Bio::Annotation
StructuredValue
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Summary
Bio::Annotation::StructuredValue - A scalar with embedded structured
information
Package variables
Privates (from "my" definitions)
$DEFAULT_CB = sub { $_[0]->value || ''}
Inherit
Synopsis
use Bio::Annotation::StructuredValue;
use Bio::Annotation::Collection;
my $col = Bio::Annotation::Collection->new();
my $sv = Bio::Annotation::StructuredValue->new(-value => 'someval');
$col->add_Annotation('tagname', $sv);
Description
Scalar value annotation object.
Methods
Methods description
Title : new
Usage : my $sv = Bio::Annotation::StructuredValue->new();
Function: Instantiate a new StructuredValue object
Returns : Bio::Annotation::StructuredValue object
Args : -value => $value to initialize the object data field [optional]
-tagname => $tag to initialize the tagname [optional] |
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 : 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 |
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 : 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 this annotation.
Set mode is here only to retain compatibility with
SimpleValue. It is equivalent to calling
add_value([0], $newval).
In get mode, this implementation allows one to pass additional
parameters that control how the structured annotation
components will be joined together to form a
string. Recognized are presently
-joins a reference to an array of join strings, the
elements at index i applying to joining
annotations at dimension i. The last element
will be re-used for dimensions higher than i.
Defaults to ['; '].
-brackets a reference to an array of two strings
denoting the opening and closing brackets for
the elements of one dimension, if there is
more than one element in the dimension.
Defaults to ['(',')'].
Returns : value of value
Args : newvalue (optional) |
Title : get_values
Usage :
Function: Get the top-level array of values. Each of the elements will
recursively be a reference to an array or a scalar, depending
on the depth of this structured value annotation.
Example :
Returns : an array
Args : none |
Title : get_all_values
Usage :
Function: Flattens all values in this structured annotation and
returns them as an array.
Example :
Returns : the (flat) array of values
Args : none |
Title : add_value
Usage :
Function: Adds the given value to the structured annotation at the
given index.
The index is multi-dimensional, with the first dimension
applying to the first level, and so forth. If a particular
dimension or a particular index does not exist yet, it will
be created. If it does exist and adding the value would
mean replacing a scalar with an array reference, we throw
an exception to prevent unintended damage. An index of -1
at any dimension means append.
If an array of values is to be added, it will create an
additional dimension at the index specified, unless the
last index value is -1, in which case they will all be
appended to the last dimension.
Example :
Returns : none
Args : the index at which to add (a reference to an array)
the value(s) to add |
Methods code
sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($value,$tag) = $self->_rearrange([qw(VALUE TAGNAME)], @args);
$self->{'values'} = [];
defined $value && $self->value($value);
defined $tag && $self->tagname($tag);
return $self;} | sub as_text
{ my ($self) = @_;
return "Value: ".$self->value; } | sub display_text
{ my ($self, $cb) = @_;
$cb ||= $DEFAULT_CB;
$self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
return $cb->($self);
}} | sub hash_tree
{ my ($self) = @_;
my $h = {};
$h->{'value'} = $self->value;} | sub tagname
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'tagname'} = $value;
}
return $self->{'tagname'};} | sub value
{ my ($self,$value,@args) = @_;
return $self->add_value([0], $value) if defined($value) && (@args == 0);
unshift(@args, $value);
my ($joins, $brackets) =
$self->_rearrange([qw(JOINS BRACKETS)], @args);
$joins = ['; '] unless $joins;
$brackets = ['(', ')'] unless $brackets;
my $txt = &_to_text($self->{'values'}, $joins, $brackets);
if((@{$self->{'values'}} == 1) &&
(length($brackets->[0]) == 1) && (length($brackets->[1]) == 1)) {
my $re = '\\'.$brackets->[0].
'([^\\'.$brackets->[1].']*)\\'.$brackets->[1];
$txt =~ s/^$re$/$1/;
}
return $txt;} | sub _to_text
{ my ($arr, $joins, $brackets, $rec_n) = @_;
$rec_n = 0 unless defined($rec_n);
my $i = $rec_n >= @$joins ? @$joins-1 : $rec_n;
my $txt = join($joins->[$i],
map {
ref($_) ?
(ref($_) eq "ARRAY" ?
&_to_text($_, $joins, $brackets, $rec_n+1) :
$_->value()) :
$_;
} @$arr);
if($rec_n && (@$arr > 1)) {
$txt = $brackets->[0] . $txt . $brackets->[1];
}
return $txt;} | sub get_values
{ my $self = shift;
return @{$self->{'values'}};} | sub get_all_values
{ my ($self) = @_;
my $txt = $self->value(-joins => ['@!@'], -brackets => ['','']);
return split(/\@!\@/, $txt);} | sub add_value
{ my ($self,$index,@values) = @_;
my $tree = $self->{'values'};
my $lastidx = pop(@$index);
foreach my $i (@$index) {
if($i < 0) {
my $subtree = [];
push(@$tree, $subtree);
$tree = $subtree;
} elsif((! $tree->[$i]) || (ref($tree->[$i]) eq "ARRAY")) {
$tree->[$i] = [] unless ref($tree->[$i]) eq "ARRAY";
$tree = $tree->[$i];
} else {
$self->throw("element $i is a scalar but not in last dimension");
}
}
if($lastidx < 0) {
push(@$tree, @values);
} elsif(@values < 2) {
$tree->[$lastidx] = shift(@values);
} else {
$tree->[$lastidx] = [@values];
}
}
1;} | 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://bioperl.org/wiki/Mailing_lists - About the mailing lists
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.
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
or the web:
https://redmine.open-bio.org/projects/bioperl/
Email hlapp-at-gmx.net
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 StructuredValue | Top |