Christopher Fields > BioPerl-1.6.921 > Bio::Annotation::Relation



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Module Version: 1.006921   Source   Latest Release: BioPerl-1.6.924


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   : confidence
 Usage   : $self->confidence($newval)
 Function: Gives the confidence value.
 Example :
 Returns : value of confidence
 Args    : newvalue (optional)


 Title   : confidence_type
 Usage   : $self->confidence_type($newtype)
 Function: Gives the confidence type.
 Example :
 Returns : type of confidence
 Args    : newtype (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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