Provided by: libbio-featureio-perl_1.6.905-2_all bug

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.