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Bio::SeqFeature::AnnotUser(Contributed Perl DocumBio::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.

perl v5.32.1			  2014-09-05	 Bio::SeqFeature::Annotated(3)

NAME | SYNOPSIS | DESCRIPTION | Implemented Interfaces | FEEDBACK | AUTHOR - Allen Day | APPENDIX | PREAMBLE | ATTRIBUTE ACCESSORS FOR Bio::SeqFeature::Annotated | SHORTCUT METHODS TO ACCESS Bio::AnnotatableI INTERFACE METHODS | INTERFACE METHODS FOR Bio::SeqFeatureI | INTERFACE METHODS FOR Bio::RangeI | INTERFACE METHODS FOR Bio::FeatureHolderI | INTERFACE METHODS FOR Bio::AnnotatableI | Bio::SeqFeatureI implemented methods

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