Commit 5941e41e authored by Marek Szuba's avatar Marek Szuba
Browse files

Document the use of ## no critic in comments

parent 3821b930
...@@ -565,6 +565,7 @@ sub _obj_from_sth { ...@@ -565,6 +565,7 @@ sub _obj_from_sth {
=cut =cut
# This method IS used, at the superclass level
sub _tables { ## no critic (Subroutines::ProhibitUnusedPrivateSubroutines) sub _tables { ## no critic (Subroutines::ProhibitUnusedPrivateSubroutines)
return (['rnaproduct', 'rp']); return (['rnaproduct', 'rp']);
} }
......
...@@ -92,6 +92,7 @@ use parent qw(Bio::EnsEMBL::RNAProduct); ...@@ -92,6 +92,7 @@ use parent qw(Bio::EnsEMBL::RNAProduct);
=cut =cut
# perlcritic doesn't know about rearrange(), silence it
sub new { ## no critic (Subroutines::RequireArgUnpacking) sub new { ## no critic (Subroutines::RequireArgUnpacking)
my $caller = shift; my $caller = shift;
......
...@@ -103,6 +103,7 @@ use parent qw(Bio::EnsEMBL::Storable); ...@@ -103,6 +103,7 @@ use parent qw(Bio::EnsEMBL::Storable);
=cut =cut
# perlcritic doesn't know about rearrange(), silence it
sub new { ## no critic (Subroutines::RequireArgUnpacking) sub new { ## no critic (Subroutines::RequireArgUnpacking)
my $caller = shift; my $caller = shift;
...@@ -524,6 +525,7 @@ sub get_all_DBEntries { ...@@ -524,6 +525,7 @@ sub get_all_DBEntries {
=cut =cut
# this is an alias, we do NOT want to unpack @_
sub get_all_DBLinks { ## no critic (Subroutines::RequireArgUnpacking) sub get_all_DBLinks { ## no critic (Subroutines::RequireArgUnpacking)
my $self = shift; my $self = shift;
return $self->get_all_DBEntries(@_); return $self->get_all_DBEntries(@_);
...@@ -554,6 +556,7 @@ sub get_all_DBLinks { ## no critic (Subroutines::RequireArgUnpacking) ...@@ -554,6 +556,7 @@ sub get_all_DBLinks { ## no critic (Subroutines::RequireArgUnpacking)
=cut =cut
# this is an alias, we do NOT want to unpack @_
sub get_all_object_xrefs { ## no critic (Subroutines::RequireArgUnpacking) sub get_all_object_xrefs { ## no critic (Subroutines::RequireArgUnpacking)
my $self = shift; my $self = shift;
return $self->get_all_DBEntries(@_); return $self->get_all_DBEntries(@_);
...@@ -580,6 +583,7 @@ sub get_all_object_xrefs { ## no critic (Subroutines::RequireArgUnpacking) ...@@ -580,6 +583,7 @@ sub get_all_object_xrefs { ## no critic (Subroutines::RequireArgUnpacking)
=cut =cut
# this is an alias, we do NOT want to unpack @_
sub get_all_xrefs { ## no critic (Subroutines::RequireArgUnpacking) sub get_all_xrefs { ## no critic (Subroutines::RequireArgUnpacking)
my $self = shift; my $self = shift;
return $self->get_all_DBLinks(@_); return $self->get_all_DBLinks(@_);
...@@ -619,6 +623,9 @@ sub modified_date { ...@@ -619,6 +623,9 @@ sub modified_date {
=cut =cut
# PBP do allow homonyms as methods but perlcritic cannot, tell these
# apart from the forbidden ones, as stated in the documentation of the
# relevant policy
sub length { ## no critic (Subroutines::ProhibitBuiltinHomonyms) sub length { ## no critic (Subroutines::ProhibitBuiltinHomonyms)
my $self = shift; my $self = shift;
my $seq = $self->seq(); my $seq = $self->seq();
......
...@@ -13,6 +13,7 @@ ...@@ -13,6 +13,7 @@
# See the License for the specific language governing permissions and # See the License for the specific language governing permissions and
# limitations under the License. # limitations under the License.
# This would go against this repository's convention for naming test files
## no critic (RequireFilenameMatchesPackage) ## no critic (RequireFilenameMatchesPackage)
package RNAProductTests; package RNAProductTests;
......
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