Bio::Annotation::Relation.3pm

Langue: en

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

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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)
 
 

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)