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

docs/ensembl_changes_spec.txt

@@ -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

modules/Bio/EnsEMBL/CircularSlice.pm

@@ -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;

modules/Bio/EnsEMBL/DBSQL/SequenceAdaptor.pm

@@ -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 

modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm

@@ -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);

modules/Bio/EnsEMBL/DBSQL/Support/BaseCache.pm

@@ -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.

modules/Bio/EnsEMBL/DBSQL/Support/LruIdCache.pm

@@ -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

modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm

@@ -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");

modules/Bio/EnsEMBL/Exon.pm

@@ -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

modules/Bio/EnsEMBL/Gene.pm

@@ -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

modules/Bio/EnsEMBL/RepeatMaskedSlice.pm

@@ -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;
 

modules/Bio/EnsEMBL/Slice.pm

@@ -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;

modules/Bio/EnsEMBL/Transcript.pm

@@ -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;

modules/Bio/EnsEMBL/Translation.pm

@@ -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;

modules/t/densityFeatureAdaptor.t

@@ -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() );