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ensembl-gh-mirror
ensembl
Commits
36ace0b8
Commit
36ace0b8
authored
Aug 07, 2014
by
Kieron Taylor
😠
Browse files
[
ENSCORESW-969
] [
ENSCORESW-901
] Massive pedantry commit.
parent
ea781cd6
Changes
14
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14 changed files
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24 additions
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24 deletions
+24
-24
docs/ensembl_changes_spec.txt
docs/ensembl_changes_spec.txt
+1
-1
modules/Bio/EnsEMBL/CircularSlice.pm
modules/Bio/EnsEMBL/CircularSlice.pm
+1
-1
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
+1
-1
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+1
-1
modules/Bio/EnsEMBL/DBSQL/Support/BaseCache.pm
modules/Bio/EnsEMBL/DBSQL/Support/BaseCache.pm
+1
-1
modules/Bio/EnsEMBL/DBSQL/Support/LruIdCache.pm
modules/Bio/EnsEMBL/DBSQL/Support/LruIdCache.pm
+1
-1
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
+1
-1
modules/Bio/EnsEMBL/Exon.pm
modules/Bio/EnsEMBL/Exon.pm
+1
-1
modules/Bio/EnsEMBL/Gene.pm
modules/Bio/EnsEMBL/Gene.pm
+2
-2
modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
+1
-1
modules/Bio/EnsEMBL/Slice.pm
modules/Bio/EnsEMBL/Slice.pm
+4
-4
modules/Bio/EnsEMBL/Transcript.pm
modules/Bio/EnsEMBL/Transcript.pm
+3
-3
modules/Bio/EnsEMBL/Translation.pm
modules/Bio/EnsEMBL/Translation.pm
+5
-5
modules/t/densityFeatureAdaptor.t
modules/t/densityFeatureAdaptor.t
+1
-1
No files found.
docs/ensembl_changes_spec.txt
View file @
36ace0b8
...
...
@@ -763,7 +763,7 @@ FeatureAdaptors
When performing a non-locational fetch (e.g. by dbID) features are still
returned in the coordinate system that they are calculated in. This is to
ensure that the feature can always be retr
e
ived in this manner of fetching
ensure that the feature can always be retri
e
ved in this manner of fetching
and so that features which are not in the database can be distinguished from
features which are simply not in the requested coordinate sytem. When a
single feature which is not in the database is requested via a non-locational
...
...
modules/Bio/EnsEMBL/CircularSlice.pm
View file @
36ace0b8
...
...
@@ -605,7 +605,7 @@ sub get_all_genotyped_VariationFeatures {
Arg [1] : none
Example : $features = $slice->get_all_DASFeatures;
Description: Retr
e
ives a hash reference to a hash of DAS feature
Description: Retri
e
ves a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
...
...
modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm
View file @
36ace0b8
...
...
@@ -157,7 +157,7 @@ sub clear_cache {
default = 1
Example : $dna = $seq_adptr->fetch_by_Slice_start_end_strand($slice, 1,
1000, -1);
Description:
r
etrieves from db the sequence for this slice
Description:
R
etrieves from db the sequence for this slice
uses AssemblyMapper to find the assembly
Returntype : string
Exceptions : endBasePair should be less or equal to length of slice
...
...
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
View file @
36ace0b8
...
...
@@ -80,7 +80,7 @@ the creation of Slice objects.
}
close FILE;
# retr
e
ive a list of slices from a file
# retri
e
ve a list of slices from a file
open( FILE, $filename ) or die("Could not open file $filename");
while ( $name = <FILE> ) {
chomp($name);
...
...
modules/Bio/EnsEMBL/DBSQL/Support/BaseCache.pm
View file @
36ace0b8
...
...
@@ -235,7 +235,7 @@ sub get_by_list {
Remember if the cache is un-aware of the key or the specific
implementation used cannot perform database lookups based on cache misses
you will not be able to retr
e
ive the object in question.
you will not be able to retri
e
ve the object in question.
Returntype : ArrayRef of found values
Exceptions : Thrown if SQL and parameters are empty and not the expected types. All
other exceptions come from DBI/SQL operations.
...
