Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Sign in
Toggle navigation
Menu
Open sidebar
ensembl-gh-mirror
ensembl
Commits
de55403a
Commit
de55403a
authored
Apr 24, 2012
by
Kieron Taylor
😠
Browse files
POD corrections
parent
d260210b
Changes
8
Hide whitespace changes
Inline
Side-by-side
Showing
8 changed files
with
42 additions
and
47 deletions
+42
-47
modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
+2
-2
modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
+1
-2
modules/Bio/EnsEMBL/DensityFeature.pm
modules/Bio/EnsEMBL/DensityFeature.pm
+2
-2
modules/Bio/EnsEMBL/DensityFeatureSet.pm
modules/Bio/EnsEMBL/DensityFeatureSet.pm
+2
-2
modules/Bio/EnsEMBL/DensityType.pm
modules/Bio/EnsEMBL/DensityType.pm
+2
-5
modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
+0
-2
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
+0
-2
modules/Bio/EnsEMBL/Feature.pm
modules/Bio/EnsEMBL/Feature.pm
+33
-30
No files found.
modules/Bio/EnsEMBL/DBSQL/MergedAdaptor.pm
View file @
de55403a
...
...
@@ -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
...
...
modules/Bio/EnsEMBL/DBSQL/MetaCoordContainer.pm
View file @
de55403a
...
...
@@ -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
...
...
modules/Bio/EnsEMBL/DensityFeature.pm
View file @
de55403a
...
...
@@ -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
...
...
modules/Bio/EnsEMBL/DensityFeatureSet.pm
View file @
de55403a
...
...
@@ -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
...
...
modules/Bio/EnsEMBL/DensityType.pm
View file @
de55403a
...
...
@@ -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
...
...
modules/Bio/EnsEMBL/DnaDnaAlignFeature.pm
View file @
de55403a
...
...
@@ -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
...
...
modules/Bio/EnsEMBL/DnaPepAlignFeature.pm
View file @
de55403a
...
...
@@ -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
...
...
modules/Bio/EnsEMBL/Feature.pm
View file @
de55403a
...
...
@@ -759,7 +759,7 @@ sub transfer {
$clone->strand, "\n";
}
Description: Returns the results of 'projecting' this feature onto another
sl
c
ie . This is useful to see where a feature
sli
c
e . This is useful to see where a feature
would lie in a coordinate system in which it
crosses a boundary.
...
...
@@ -779,7 +779,7 @@ sub transfer {
If the feature projects entirely into a gap then a reference to
an empty list is returned.
Returntype : list
ref
erence
of Bio::EnsEMBL::ProjectionSegments
Returntype : listref of Bio::EnsEMBL::ProjectionSegments
which can also be used as [$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
ref
erence
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 : list
ref
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
");
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment