Commit 3bcb7a52 authored by Marek Szuba's avatar Marek Szuba
Browse files

MicroRNA: get rid of FIXMEs from class documentation

1. List of arguments passed to the constructor now references the
superclass (a'la Feature class hierarchy) instead of listing them
explicitly.

2. Arm documentation now correctly lists values this property can take.
parent 91202fa8
......@@ -71,31 +71,18 @@ use parent qw(Bio::EnsEMBL::RNAProduct);
=head2 new
Arg [-SEQ_START] : The offset in the Translation indicating the start
position of the product sequence.
Arg [-SEQ_END] : The offset in the Translation indicating the end
position of the product sequence.
Arg [-STABLE_ID] : The stable identifier for this RNAPRoduct
Arg [-VERSION] : The version of the stable identifier
Arg [-DBID] : The internal identifier of this MicroRNA
Arg [-ADAPTOR] : The TranslationAdaptor for this MicroRNA
Arg [-SEQ] : Manually sets the nucleotide sequence of this
rnaproduct. May be useful if this rnaproduct is not
stored in a database.
Arg [-CREATED_DATE] : the date the rnaproduct was created
Arg [-MODIFIED_DATE]: the date the rnaproduct was modified
# FIXME: does all of the above have to be repeated here or can we somehow pull this from the superclass?
Arg: [-ARM] : which arm of the hairpin precursor this miRNA comes
from. Negative values indicate 3', positive ones - 5'.
FIXME: is this right?
from. Returns 3 and 5 for 3' and 5', respectively.
Arg [...] : Named arguments to superclass constructor
(see Bio::EnsEMBL::RNAProduct)
Example : my $miR = Bio::EnsEMBL::MicroRNA->new(
-SEQ_START => 36,
-SEQ_END => 58,
-ARM => -1
-ARM => 3
);
Description: Constructor. Creates a new MicroRNA object
Returntype : Bio::EnsEMBL::MicroRNA
Exceptions : none
Exceptions : throw if ARM value is out of bounds
Caller : general
Status : In Development
......@@ -123,12 +110,16 @@ sub new { ## no critic (Subroutines::RequireArgUnpacking)
=head2 arm
Arg [1] : (optional) int $arm which arm of the hairpin precursor
this miRNA comes from
Example : $mirna_arm = $mirna->arm();
Description : Returns the arm of the hairpin this miRNA comes from.
Negative values indicate the 3' end, positive ones
- the 5' one. FIXME: is this right?
$mirna->arm(3);
Description : Sets or returns the arm of the hairpin this miRNA comes
from. Accepted values are 3 and 5 for 3' and 5',
respectively.
Return type : Integer
Exceptions : warn if multiple 'mirna_arm' attributes exist
Exceptions : throw if setter is passed an incorrect value;
warn if multiple 'mirna_arm' attributes exist.
Caller : General
Status : Stable
......
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