENT',
+ 'DIRECT', 'INFERRED_PAIR', 'MISC', 'NONE', 'PROBE',
+ 'PROJECTION', 'SEQUENCE_MATCH' AND 'UNMAPPED'.
Returntype : String
Exceptions : none
Caller : general
@@ -411,6 +416,8 @@ sub info_type {
Arg [1] : String $info_text
Example : none
Description: Getter/setter for attribute 'info_text'.
+ Additional information recorded during the xref
+ association. Intended to be used as metadata.
Returntype : String
Exceptions : none
Caller : general
@@ -430,6 +437,7 @@ sub info_text {
Arg [1] : String $object_xref_text
Example : none
Description: Getter/setter for attribute 'linkage_annotation'.
+ The object xref 'linkage annotation'.
Returntype : String
Exceptions : none
Caller : general
@@ -450,6 +458,7 @@ sub linkage_annotation {
Arg [1] : String $type
Example : none
Description: Getter/setter for attribute 'type'.
+ The external database type.
Returntype : String
Exceptions : none
Caller : general
@@ -468,6 +477,7 @@ sub type {
Arg [1] : String $secondary_db_name
Description: Getter/setter for attribute 'secondary_db_name'.
+ The external database 'secondary' database name.
Returntype : String
Exceptions : none
Caller : general
@@ -487,6 +497,7 @@ sub secondary_db_name {
Arg [1] : String $secondary_db_table
Description: Getter/setter for attribute 'secondary_db_table'.
+ The external database 'secondary' database table.
Returns : String
Exceptions : none
Caller : general
@@ -513,7 +524,6 @@ sub secondary_db_table {
=cut
-
sub add_synonym {
my ( $self, $arg ) = @_;
if( defined $arg ) {
@@ -612,6 +622,7 @@ sub flush_synonyms {
Arg [1] : (optional) String $arg - value to set
Description: Getter/setter for attribute 'status'.
+ The external database status.
Returntype : String
Exceptions : none
Caller : general
@@ -619,7 +630,6 @@ sub flush_synonyms {
=cut
-
sub status{
my ( $self, $arg ) = @_;
if( defined $arg ) {
@@ -632,6 +642,9 @@ sub status{
Arg [1] : (optional) String $arg - value to set
Description: Getter/setter for attribute ensembl_object_type.
+ The object xref ensembl object type, one of 'Gene',
+ 'Marker', 'Operon', 'OperonTranscript', 'RawContig',
+ 'Transcript' or 'Translation'.
Returntype : String
Exceptions : none
Caller : general
@@ -639,7 +652,6 @@ sub status{
=cut
-
sub ensembl_object_type{
my ( $self, $arg ) = @_;
if( defined $arg ) {
@@ -652,6 +664,10 @@ sub ensembl_object_type{
Arg [1] : (optional) String $arg - value to set
Description: Getter/setter for attribute ensembl_id.
+ The ensembl_id is the internal identifier of the object
+ linked via object_xref. This should be used in
+ conjunction with ensembl_object_type to identify the
+ correct object type.
Returntype : String
Exceptions : none
Caller : general
@@ -659,7 +675,6 @@ sub ensembl_object_type{
=cut
-
sub ensembl_id{
my ( $self, $arg ) = @_;
if( defined $arg ) {
--
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