Commit de55403a authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

POD corrections

parent d260210b
......@@ -53,13 +53,13 @@ my $reg = "Bio::EnsEMBL::Registry";
=head2 new
Example : $MergedAdaptor = new
: Bio::EnsEMBL::DBSQL::MergedAdaptor(-species=> 'human', -type =>'Population', -groups => ['Sanger','Ensembl']);
Arg [SPECIES]: (optional) string
species name to get adaptors for
Arg [TYPE] : (optional) string
type to get adaptors for
Arg [GROUPS] : (optional) ref to list
Example : $MergedAdaptor = new
: Bio::EnsEMBL::DBSQL::MergedAdaptor(-species=> 'human', -type =>'Population', -groups => ['Sanger','Ensembl']);
Description: Creates a new MergedAdaptor
Returntype : Bio::EnsEMBL::DBSQL::MergedAdaptor
......
......@@ -124,8 +124,7 @@ sub fetch_all_CoordSystems_by_feature_type {
Arg [1] : Bio::EnsEMBL::CoordSystem $cs
Arg [2] : string $table
Example : $max_len =
$mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');
Example : $max_len = $mcc->fetch_max_length_by_CoordSystem_feature_type($cs,'gene');
Description: Returns the maximum length of features of a given type in
a given coordinate system.
Returntype : int or undef
......
......@@ -255,7 +255,7 @@ sub density_type{
Title : scaledvalue
Usage : $obj->scaledvalue($newval)
Function:
Returns : this objects scaled value
Returns : scalar - object's scaled value
Args : newvalue (optional)
Status : Stable
......@@ -277,7 +277,7 @@ sub scaledvalue{
Title : url
Usage : $obj->url($newval)
Function:
Returns : this object's url
Returns : String containing this object's url
Args : newvalue (optional)
Status : Stable
......
......@@ -150,7 +150,7 @@ sub colour{
Title : label
Usage : $obj->label($newval)
Function:
Returns : value of label
Returns : String containing label
Args : newvalue (optional)
Status : Stable
......@@ -170,7 +170,7 @@ sub label{
Title : label2
Usage : $obj->label2($newval)
Function:
Returns : value of label2
Returns : String containing label2
Args : newvalue (optional)
Status : Stable
......
......@@ -116,8 +116,7 @@ sub new {
=head2 analysis
Arg [1] : Bio::EnsEMBL::Analysi
Example : none
Arg [1] : Bio::EnsEMBL::Analysis
Description: get/set for attribute analysis
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
......@@ -142,8 +141,7 @@ sub analysis{
=head2 value_type
Arg [1] : string $value_type
Example : none
Description: gettter/setter for the
Description: gettter/setter for the type
Returntype : float
Exceptions : none
Caller : general
......@@ -161,7 +159,6 @@ sub value_type{
=head2 block_size
Arg [1] : int
Example : none
Description: getter/setter for attribute block_size
Returntype : int
Exceptions : none
......
......@@ -99,7 +99,6 @@ sub pair_dna_align_feature_id{
=head2 _hit_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method. Returns
1 as the 'unit' used for the hit sequence.
Returntype : int
......@@ -118,7 +117,6 @@ sub _hit_unit {
=head2 _query_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method Returns
1 as the 'unit' used for the hit sequence.
Returntype : int
......
......@@ -72,7 +72,6 @@ sub new_fast {
=head2 _hit_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method. Returns
1 as the 'unit' used for the hit sequence.
Returntype : int
......@@ -91,7 +90,6 @@ sub _hit_unit {
=head2 _query_unit
Arg [1] : none
Example : none
Description: PRIVATE implementation of abstract superclass method. Returns
3 as the 'unit' used for the query sequence.
Returntype : int
......
......@@ -759,7 +759,7 @@ sub transfer {
$clone->strand, "\n";
}
Description: Returns the results of 'projecting' this feature onto another
slcie . This is useful to see where a feature
slice . This is useful to see where a feature
would lie in a coordinate system in which it
crosses a boundary.
......@@ -779,7 +779,7 @@ sub transfer {
If the feature projects entirely into a gap then a reference to
an empty list is returned.
Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
Returntype : listref of Bio::EnsEMBL::ProjectionSegments
which can also be used as [$start,$end,$slice] triplets
Exceptions : slice does not have an adaptor
Caller : general
......@@ -853,7 +853,7 @@ sub project_to_slice {
If the feature projects entirely into a gap then a reference to
an empty list is returned.
Returntype : list reference of Bio::EnsEMBL::ProjectionSegments
Returntype : listref of Bio::EnsEMBL::ProjectionSegments
which can also be used as [$start,$end,$slice] triplets
Exceptions : slice does not have an adaptor
Caller : general
......@@ -1024,7 +1024,7 @@ sub seq_region_name {
Example : print $feature->seq_region_length();
Description: Returns the length of the seq_region which this feature is on
Returns undef if this Feature is not on a slice.
Returntype : unsigned int or undef
Returntype : int (unsigned) or undef
Exceptions : none
Caller : general
Status : Stable
......@@ -1242,7 +1242,7 @@ sub seq {
haplotypes will give you back the reference location, but not
locations on the other alternate haplotypes).
Returntype : reference to list of features of the same type of this feature.
Returntype : listref of features of the same type of this feature.
Exceptions : none
Caller : general
Status : Stable
......@@ -1465,11 +1465,11 @@ sub species {
##############################################
# contig
#
# This method is included for backwards compatibility.
# Use slice() instead
#
=head2 contig
This method is deprecated and included for backwards compatibility only.
Use slice() instead
=cut
sub contig {
deprecate('Use slice() instead');
slice(@_);
......@@ -1477,21 +1477,21 @@ sub contig {
# sub_SeqFeature
#
# This method is only for genebuild backwards compatibility.
# Avoid using it if possible
#
=head2 sub_SeqFeature
This method is deprecated and only for genebuild backwards compatibility.
Avoid using it if possible
=cut
sub sub_SeqFeature{
my ($self) = @_;
return @{$self->{'_gsf_sub_array'}} if($self->{'_gsf_sub_array'});
}
# add_sub_SeqFeature
#
# This method is only for genebuild backwards compatibility.
# Avoid using it if possible
#
=head2 add_sub_SeqFeature
This method is deprecated and only for genebuild backwards compatibility.
Avoid using it if possible
=cut
sub add_sub_SeqFeature{
my ($self,$feat,$expand) = @_;
my ($p, $f, $l) = caller;
......@@ -1521,11 +1521,11 @@ sub add_sub_SeqFeature{
push(@{$self->{'_gsf_sub_array'}},$feat);
}
# flush_sub_SeqFeature
#
# This method is only for genebuild backwards compatibility.
# Avoid using it isf possible
#
=head2 flush_sub_SeqFeature
This method is deprecated and only for genebuild backwards compatibility.
Avoid using it isf possible
=cut
sub flush_sub_SeqFeature {
my ($self) = @_;
$self->{'_gsf_sub_array'} = [];
......@@ -1562,11 +1562,14 @@ sub _deprecated_transform {
return $self;
}
# id
#
# This method is included for backwards compatibility only.
# Use hseqname or dbID or stable_id instead
#
=head2 id
This method is deprecated and only included for backwards compatibility.
Use display_id, hseqname, dbID or stable_id instead
=cut
sub id {
my $self = shift;
deprecate("id method is not used - use display_id instead");
......
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