...
modules/Bio/EnsEMBL/DBSQL/Support/LruIdCache.pm
View file @
36ace0b8
...
...
@@ -156,7 +156,7 @@ sub get {
Arg [2] : Bio::EnsEMBL::Slice optional attribute for
C<_uncached_fetch_all_by_dbID_list()> delegation
Example : is($cache->get_by_list([1,2]), ['a','b']);
Description: Attempts to retr
e
ive all values currently available in the cache,
Description: Attempts to retri
e
ve all values currently available in the cache,
fetches any remaining values and stores these in the cache.
Returntype : ArrayRef of found values
Exceptions : None
...
...
modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm
View file @
36ace0b8
...
...
@@ -2061,7 +2061,7 @@ sub fetch_all_by_transcript_supporting_evidence {
sub
get_display_xref
{
my
(
$self
,
$transcript
)
=
@_
;
deprecate
("
display_xref should be retr
e
ived from Transcript object directly.
");
deprecate
("
display_xref should be retri
e
ved from Transcript object directly.
");
if
(
!
defined
$transcript
)
{
throw
("
Must call with a Transcript object
");
...
...
modules/Bio/EnsEMBL/Exon.pm
View file @
36ace0b8
...
...
@@ -1032,7 +1032,7 @@ sub flush_supporting_features {
Arg [1] : none
Example : @evidence = @{$exon->get_all_supporting_features()};
Description: Retr
e
ives any supporting features added manually by
Description: Retri
e
ves any supporting features added manually by
calls to add_supporting_features. If no features have been
added manually and this exon is in a database (i.e. it has
an adaptor), fetch from the database
...
...
modules/Bio/EnsEMBL/Gene.pm
View file @
36ace0b8
...
...
@@ -439,7 +439,7 @@ sub equals {
=head2 canonical_transcript
Arg [1] : (optional) Bio::EnsEMBL::Transcipt - canonical_transcript object
Arg [1] : (optional) Bio::EnsEMBL::Transc
r
ipt - canonical_transcript object
Example : $gene->canonical_transcript($canonical_transcript);
Description: Getter/setter for the canonical_transcript
Returntype : Bio::EnsEMBL::Transcript
...
...
@@ -1361,7 +1361,7 @@ sub get_all_DASFactories {
=head2 get_all_DAS_Features
Example : $features = $prot->get_all_DAS_Features;
Description: Retr
e
ives a hash reference to a hash of DAS feature
Description: Retri
e
ves a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features
...
...
modules/Bio/EnsEMBL/RepeatMaskedSlice.pm
View file @
36ace0b8
...
...
@@ -68,7 +68,7 @@ use vars qw(@ISA);
@ISA
=
('
Bio::EnsEMBL::Slice
');
# The BLOCK_PWR is the lob_bin of the chunksize where you want your repeat features
# to be retr
e
ived. This will create repeat feature retrieval calls that are likely
# to be retri
e
ved. This will create repeat feature retrieval calls that are likely
# to be on the same slice and hopefully create cache hits and less database traffic
my
$BLOCK_PWR
=
18
;
...
...
modules/Bio/EnsEMBL/Slice.pm
View file @
36ace0b8
...
...
@@ -2993,7 +2993,7 @@ sub _mask_features {
Arg [1] : scalar $ticket_ids
Example : $slice->get_all_SearchFeatures('BLA_KpUwwWi5gY');
Description: Retr
e
ives all search features for stored blast
Description: Retri
e
ves all search features for stored blast
results for the ticket that overlap this slice
Returntype : listref of Bio::EnsEMBL::SeqFeatures
Exceptions : none
...
...
@@ -3032,7 +3032,7 @@ sub get_all_SearchFeatures {
=head2 get_all_AssemblyExceptionFeatures
Example : $slice->get_all_AssemblyExceptionFeatures();
Description: Retr
e
ives all misc features which overlap this slice. If
Description: Retri
e
ves all misc features which overlap this slice. If
a set code is provided only features which are members of
the requested set are returned.
Returntype : listref of Bio::EnsEMBL::AssemblyExceptionFeatures
...
...
