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ensembl-gh-mirror
ensembl
Commits
3a551aa7
Commit
3a551aa7
authored
Mar 19, 2019
by
Marek Szuba
Browse files
Documentation of private methods is now in PODs rather than comments
parent
443d4117
Changes
3
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3 changed files
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62 additions
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46 deletions
+62
-46
modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
+39
-30
modules/Bio/EnsEMBL/MicroRNA.pm
modules/Bio/EnsEMBL/MicroRNA.pm
+11
-9
modules/Bio/EnsEMBL/Utils/RNAProductTypeMapper.pm
modules/Bio/EnsEMBL/Utils/RNAProductTypeMapper.pm
+12
-7
No files found.
modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
View file @
3a551aa7
...
...
@@ -448,19 +448,21 @@ SQL
}
# _fetch_direct_query
# Arg [1] : reference to an array consisting of:
# - the name of the column to use in the WHERE clause,
# - the value fields from that column are to be equal to,
# - the data type of that column (e.g. SQL_INTEGER)
# Description: PRIVATE internal method shared between public fetch methods
# in order to avoid duplication of SQL-query logic. NOT SAFE
# to be handed directly to users because in its current form
# it can be trivially exploited to inject arbitrary SQL.
# Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs
# Exceptions : throws if RNAProduct type is absent or unknown
# Caller : internal
# Status : At Risk (In Development)
=head2 _fetch_direct_query
Arg [1] : reference to an array consisting of:
- the name of the column to use in the WHERE clause,
- the value fields from that column are to be equal to,
- the data type of that column (e.g. SQL_INTEGER)
Description: PRIVATE internal method shared between public fetch methods
in order to avoid duplication of SQL-query logic. NOT SAFE
to be handed directly to users because in its current form
it can be trivially exploited to inject arbitrary SQL.
Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs
Exceptions : throws if RNAProduct type is absent or unknown
Caller : internal
Status : At Risk (In Development)
=cut
sub
_fetch_direct_query
{
my
(
$self
,
$where_args
)
=
@_
;
...
...
@@ -488,15 +490,18 @@ sub _fetch_direct_query {
}
# _obj_from_sth
# Arg [1] : DBI statement handle
# Description: PRIVATE internal method shared between public SQL-query
# methods in order to avoid duplication of object-creation
# logic.
# Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs
# Exceptions : throws if RNAProduct type is absent or unknown
# Caller : internal
# Status : At Risk (In Development)
=head2 _obj_from_sth
Arg [1] : DBI statement handle
Description: PRIVATE internal method shared between public SQL-query
methods in order to avoid duplication of object-creation
logic.
Returntype : ArrayRef of either Bio::EnsEMBL::RNAProducts or undefs
Exceptions : throws if RNAProduct type is absent or unknown
Caller : internal
Status : At Risk (In Development)
=cut
sub
_obj_from_sth
{
my
(
$self
,
$sth
)
=
@_
;
my
@return_data
;
...
...
@@ -548,17 +553,21 @@ sub _obj_from_sth {
}
# _tables
# Arg [1] : none
# Description: PROTECTED implementation of superclass abstract method.
# Returns the names, aliases of the tables to use for queries.
# Returntype : list of listrefs of strings
# Exceptions : none
# Caller : internal
# Status : Stable
=head2 _tables
Arg [1] : none
Description: PROTECTED implementation of superclass abstract method.
Returns the names, aliases of the tables to use for queries.
Returntype : list of listrefs of strings
Exceptions : none
Caller : internal
Status : Stable
=cut
sub
_tables
{
## no critic (Subroutines::ProhibitUnusedPrivateSubroutines)
return
(['
rnaproduct
',
'
rp
']);
}
1
;
modules/Bio/EnsEMBL/MicroRNA.pm
View file @
3a551aa7
...
...
@@ -165,15 +165,17 @@ sub summary_as_hash {
}
# _validate_arm_value
# Arg [1] : int $arm which arm of the hairpin precursor this miRNA
# comes from
# Description: PRIVATE validates if its argument has one of the accepted
# values for specifying the miRNA hairpin arm.
# Returntype : none
# Exceptions : throw if the argument is out of bounds
# Caller : internal
# Status : Stable
=head2 _validate_arm_value
Arg [1] : int $arm which arm of the hairpin precursor this miRNA
comes from
Description: PRIVATE validates if its argument has one of the accepted
values for specifying the miRNA hairpin arm.
Returntype : none
Exceptions : throw if the argument is out of bounds
Caller : internal
Status : Stable
=cut
sub
_validate_arm_value
{
my
(
$arm
)
=
@_
;
...
...
modules/Bio/EnsEMBL/Utils/RNAProductTypeMapper.pm
View file @
3a551aa7
...
...
@@ -132,6 +132,7 @@ sub new {
return
$self
;
}
=head2 class_attribute_cache_map
Arg [1] : string $class_name - fully qualified RNA-product class name
...
...
@@ -158,6 +159,7 @@ sub class_attribute_cache_map {
return
$map
{
$class_name
};
}
=head2 class_to_type_code
Arg [1] : string $class_name - fully qualified RNA-product class name
...
...
@@ -213,14 +215,17 @@ sub type_code_to_class {
return
$map
{
$type_code
};
}
# _generate_reverse_map
# Description: PRIVATE generates class_name->type_code map from the
# type_code->class_name one.
# Returntype : none
# Exceptions : none
# Caller : internal
# Status : Stable
=head2 _generate_reverse_map
Description: PRIVATE generates class_name->type_code map from the
type_code->class_name one.
Returntype : none
Exceptions : none
Caller : internal
Status : Stable
=cut
sub
_generate_reverse_map
{
my
(
$self
)
=
@_
;
...
...
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