AnnotationCollectionI documentation.

Title : get_value
Usage : $ac->get_value($tagname) -or-
$ac->get_value( $tag_level1, $tag_level2,... )
Function: access the annotation value assocated with the given tags
Example :
Returns : a scalar
Args : an array of tagnames that descend into the annotation tree

Title : put_value
Usage : $ac->put_value($tagname, $value) -or-
$ac->put_value([$tag_level1, $tag_level2, ...], $value) -or-
$ac->put_value( [$tag_level1, $tag_level2, ...] )
Function: create a node in an annotation tree, and assign a scalar value to it
if a value is specified
Example :
Returns : scalar or a Bio::AnnotationCollection object
Args : $tagname, $value scalars (can be specified as -KEYS=>$tagname,
-VALUE=>$value) -or-
\@tagnames, $value (or as -KEYS=>\@tagnames, -VALUE=>$value )
Note : If intervening nodes do not exist, put_value creates them, replacing
existing nodes. So if $ac->put_value('x', 10) was done, then later,
$ac->put_value(['x', 'y'], 20), the original value of 'x' is trashed, and $ac->get_value('x') will now return the annotation collection
with tagname 'y'.

Title : get_keys
Usage : $ac->get_keys($tagname_level_1, $tagname_level_2,...)
Function: Get an array of tagnames underneath the named tag nodes
Example : # prints the values of the members of Category 1...
print map { $ac->get_value($_) } $ac->get_keys('Category 1') ;
Returns : array of tagnames or empty list if the arguments represent a leaf
Args : [array of] tagname[s]

sub get_value {

    local $_;
    my $self = shift;
    my @args = @_;
    my @h;
    return "" unless @_;
    while ($_ = shift @args) {
	@h = $self->get_Annotations($_);
	if (ref($h[0]->{value})) {
	    $self = $h[0]->{value}; # must be another Bio::AnnotationCollectionI
	}
	else {
	    last;
	}
    }
	return $h[0] && $h[0]->{value} ; # now the last value.

}

sub put_value {

    local $_;
    my $self = shift;
    my @args = @_;
    my ($keys, $value) = $self->_rearrange([qw( KEYS VALUE )], @args);
    my (@keys, $lastkey);
#    $value ||= new Bio::Annotation::Collection;
    @keys = (ref($keys) eq 'ARRAY') ? @$keys : ($keys);
    $lastkey = pop @keys;
    foreach (@keys) {
	my $a = $self->get_value($_);
	if (ref($a) && $a->isa('Bio::Annotation::Collection')) {
	    $self = $a;
	}
	else {
	    # replace an old value
	    $self->remove_Annotations($_) if $a;
	    my $ac = new Bio::Annotation::Collection;
	    $self->add_Annotation(new Bio::Annotation::SimpleValue(
				      -tagname => $_,
				      -value => $ac
				  )
		);
	    $self = $ac;
	}
    }
    if ($self->get_value($lastkey)) {
	# replace existing value
	($self->get_Annotations($lastkey))[0]->{value} = $value;
    }
    else {
	$self->add_Annotation(new Bio::Annotation::SimpleValue(
				  -tagname=>$lastkey,
				  -value=>$value
			      ));
    }
    return $value;

}

sub get_keys {

    my $self = shift;
    my @keys = @_;
    foreach (@keys) {
	my $a = $self->get_value($_);
	if (ref($a) && $a->isa('Bio::Annotation::Collection')) {
	    $self = $a;
	}
	else {
	    return ();
	}
    }
    return $self->get_all_annotation_keys();
}

1;

}

get_value	Description	Code
put_value	Description	Code
get_keys	Description	Code