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PDoc Bio::Annotation::Relation
CPAN Bio::Annotation::Relation
metaCPAN Bio::Annotation::Relation

this is a temporary document, it will be gone once the PDoc link is in work.


   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)
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