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Bio::Annotation::SimpleValue.3pm

NAME

Bio::Annotation::SimpleValue - A simple scalar

SYNOPSIS

    use Bio::Annotation::SimpleValue;
    use Bio::Annotation::Collection;
 
    my $col = new Bio::Annotation::Collection;
    my $sv = new Bio::Annotation::SimpleValue(-value => 'someval');
    $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
 
 

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 - Ewan Birney

Email birney@ebi.ac.uk

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 = new Bio::Annotation::SimpleValue;
  Function: Instantiate a new SimpleValue object
  Returns : Bio::Annotation::SimpleValue object
  Args    : -value    => $value to initialize the object data field [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
 
 

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 SimpleValue

value

  Title   : value
  Usage   : $obj->value($newval)
  Function: Get/Set the value for simplevalue
  Returns : value of value
  Args    : newvalue (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)