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Commit 443d4117 authored by Marek Szuba's avatar Marek Szuba
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s/rnaproduct/RNAProduct/ in comments

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Showing with 52 additions and 52 deletions
modules/Bio/EnsEMBL/DBSQL/RNAProductAdaptor.pm
View file @ 443d4117
......@@ -103,7 +103,7 @@ sub fetch_all_by_Transcript {
=head2 fetch_all_by_external_name
Arg [1] : String $external_name
An external identifier of the rnaproduct to be obtained
An external identifier of the RNAProduct to be obtained
Arg [2] : (optional) String $external_db_name
The name of the external database from which the
identifier originates.
......@@ -113,11 +113,11 @@ sub fetch_all_by_Transcript {
@{ $rp_a->fetch_all_by_external_name('MIMAT0000416') };
my @more_rnaproducts =
@{ $rp_a->fetch_all_by_external_name('hsa-miR-1-__') };
Description: Retrieves all rnaproducts which are associated with
Description: Retrieves all RNAProducts which are associated with
an external identifier such as a GO term, miRBase
identifer, etc. Usually there will only be a single
rnaproduct returned in the list reference, but not
always. If no rnaproducts with the external identifier
RNAProduct returned in the list reference, but not
always. If no RNAProducts with the external identifier
are found, a reference to an empty list is returned.
SQL wildcards % and _ are supported in the $external_name
but their use is somewhat restricted for performance reasons.
......@@ -192,10 +192,10 @@ sub fetch_all_by_type {
The internal identifier of the RNAProduct to obtain
Example : $rnaproduct = $rnaproduct_adaptor->fetch_by_dbID(1234);
Description: This fetches a RNAProduct object via its internal id.
This is only debatably useful since rnaproducts do
This is only debatably useful since RNAProducts do
not make much sense outside of the context of their
Transcript. Consider using fetch_by_Transcript instead.
Returntype : Bio::EnsEMBL::RNAProduct, or undef if the rnaproduct is not
Returntype : Bio::EnsEMBL::RNAProduct, or undef if the RNAProduct is not
found.
Caller : ?
Status : Stable
......@@ -219,7 +219,7 @@ sub fetch_by_dbID {
The stable identifier of the RNAProduct to obtain
Example : $rnaproduct = $rnaproduct_adaptor->fetch_by_stable_id("ENSM00001");
Description: This fetches a RNAProduct object via its stable id.
Returntype : Bio::EnsEMBL::RNAProduct, or undef if the rnaproduct is not
Returntype : Bio::EnsEMBL::RNAProduct, or undef if the RNAProduct is not
found.
Caller : ?
Status : Stable
......@@ -241,7 +241,7 @@ sub fetch_by_stable_id {
Arg [1] : none
Example : @rnaproduct_ids = @{$rnaproduct_adaptor->list_dbIDs()};
Description: Gets an array of internal ids for all rnaproducts in the current db
Description: Gets an array of internal ids for all RNAProducts in the current db
Returntype : list of ints
Exceptions : none
Caller : ?
......@@ -259,9 +259,9 @@ sub list_dbIDs {
=head2 remove
Arg [1] : Bio::EnsEMBL::RNAProduct $rnaproduct
The rnaproduct to be removed from the database
The RNAProduct to be removed from the database
Example : $rpID = $rp_adaptor->remove($rnaproduct, $transcript->dbID());
Description: Removes a rnaproduct, along with all associated information
Description: Removes a RNAProduct, along with all associated information
from the database.
Returntype : none
Exceptions : throw on incorrect arguments
......@@ -311,13 +311,13 @@ sub remove {
=head2 store
Arg [1] : Bio::EnsEMBL::RNAProduct $rnaproduct
The rnaproduct to be written to the database
The RNAProduct to be written to the database
Arg [2] : Int $transcript_dbID
The identifier of the transcript that this rnaproduct is
The identifier of the transcript that this RNAProduct is
associated with
Example : $rpID = $rp_adaptor->store($rnaproduct, $transcript->dbID());
Description: Stores a rnaproduct in the database and returns the new
internal identifier for the stored rnaproduct.
