Sendu Bala
and 1 contributors

NAME

Bio::SeqFeature::Annotated - PLEASE PUT SOMETHING HERE

SYNOPSIS

    # none yet, complain to authors

DESCRIPTION

None yet, complain to authors.

Implemented Interfaces

This class implementes 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

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 _

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 : a Bio::Annotation::SimpleValue object 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.
 Args    : on set, a SOFA name, identifier, or Bio::Annotation::OntologyTerm object.

source()

 Usage   : $obj->source($newval)
 Function: holds a string corresponding to the source of the feature.
 Returns : a Bio::Annotation::SimpleValue object representing the source.
 Args    : on set, some scalar or a Bio::Annotation::SimpleValue object.

score()

 Usage   : $score = $feat->score()
           $feat->score($score)
 Function: holds a value corresponding to the score of the feature.
 Returns : a Bio::Annotation::SimpleValue object 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 Bio::Annotation::SimpleValue object holdig one of 0,1,2,'.'
           as its value.
 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 Bio::Annotation::SimpleValue object holdig one of 0,1,2,'.'
           as its value.
 Args    : on set, one of 0,1,2,'.' or a Bio::Annotation::SimpleValue
           object holding one of 0,1,2,'.' as its value.

SHORTCUT METHDODS 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

display_name()

 Deprecated, use L<Bio::SeqFeatureI/name()>.  Will raise a warning.

primary_tag()

 Deprecated, use L<Bio::SeqFeatureI/type()>.  Will raise a warning.

source_tag()

 Deprecated, use L<Bio::SeqFeatureI/source()>.  Will raise a warning.

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

has_tag()

 See Bio::AnnotatableI::has_tag().

add_tag_value()

 See Bio::AnnotatableI::add_tag_value().

get_tag_values()

 See Bio::AnnotationCollectionI::get_tag_values().

get_all_tags()

 See Bio::AnnotationCollectionI::get_all_annotation_keys().

remove_tag()

 See Bio::AnnotationCollectionI::remove_tag().

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    : ???

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.