Bio::SeqFeature::Annotated(3)

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 <allenday at ucla.edu>

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<Bio::SeqFeature::Generic> 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</location()>.
 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.