Description: Stores a RNAProduct in the database and returns the new
internal identifier for the stored RNAProduct.
Returntype : Int
Exceptions : throw on incorrect arguments
Caller : general
......@@ -418,7 +418,7 @@ sub store {
Arg[1] : String $table
Arg[2] : String $column
Example : $rnaproduct_adaptor->_list_dbIDs('rnaproduct', 'rnaproduct_id');
Description : Local reimplementation to ensure multi-species rnaproducts
Description : Local reimplementation to ensure multi-species RNAProducts
are limited to their species alone
Returntype : ArrayRef of specified IDs
Caller : Internal
......@@ -458,7 +458,7 @@ SQL
# 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
# Exceptions : throws if RNAProduct type is absent or unknown
# Caller : internal
# Status : At Risk (In Development)
......@@ -494,7 +494,7 @@ sub _fetch_direct_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
# Exceptions : throws if RNAProduct type is absent or unknown
# Caller : internal
# Status : At Risk (In Development)
sub _obj_from_sth {
......
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
View file @ 443d4117
......@@ -253,11 +253,11 @@ sub fetch_all_versions_by_stable_id {
=head2 fetch_by_rnaproduct_id
Arg [1] : Int $id
The internal identifier of the rnaproduct whose transcript
The internal identifier of the RNAProduct whose transcript
is to be retrieved
Example : my $tr = $tr_adaptor->fetch_by_rnaproduct_id($rnap->dbID);
Description: Given the internal identifier of a rnaproduct this method
retrieves the transcript associated with that rnaproduct.
Description: Given the internal identifier of a RNAProduct this method
retrieves the transcript associated with that RNAProduct.
If the transcript cannot be found undef is returned instead.
Returntype : Bio::EnsEMBL::Transcript or undef
Exceptions : none
......
modules/Bio/EnsEMBL/RNAProduct.pm
View file @ 443d4117
......@@ -77,17 +77,17 @@ use parent qw(Bio::EnsEMBL::Storable);
position of the product sequence.
Arg [-SEQ_END] : The offset in the Transcript indicating the end
position of the product sequence.
Arg [-START_EXON] : The Exon object in which the rnaproduct starts
Arg [-END_EXON] : The Exon object in which the rnaproduct ends
Arg [-START_EXON] : The Exon object in which the RNAProduct starts
Arg [-END_EXON] : The Exon object in which the RNAProduct ends
Arg [-STABLE_ID] : The stable identifier for this RNAPRoduct
Arg [-VERSION] : The version of the stable identifier
Arg [-DBID] : The internal identifier of this RNAProduct
Arg [-ADAPTOR] : The RNAProductAdaptor for this RNAProduct
Arg [-SEQ] : Manually sets the nucleotide sequence of this
rnaproduct. May be useful if this rnaproduct is not
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
Arg [-CREATED_DATE] : the date the RNAProduct was created
Arg [-MODIFIED_DATE]: the date the RNAProduct was modified
Example : my $rp = Bio::EnsEMBL::RNAProduct->new(
-SEQ_START => 36,
-SEQ_END => 58
......@@ -181,9 +181,9 @@ sub add_Attributes {
Arg [1] : Bio::EnsEMBL::DBEntry $dbe
The dbEntry to be added
Example : $rnaproduct->add_DBEntry($xref);
Description: Associates a DBEntry with this rnaproduct. Note that adding
Description: Associates a DBEntry with this RNAProduct. Note that adding
DBEntries will prevent future lazy-loading of DBEntries for this
rnaproduct (see get_all_DBEntries).
RNAProduct (see get_all_DBEntries).
Returntype : none
Exceptions : thrown on incorrect argument type
Caller : general
......@@ -208,9 +208,9 @@ sub add_DBEntry {
=head2 cdna_end
Example : $rnaproduct_cdna_end = $rnaproduct->cdna_end();
Description : Returns the end position of the rnaproduct in cDNA
Description : Returns the end position of the RNAProduct in cDNA
coordinates.
