Commit 3a551aa7 authored by Marek Szuba's avatar Marek Szuba
Browse files

Documentation of private methods is now in PODs rather than comments

parent 443d4117
......@@ -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;
......@@ -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) = @_;
......
......@@ -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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