diff --git a/modules/Bio/EnsEMBL/Feature.pm b/modules/Bio/EnsEMBL/Feature.pm index f83de136e28fbb18159542728627c2be15acab4c..ebc712c200bf3fbd49884cd86e8cb40a12060894 100644 --- a/modules/Bio/EnsEMBL/Feature.pm +++ b/modules/Bio/EnsEMBL/Feature.pm @@ -28,7 +28,8 @@ Bio::EnsEMBL::Feature - Ensembl specific sequence feature. -start => 100, -end => 220, -strand => -1, - -slice => $slice -analysis => $analysis + -slice => $slice, + -analysis => $analysis ); my $start = $feat->start(); @@ -273,7 +274,6 @@ sub strand { Arg [1] : int start Arg [2] : int end Arg [3] : (optional) int strand - Example : None Description: Sets the start, end and strand in one call rather than in 3 seperate calls to the start(), end() and strand() methods. This is for convenience and for speed when this needs to be @@ -1412,7 +1412,7 @@ sub get_overlapping_Genes{ =head2 get_nearest_Gene - Description: Get all the nearest gene to the feature + Description: Get the nearest gene to the feature Returntype : Bio::EnsEMBL::Gene Caller : general Status : UnStable @@ -1434,7 +1434,7 @@ sub get_nearest_Gene { Example : $feature_summary = $feature->summary_as_hash(); Description : Retrieves a textual summary of this Feature. - Should be overidden by subclasses for specific tweaking + Should be overidden by subclasses for specific tweaking Returns : hashref of arrays of descriptive strings Status : Intended for internal use =cut @@ -1474,7 +1474,7 @@ sub species { =head2 contig - This method is deprecated and included for backwards compatibility only. + Deprecated - Included for backwards compatibility only. Use slice() instead =cut sub contig { @@ -1486,7 +1486,7 @@ sub contig { =head2 sub_SeqFeature - This method is deprecated and only for genebuild backwards compatibility. + Deprecated - For genebuild backwards compatibility. Avoid using it if possible =cut sub sub_SeqFeature{ @@ -1496,7 +1496,7 @@ sub sub_SeqFeature{ =head2 add_sub_SeqFeature - This method is deprecated and only for genebuild backwards compatibility. + Deprecated - only for genebuild backward compatibility. Avoid using it if possible =cut sub add_sub_SeqFeature{ @@ -1530,8 +1530,8 @@ sub add_sub_SeqFeature{ =head2 flush_sub_SeqFeature - This method is deprecated and only for genebuild backwards compatibility. - Avoid using it isf possible + Deprecated - Only for genebuild backwards compatibility. + Avoid using it if possible =cut sub flush_sub_SeqFeature { my ($self) = @_; @@ -1572,7 +1572,7 @@ sub _deprecated_transform { =head2 id -This method is deprecated and only included for backwards compatibility. +Deprecated - only included for backwards compatibility. Use display_id, hseqname, dbID or stable_id instead =cut