--- name: "Bio::SeqFeature::Annotated" section: "3pm" platform: "linux" package: "libbio-featureio-perl" version: "1.6.905-2" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::SeqFeature::Annotated" --- # Bio::SeqFeature::Annotated(3pm) PLEASE PUT SOMETHING HERE ## NAME Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE ## SYNOPSIS ``` # none yet, complain to authors ``` ## DESCRIPTION None yet, complain to authors. ## Implemented Interfaces This class implements the following interfaces. - Bio::SeqFeatureI Note that this includes implementing Bio::RangeI. - Bio::AnnotatableI - Bio::FeatureHolderI Features held by a feature are essentially sub-features. ## FEEDBACK ### Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. ``` bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists ``` ### Support Please direct usage questions or support issues to the mailing list: *bioperl-l@bioperl.org* rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. ### Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: ``` http://bugzilla.open-bio.org/ ``` ## AUTHOR - Allen Day Allen Day \ ## APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_ ## PREAMBLE Okay, where to start... The original idea for this class appears to lump all SeqFeatureI data (primary\_tag, source\_tag, etc) into AnnotationI objects into an Bio::Annotation::Collection. The type is then checked against SOFA. There have been several requests to have type checking be optionally run. Bio::FeatureHolderI::create\_hierarchy\_from\_ParentIDs Bio::FeatureHolderI::feature\_count Bio::FeatureHolderI::get\_all\_SeqFeatures Bio::FeatureHolderI::set\_ParentIDs\_from\_hierarchy Bio::RangeI::contains Bio::RangeI::disconnected\_ranges Bio::RangeI::equals Bio::RangeI::intersection Bio::RangeI::offsetStranded Bio::RangeI::overlap\_extent Bio::RangeI::overlaps Bio::RangeI::subtract Bio::RangeI::union Bio::SeqFeature::Annotated::Dumper Bio::SeqFeature::Annotated::MAX\_TYPE\_CACHE\_MEMBERS Bio::SeqFeature::Annotated::add\_Annotation Bio::SeqFeature::Annotated::add\_SeqFeature Bio::SeqFeature::Annotated::add\_tag\_value Bio::SeqFeature::Annotated::add\_target Bio::SeqFeature::Annotated::annotation Bio::SeqFeature::Annotated::attach\_seq Bio::SeqFeature::Annotated::display\_name Bio::SeqFeature::Annotated::each\_target Bio::SeqFeature::Annotated::end Bio::SeqFeature::Annotated::entire\_seq Bio::SeqFeature::Annotated::frame Bio::SeqFeature::Annotated::from\_feature Bio::SeqFeature::Annotated::get\_Annotations Bio::SeqFeature::Annotated::get\_SeqFeatures Bio::SeqFeature::Annotated::get\_all\_tags Bio::SeqFeature::Annotated::get\_tag\_values Bio::SeqFeature::Annotated::get\_tagset\_values Bio::SeqFeature::Annotated::has\_tag Bio::SeqFeature::Annotated::length Bio::SeqFeature::Annotated::location Bio::SeqFeature::Annotated::name Bio::SeqFeature::Annotated::new Bio::SeqFeature::Annotated::phase Bio::SeqFeature::Annotated::primary\_tag Bio::SeqFeature::Annotated::remove\_Annotations Bio::SeqFeature::Annotated::remove\_SeqFeatures Bio::SeqFeature::Annotated::remove\_tag Bio::SeqFeature::Annotated::score Bio::SeqFeature::Annotated::seq Bio::SeqFeature::Annotated::seq\_id Bio::SeqFeature::Annotated::source Bio::SeqFeature::Annotated::source\_tag Bio::SeqFeature::Annotated::start Bio::SeqFeature::Annotated::strand Bio::SeqFeature::Annotated::type Bio::SeqFeature::Annotated::uri\_escape Bio::SeqFeature::Annotated::uri\_unescape Bio::SeqFeature::TypedSeqFeatureI::croak Bio::SeqFeature::TypedSeqFeatureI::ontology\_term Bio::SeqFeatureI::generate\_unique\_persistent\_id Bio::SeqFeatureI::gff\_string Bio::SeqFeatureI::primary\_id Bio::SeqFeatureI::spliced\_seq ## ATTRIBUTE ACCESSORS FOR Bio::SeqFeature::Annotated ### from\_feature ``` Usage: $obj->from_feature($myfeature); Desc : initialize this object with the contents of another feature object. Useful for converting objects like L to this class Ret : nothing meaningful Args : a single object of some other feature type, Side Effects: throws error on failure Example: ``` ### seq\_id() ``` Usage : $obj->seq_id($newval) Function: holds a string corresponding to the unique seq_id of the sequence underlying the feature (e.g. database accession or primary key). Returns : string representing the seq_id. Args : on set, some string or a Bio::Annotation::SimpleValue object. ``` ### name() ``` Usage : $obj->name($newval) Function: human-readable name for the feature. Returns : value of name (a scalar) Args : on set, new value (a scalar or undef, optional) ``` ### type() ``` Usage : $obj->type($newval) Function: a SOFA type for the feature. Returns : Bio::Annotation::OntologyTerm object representing the type. NB: to get a string, use primary_tag(). Args : on set, Bio::Annotation::OntologyTerm object. NB: to set a string (SOFA name or identifier), use primary_tag() ``` ### source() ``` Usage : $obj->source($newval) Function: holds the source of the feature. Returns : a Bio::Annotation::SimpleValue representing the source. NB: to get a string, use source_tag() Args : on set, a Bio::Annotation::SimpleValue object. NB: to set a string, use source_tag() ``` ### score() ``` Usage : $score = $feat->score() $feat->score($score) Function: holds a value corresponding to the score of the feature. Returns : a string representing the score. Args : on set, a scalar or a Bio::Annotation::SimpleValue object. ``` ### phase() ``` Usage : $phase = $feat->phase() $feat->phase($phase) Function: get/set on phase information Returns : a string 0,1,2,'.' Args : on set, one of 0,1,2,'.' or a Bio::Annotation::SimpleValue object holding one of 0,1,2,'.' as its value. ``` ### frame() ``` Usage : $frame = $feat->frame() $feat->frame($phase) Function: get/set on phase information Returns : a string 0,1,2,'.' Args : on set, one of 0,1,2,'.' or a Bio::Annotation::SimpleValue object holding one of 0,1,2,'.' as its value. ``` ## SHORTCUT METHODS TO ACCESS Bio::AnnotatableI INTERFACE METHODS ### add\_Annotation() ``` Usage : Function: $obj->add_Annotation() is a shortcut to $obj->annotation->add_Annotation Returns : Args : ``` ### remove\_Annotations() ``` Usage : Function: $obj->remove_Annotations() is a shortcut to $obj->annotation->remove_Annotations Returns : Args : ``` ## INTERFACE METHODS FOR Bio::SeqFeatureI Note that no methods are deprecated. Any SeqFeatureI methods must return strings (no objects). ### display\_name() ### primary\_tag() ### source\_tag() ### attach\_seq() ``` Usage : $sf->attach_seq($seq) Function: Attaches a Bio::Seq object to this feature. This Bio::Seq object is for the *entire* sequence: ie from 1 to 10000 Returns : TRUE on success Args : a Bio::PrimarySeqI compliant object ``` ### seq() ``` Usage : $tseq = $sf->seq() Function: returns a truncated version of seq() with bounds matching this feature Returns : sub seq (a Bio::PrimarySeqI compliant object) on attached sequence bounded by start & end, or undef if there is no sequence attached Args : none ``` ### entire\_seq() ``` Usage : $whole_seq = $sf->entire_seq() Function: gives the entire sequence that this seqfeature is attached to Returns : a Bio::PrimarySeqI compliant object, or undef if there is no sequence attached Args : none ``` ## INTERFACE METHODS FOR Bio::RangeI ``` as inherited via Bio::SeqFeatureI ``` ### length() ``` Usage : $feature->length() Function: Get the feature length computed as $feat->end - $feat->start + 1 Returns : integer Args : none ``` ### start() ``` Usage : $obj->start($newval) Function: Get/set on the start coordinate of the feature Returns : integer Args : on set, new value (a scalar or undef, optional) ``` ### end() ``` Usage : $obj->end($newval) Function: Get/set on the end coordinate of the feature Returns : integer Args : on set, new value (a scalar or undef, optional) ``` ### strand() ``` Usage : $strand = $feat->strand($newval) Function: get/set on strand information, being 1,-1 or 0 Returns : -1,1 or 0 Args : on set, new value (a scalar or undef, optional) ``` ## INTERFACE METHODS FOR Bio::FeatureHolderI This includes methods for retrieving, adding, and removing features. Since this is already a feature, features held by this feature holder are essentially sub-features. ### get\_SeqFeatures ``` Usage : @feats = $feat->get_SeqFeatures(); Function: Returns an array of Bio::SeqFeatureI objects Returns : An array Args : none ``` ### add\_SeqFeature() ``` Usage : $feat->add_SeqFeature($subfeat); $feat->add_SeqFeature($subfeat,'EXPAND') Function: adds a SeqFeature into the subSeqFeature array. with no 'EXPAND' qualifer, subfeat will be tested as to whether it lies inside the parent, and throw an exception if not. If EXPAND is used, the parent''s start/end/strand will be adjusted so that it grows to accommodate the new subFeature