Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

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

SYNOPSIS

          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);

DESCRIPTION

       Scalar value annotation object

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   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:

         https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Mira Han

       Email mirhan@indiana.edu

APPENDIX

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

   new
        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

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

   display_text
        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
                  returned
        Example :
        Returns : a string
        Args    : [optional] callback

   hash_tree
        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

   tagname
        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
                  object.

        Example :
        Returns : value of tagname (a scalar)
        Args    : new value (a scalar, optional)

Specific accessors for Relation

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

   to
        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)

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

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

   tag_term
        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)