Bio::Annotation
SimpleValue
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Summary
Bio::Annotation::SimpleValue - A simple scalar
Package variables
No package variables defined.
Included modules
Inherit
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
Methods
Methods description
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 : 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 : 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] |
Title : tag_term
Usage : $obj->tag_term($newval)
Function: Get/set the 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 Bio::Ontology::TermI compliant object, or undef
Args : on set, new value (a Bio::Ontology::TermI compliant
object or undef, optional) |
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) |
Title : value
Usage : $obj->value($newval)
Function: Get/Set the value for simplevalue
Returns : value of value
Args : newvalue (optional) |
Methods code
sub as_text
{ my ($self) = @_;
return "Value: ".$self->value; } | sub hash_tree
{ my ($self) = @_;
my $h = {};
$h->{'value'} = $self->value;} | sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($value,$tag,$term) =
$self->_rearrange([qw(VALUE TAGNAME TAG_TERM)], @args);
defined $term && $self->tag_term($term);
defined $value && $self->value($value);
defined $tag && $self->tagname($tag);
return $self;} | sub tag_term
{ my $self = shift;
return $self->{'_tag_term'} = shift if @_;
return $self->{'_tag_term'};
}
1;} | sub tagname
{ my $self = shift;
if($self->{'_tag_term'}) {
$self->{'tagname'} = $_[0] if @_;
return $self->tag_term->name(@_);
}
return $self->{'tagname'} = shift if @_;
return $self->{'tagname'};} | sub value
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'value'} = $value;
}
return $self->{'value'};} | General documentation
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://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
| AnnotationI implementing functions | Top |
| Specific accessors for SimpleValue | Top |