Example : Returns : nothing Args : a Bio::SeqFeatureI object ``` ### remove\_SeqFeatures() ``` Usage : $obj->remove_SeqFeatures Function: Removes all sub SeqFeatures. If you want to remove only a subset, remove that subset from the returned array, and add back the rest. Returns : The array of Bio::SeqFeatureI implementing sub-features that was deleted from this feature. Args : none ``` ## INTERFACE METHODS FOR Bio::AnnotatableI ### annotation() ``` Usage : $obj->annotation($annot_obj) Function: Get/set the annotation collection object for annotating this feature. Returns : A Bio::AnnotationCollectionI object Args : newvalue (optional) ``` ### location() ``` Usage : my $location = $seqfeature->location() Function: returns a location object suitable for identifying location of feature on sequence or parent feature Returns : Bio::LocationI object Args : [optional] Bio::LocationI object to set the value to. ``` ### add\_target() ``` Usage : $seqfeature->add_target(Bio::LocatableSeq->new(...)); Function: adds a target location on another reference sequence for this feature Returns : true on success Args : a Bio::LocatableSeq object ``` ### each\_target() ``` Usage : @targets = $seqfeature->each_target(); Function: Returns a list of Bio::LocatableSeqs which are the locations of this object. To obtain the "primary" location, see L. Returns : a list of 0..N Bio::LocatableSeq objects Args : none ``` ### \_expand\_region ``` Title : _expand_region Usage : $self->_expand_region($feature); Function: Expand the total region covered by this feature to accomodate for the given feature. May be called whenever any kind of subfeature is added to this feature. add_SeqFeature() already does this. Returns : Args : A Bio::SeqFeatureI implementing object. ``` ### get\_Annotations ``` Usage : my $parent = $obj->get_Annotations('Parent'); my @parents = $obj->get_Annotations('Parent'); Function: a wrapper around Bio::Annotation::Collection::get_Annotations(). Returns : returns annotations as Bio::Annotation::Collection::get_Annotations() does, but additionally returns a single scalar in scalar context instead of list context so that if an annotation tag contains only a single value, you can do: $parent = $feature->get_Annotations('Parent'); instead of: ($parent) = ($feature->get_Annotations('Parent'))[0]; if the 'Parent' tag has multiple values and is called in a scalar context, the number of annotations is returned. Args : an annotation tag name. ``` ## Bio::SeqFeatureI implemented methods These are specialized implementations of SeqFeatureI methods which call the internal Bio::Annotation::AnnotationCollection object. Just prior to the 1.5 release the below methods were moved from Bio::SeqFeatureI to Bio::AnnotatableI, and having Bio::SeqFeatureI inherit Bio::AnnotatableI. This behavior forced all Bio::SeqFeatureI-implementing classes to use Bio::AnnotationI objects for any data. It is the consensus of the core developers that this be rolled back in favor of a more flexible approach by rolling back the above changes and making this class Bio::AnnotatableI. The SeqFeatureI tag-related methods are reimplemented in order to approximate the same behavior as before. The methods below allow mapping of the "**get\_tag\_values()**"-style annotation access to Bio::AnnotationCollectionI. These need not be implemented in a Bio::AnnotationCollectionI compliant class, as they are built on top of the methods. For usage, see Bio::SeqFeatureI. ### has\_tag ### add\_tag\_value ### get\_tag\_values ``` Usage : @annotations = $obj->get_tag_values($tag) Function: returns annotations corresponding to $tag Returns : a list of scalars Args : tag name ``` ### get\_tagset\_values ``` Usage : @annotations = $obj->get_tagset_values($tag1,$tag2) Function: returns annotations corresponding to a list of tags. this is a convenience method equivalent to multiple calls to get_tag_values with each tag in the list. Returns : a list of Bio::AnnotationI objects. Args : a list of tag names ``` ### get\_all\_tags ``` Usage : @tags = $obj->get_all_tags() Function: returns a list of annotation tag names. Returns : a list of tag names Args : none ``` ### remove\_tag ``` Usage : See remove_Annotations(). Function: Returns : Args : Note : Contrary to what the name suggests, this method removes all annotations corresponding to $tag, not just a single anntoation. ```