@@ -3057,7 +3057,7 @@ sub get_all_AssemblyExceptionFeatures {
Arg [1] : string $set (optional)
Arg [2] : string $database (optional)
Example : $slice->get_all_MiscFeatures('cloneset');
Description: Retr
e
ives all misc features which overlap this slice. If
Description: Retri
e
ves all misc features which overlap this slice. If
a set code is provided only features which are members of
the requested set are returned.
Returntype : listref of Bio::EnsEMBL::MiscFeatures
...
...
@@ -3295,7 +3295,7 @@ sub get_all_DASFeatures_dsn {
Arg [1] : none
Example : $features = $slice->get_all_DASFeatures;
Description: Retr
e
ives a hash reference to a hash of DAS feature
Description: Retri
e
ves a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
...
...
modules/Bio/EnsEMBL/Transcript.pm
View file @
36ace0b8
...
...
@@ -99,7 +99,7 @@ use vars qw(@ISA);
Arg [-MODIFIED_DATE]:
string - the date the transcript was last modified
Arg [-DESCRIPTION]:
string - the transcipts description
string - the transc
r
ipts description
Arg [-BIOTYPE]:
string - the biotype e.g. "protein_coding"
Arg [-STATUS]:
...
...
@@ -393,7 +393,7 @@ sub add_DBEntry {
=head2 get_all_supporting_features
Example : my @evidence = @{ $transcript->get_all_supporting_features };
Description: Retr
e
ives any supporting features added manually by
Description: Retri
e
ves any supporting features added manually by
calls to add_supporting_features.
Returntype : Listref of Bio::EnsEMBL::FeaturePair objects
Exceptions : none
...
...
@@ -2794,7 +2794,7 @@ sub get_all_DASFactories {
Arg [1] : none
Example : $features = $prot->get_all_DAS_Features;
Description: Retr
e
ives a hash reference to a hash of DAS feature
Description: Retri
e
ves a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
...
...
modules/Bio/EnsEMBL/Translation.pm
View file @
36ace0b8
...
...
@@ -1043,10 +1043,10 @@ sub add_Attributes {
=head2 get_all_SeqEdits
Arg [1] : ArrayRef $edits. Specify the name of the edits to fetch
Example : my @seqeds = @{$trans
cript
->get_all_SeqEdits()};
my @seqeds = @{$trans
cript
->get_all_SeqEdits('_selenocysteine')};
Example : my @seqeds = @{$trans
lation
->get_all_SeqEdits()};
my @seqeds = @{$trans
lation
->get_all_SeqEdits('_selenocysteine')};
Description: Retrieves all post transcriptional sequence modifications for
this trans
cript
.
this trans
lation
.
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : none
Caller : spliced_seq()
...
...
@@ -1078,7 +1078,7 @@ sub get_all_SeqEdits {
=head2 get_all_selenocysteine_SeqEdits
Example : my @edits = @{$trans
cript
->get_all_selenocysteine_SeqEdits()};
Example : my @edits = @{$trans
lation
->get_all_selenocysteine_SeqEdits()};
Description: Retrieves all post transcriptional sequence modifications related
to selenocysteine PTMs
Returntype : Bio::EnsEMBL::SeqEdit
...
...
@@ -1198,7 +1198,7 @@ sub get_all_DASFactories {
=head2 get_all_DAS_Features
Example : $features = $prot->get_all_DAS_Features;
Description: Retr
e
ives a hash reference to a hash of DAS feature
Description: Retri
e
ves a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
...
...
modules/t/densityFeatureAdaptor.t
View file @
36ace0b8
...
...
@@ -157,7 +157,7 @@ debug( "Created ".scalar( @density_features )." density features on chr 20" );
@stored_features
=
@
{
$dfa
->
fetch_all_by_Slice
(
$chr_20_slice
,'
GeneDensityTest
',
100
,
"
interpolate
"
)};
ok
(
scalar
(
@stored_features
)
==
100
);
debug
(
"
Interpolated retr
e
ived
"
.
scalar
(
@stored_features
));
debug
(
"
Interpolated retri
e
ved
"
.
scalar
(
@stored_features
));
ok
(
abs
(
$stored_features
[
0
]
->
density_value
()
-
15
)
<
0.0001
);
debug
(
"
Density value =
"
.
$stored_features
[
0
]
->
density_value
()
);
...
...
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