Since rnaproducts do not span multiple exons, this is
Since RNAProducts do not span multiple exons, this is
simply an alias for end().
Return type : Integer
Caller : General
......@@ -228,9 +228,9 @@ sub cdna_end {
=head2 cdna_start
Example : $rnaproduct_cdna_start = $rnaproduct->cdna_start();
Description : Returns the start position of the rnaproduct in cDNA
Description : Returns the start position of the RNAProduct in cDNA
coordinates.
Since rnaproducts do not span multiple exons, this is
Since RNAProducts do not span multiple exons, this is
simply an alias for start().
Return type : Integer
Caller : General
......@@ -270,7 +270,7 @@ sub created_date {
Example : print $rnaproduct->display_id();
Description: This method returns a string that is considered to be
the 'display' identifier. For rnaproducts this is (depending on
the 'display' identifier. For RNAProducts this is (depending on
availability and in this order) the stable ID, the dbID or an
empty string.
Returntype : string
......@@ -313,7 +313,7 @@ sub end {
Arg [1] : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign
Example : $rnaproduct->end_Exon($exon1);
Description: Getter/setter for the value of end_Exon, which denotes the
exon at which rnaproduct ends.
exon at which RNAProduct ends.
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
......@@ -344,7 +344,7 @@ sub end_Exon {
Args : None
Example : $rnaproduct_genomic_end = $rnaproduct->genomic_end();
Description : Returns the end position of the rnaproduct in genomic
Description : Returns the end position of the RNAProduct in genomic
coordinates on the forward strand.
Return type : Integer
Exceptions : None
......@@ -376,7 +376,7 @@ sub genomic_end {
Args : None
Example : $rnaproduct_genomic_start = $rnaproduct->genomic_start();
Description : Returns the start position of the rnaproduct in
Description : Returns the start position of the RNAProduct in
genomic coordinates on the forward strand.
Return type : Integer
Exceptions : None
......@@ -410,7 +410,7 @@ sub genomic_start {
The code of the attribute type to retrieve values for.
Example : ($n_attr) = @{$tl->get_all_Attributes('note')};
@rp_attributes = @{$rnaproduct->get_all_Attributes()};
Description: Gets a list of Attributes of this rnaproduct.
Description: Gets a list of Attributes of this RNAProduct.
Optionally just get Attributes for given code.
Returntype : listref Bio::EnsEMBL::Attribute
Exceptions : none
......@@ -422,7 +422,7 @@ sub genomic_start {
sub get_all_Attributes {
my ($self, $attrib_code) = @_;
# if not cached, retrieve all of the attributes for this rnaproduct
# If not cached, retrieve all of the attributes for this RNAProduct
if (!defined($self->{'attributes'}) && defined($self->adaptor())) {
my $aa = $self->adaptor->db->get_AttributeAdaptor();
$self->{'attributes'} = $aa->fetch_all_by_RNAProduct($self);
......@@ -453,11 +453,11 @@ sub get_all_Attributes {
@dbentries = @{ $rnaproduct->get_all_DBEntries('Uniprot%') };
@dbentries = @{ $rnaproduct->get_all_DBEntries('%', 'ENSEMBL') };
Description: Retrieves DBEntries (xrefs) for this rnaproduct.
Description: Retrieves DBEntries (xrefs) for this RNAProduct.
This method will attempt to lazy-load DBEntries
from a database if an adaptor is available and no
DBEntries are present on the rnaproduct (i.e. they
DBEntries are present on the RNAProduct (i.e. they
have not already been added or loaded).
Returntype : Listref to Bio::EnsEMBL::DBEntry objects
......@@ -480,7 +480,7 @@ sub get_all_DBEntries {
$cache_name .= $ex_db_type;
}
# if not cached, retrieve all of the xrefs for this rnaproduct
# If not cached, retrieve all of the xrefs for this RNAProduct
if (!defined($self->{$cache_name}) && defined($self->adaptor())) {
$self->{$cache_name} = $self->adaptor()->db()->get_DBEntryAdaptor()->
fetch_all_by_RNAProduct( $self, $ex_db_exp, $ex_db_type );
......@@ -535,11 +535,11 @@ sub get_all_DBLinks { ## no critic (Subroutines::RequireArgUnpacking)
Example : @oxrefs = @{ $rnaproduct->get_all_object_xrefs() };
Description: Retrieves xrefs for this rnaproduct.
