Commit 36ace0b8 authored by Kieron Taylor's avatar Kieron Taylor 😠
Browse files

[ENSCORESW-969] [ENSCORESW-901] Massive pedantry commit.

parent ea781cd6
......@@ -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 retreived in this manner of fetching
ensure that the feature can always be retrieved 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
......
......@@ -605,7 +605,7 @@ sub get_all_genotyped_VariationFeatures {
Arg [1] : none
Example : $features = $slice->get_all_DASFeatures;
Description: Retreives a hash reference to a hash of DAS feature
Description: Retrieves 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;
......
......@@ -157,7 +157,7 @@ sub clear_cache {
default = 1
Example : $dna = $seq_adptr->fetch_by_Slice_start_end_strand($slice, 1,
1000, -1);
Description: retrieves from db the sequence for this slice
Description: Retrieves 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
......
......@@ -80,7 +80,7 @@ the creation of Slice objects.
}
close FILE;
# retreive a list of slices from a file
# retrieve a list of slices from a file
open( FILE, $filename ) or die("Could not open file $filename");
while ( $name = <FILE> ) {
chomp($name);
......
......@@ -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 retreive the object in question.
you will not be able to retrieve 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.
......
......@@ -156,7 +156,7 @@ sub get {
Arg [2] : Bio::EnsEMBL::Slice optional attribute for
C<_uncached_fetch_all_by_dbID_list()> delegation
Example : is($cache->get_by_list([1,2]), ['a','b']);
Description: Attempts to retreive all values currently available in the cache,
Description: Attempts to retrieve all values currently available in the cache,
fetches any remaining values and stores these in the cache.
Returntype : ArrayRef of found values
Exceptions : None
......
......@@ -2061,7 +2061,7 @@ sub fetch_all_by_transcript_supporting_evidence {
sub get_display_xref {
my ($self, $transcript) = @_;
deprecate("display_xref should be retreived from Transcript object directly.");
deprecate("display_xref should be retrieved from Transcript object directly.");
if ( !defined $transcript ) {
throw("Must call with a Transcript object");
......
......@@ -1032,7 +1032,7 @@ sub flush_supporting_features {
Arg [1] : none
Example : @evidence = @{$exon->get_all_supporting_features()};
Description: Retreives any supporting features added manually by
Description: Retrieves 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
......
......@@ -439,7 +439,7 @@ sub equals {
=head2 canonical_transcript
Arg [1] : (optional) Bio::EnsEMBL::Transcipt - canonical_transcript object
Arg [1] : (optional) Bio::EnsEMBL::Transcript - 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: Retreives a hash reference to a hash of DAS feature
Description: Retrieves 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
......
......@@ -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 retreived. This will create repeat feature retrieval calls that are likely
# to be retrieved. 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;
......
......@@ -2993,7 +2993,7 @@ sub _mask_features {
Arg [1] : scalar $ticket_ids
Example : $slice->get_all_SearchFeatures('BLA_KpUwwWi5gY');
Description: Retreives all search features for stored blast
Description: Retrieves 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: Retreives all misc features which overlap this slice. If
Description: Retrieves 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: Retreives all misc features which overlap this slice. If
Description: Retrieves 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: Retreives a hash reference to a hash of DAS feature
Description: Retrieves 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;
......
......@@ -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 transcripts 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: Retreives any supporting features added manually by
Description: Retrieves 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: Retreives a hash reference to a hash of DAS feature
Description: Retrieves 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;
......
......@@ -1043,10 +1043,10 @@ sub add_Attributes {
=head2 get_all_SeqEdits
Arg [1] : ArrayRef $edits. Specify the name of the edits to fetch
Example : my @seqeds = @{$transcript->get_all_SeqEdits()};
my @seqeds = @{$transcript->get_all_SeqEdits('_selenocysteine')};
Example : my @seqeds = @{$translation->get_all_SeqEdits()};
my @seqeds = @{$translation->get_all_SeqEdits('_selenocysteine')};
Description: Retrieves all post transcriptional sequence modifications for
this transcript.
this translation.
Returntype : Bio::EnsEMBL::SeqEdit
Exceptions : none
Caller : spliced_seq()
......@@ -1078,7 +1078,7 @@ sub get_all_SeqEdits {
=head2 get_all_selenocysteine_SeqEdits
Example : my @edits = @{$transcript->get_all_selenocysteine_SeqEdits()};
Example : my @edits = @{$translation->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 = $prot->get_all_DAS_Features;
Description: Retreives a hash reference to a hash of DAS feature
Description: Retrieves a hash reference to a hash of DAS feature
sets, keyed by the DNS, NOTE the values of this hash
are an anonymous array containing:
(1) a pointer to an array of features;
......
......@@ -157,7 +157,7 @@ debug( "Created ".scalar( @density_features )." density features on chr 20" );
@stored_features = @{$dfa->fetch_all_by_Slice($chr_20_slice,'GeneDensityTest', 100, "interpolate" )};
ok( scalar( @stored_features ) == 100 );
debug( "Interpolated retreived ".scalar( @stored_features ));
debug( "Interpolated retrieved ".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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