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Bio::SeqFeature::Annotated.3pm

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.