Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)


Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI;


    use Bio::Annotation::Relation;
    use Bio::Annotation::Collection;
    my $col = Bio::Annotation::Collection->new();
    my $sv = Bio::Annotation::Relation->new(-type => "paralogy" -to => "someSeqI");
    $col->add_Annotation('tagname', $sv);


Scalar value annotation object


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AUTHOR - Mira Han



The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _


  Title   : new
  Usage   : my $sv = Bio::Annotation::Relation->new();
  Function: Instantiate a new Relation object
  Returns : Bio::Annotation::Relation object
  Args    : -type    => $type of relation [optional]
            -to     => $obj which $self is in relation to [optional]
            -tagname  => $tag to initialize the tagname [optional]
            -tag_term => ontology term representation of the tag [optional]

AnnotationI implementing functions


  Title   : as_text
  Usage   : my $text = $obj->as_text
  Function: return the string "Value: $v" where $v is the value
  Returns : string
  Args    : none


  Title   : display_text
  Usage   : my $str = $ann->display_text();
  Function: returns a string. Unlike as_text(), this method returns a string
            formatted as would be expected for te specific implementation.
            One can pass a callback as an argument which allows custom text
            generation; the callback is passed the current instance and any text
  Example :
  Returns : a string
  Args    : [optional] callback


  Title   : hash_tree
  Usage   : my $hashtree = $value->hash_tree
  Function: For supporting the AnnotationI interface just returns the value
            as a hashref with the key 'value' pointing to the value
  Returns : hashrf
  Args    : none


  Title   : tagname
  Usage   : $obj->tagname($newval)
  Function: Get/set the tagname for this annotation value.
            Setting this is optional. If set, it obviates the need to
            provide a tag to AnnotationCollection when adding this
  Example :
  Returns : value of tagname (a scalar)
  Args    : new value (a scalar, optional)

Specific accessors for Relation


  Title   : type 
  Usage   : $obj->type($newval)
  Function: Get/Set the type
  Returns : type of relation
  Args    : newtype (optional)


  Title   : to
  Usage   : $obj->to($newval)
  Function: Get/Set the object which $self is in relation to
  Returns : the object which the relation applies to
  Args    : new target object (optional)


  Title   : tag_term
  Usage   : $obj->tag_term($newval)
  Function: Get/set the L<Bio::Ontology::TermI> object representing
            the tag name.
            This is so you can specifically relate the tag of this
            annotation to an entry in an ontology. You may want to do
            this to associate an identifier with the tag, or a
            particular category, such that you can better match the tag
            against a controlled vocabulary.
            This accessor will return undef if it has never been set
            before in order to allow this annotation to stay
            light-weight if an ontology term representation of the tag
            is not needed. Once it is set to a valid value, tagname()
            will actually delegate to the name() of this term.
  Example :
  Returns : a L<Bio::Ontology::TermI> compliant object, or undef
  Args    : on set, new value (a L<Bio::Ontology::TermI> compliant
            object or undef, optional)