Description: Retrieves xrefs for this RNAProduct.
This method will attempt to lazy-load xrefs from a
database if an adaptor is available and no xrefs
are present on the rnaproduct (i.e. they have not
are present on the RNAProduct (i.e. they have not
already been added or loaded).
NB: This method is an alias for the
......@@ -722,7 +722,7 @@ sub stable_id {
Arg [1] : (optional) String - the stable ID with version to set
Example : $rnaproduct->stable_id("ENSM0059890.3");
Description: Getter/setter for stable id with version for this rnaproduct.
Description: Getter/setter for stable id with version for this RNAProduct.
If the input string omits the version part, the version gets reset
to undef; use stable_id() if you want to avoid this.
Returntype : String
......@@ -780,7 +780,7 @@ sub start {
Arg [1] : (optional) Bio::EnsEMBL::Exon || undef - start exon to assign
Example : $rnaproduct->start_Exon($exon1);
Description: Getter/setter for the value of start_Exon, which denotes the
exon at which rnaproduct starts.
exon at which RNAProduct starts.
Returntype : Bio::EnsEMBL::Exon
Exceptions : thrown on wrong argument type
Caller : general
......@@ -898,9 +898,9 @@ sub synchronise_attributes {
Arg [1] : Transcript object (optional)
Description : Sets or retrieves the transcript object associated
with this rnaproduct object.
with this RNAProduct object.
Exceptions : Throws if there is no adaptor or no dbID defined for
the rnaproduct object.
the RNAProduct object.
Returntype : Bio::EnsEMBL::Transcript
=cut
......@@ -923,12 +923,12 @@ sub transcript {
} elsif (!defined($self->{'transcript'})) {
my $adaptor = $self->{'adaptor'};
if (!defined($adaptor)) {
throw("Adaptor not set for rnaproduct, cannot fetch its transcript");
throw("Adaptor not set for RNAProduct, cannot fetch its transcript");
}
my $dbID = $self->{'dbID'};
if (!defined($dbID)) {
throw("dbID not set for rnaproduct, cannot fetch its transcript.");
throw("dbID not set for RNAProduct, cannot fetch its transcript.");
}
$self->{'transcript'} =
......@@ -936,7 +936,7 @@ sub transcript {
->fetch_by_rnaproduct_id($dbID);
# Do not weaken the reference if we had to get the transcript from the
# database. The user is probably working on rnaproducts directly,
# database. The user is probably working on RNA products directly,
# not going through transcripts.
}
......
modules/Bio/EnsEMBL/Utils/RNAProductTypeMapper.pm
View file @ 443d4117
......@@ -134,7 +134,7 @@ sub new {
=head2 class_attribute_cache_map
Arg [1] : string $class_name - fully qualified rnaproduct class name
Arg [1] : string $class_name - fully qualified RNA-product class name
Example : my $attr_cache_map
= $mapper->class_attribute_cache_map( 'Bio::EnsEMBL::MicroRNA' );
Description: For the given name of a class representing a mature RNA
......@@ -160,7 +160,7 @@ sub class_attribute_cache_map {
=head2 class_to_type_code
Arg [1] : string $class_name - fully qualified rnaproduct class name
Arg [1] : string $class_name - fully qualified RNA-product class name
Example : my $type_code
= $mapper->class_to_type_code( 'Bio::EnsEMBL::MicroRNA' );
Description: For the given name of a class representing a mature RNA
......@@ -191,7 +191,7 @@ sub class_to_type_code {
=head2 type_code_to_class
Arg [1] : string $type_code - type code of rnaproduct
Arg [1] : string $type_code - type code of RNA product
Example : my $class_name = $mapper->class_to_type_code( 1 );
Description: For the type code representing a mature RNA product in the
Ensembl database, return its API class name
......
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