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
Bio::Annotation::SimpleValue
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
newDescriptionCode
as_textDescriptionCode
display_textDescriptionCode
hash_treeDescriptionCode
tagnameDescriptionCode
valueDescriptionCode
_to_text
No description
Code
get_valuesDescriptionCode
get_all_valuesDescriptionCode
add_valueDescriptionCode
Methods description
newcode    nextTop
 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]
as_textcodeprevnextTop
 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_textcodeprevnextTop
 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_treecodeprevnextTop
 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
tagnamecodeprevnextTop
 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)
valuecodeprevnextTop
 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)
get_valuescodeprevnextTop
 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
get_all_valuescodeprevnextTop
 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
add_valuecodeprevnextTop
 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
newdescriptionprevnextTop
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 $self;
}
as_textdescriptionprevnextTop
sub as_text {
   my ($self) = @_;

   return "Value: ".$self->value;
}
display_textdescriptionprevnextTop
sub display_text {
    my ($self, $cb) = @_;
    $cb ||= $DEFAULT_CB;
    $self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
    return $cb->($self);
  }
}
hash_treedescriptionprevnextTop
sub hash_tree {
   my ($self) = @_;

   my $h = {};
   $h->{'value'} = $self->value;
}
tagnamedescriptionprevnextTop
sub tagname {
    my ($self,$value) = @_;
    if( defined $value) {
	$self->{'tagname'} = $value;
    }
    return $self->{'tagname'};
}
valuedescriptionprevnextTop
sub value {
    my ($self,$value,@args) = @_;

    # set mode?
return $self->add_value([0], $value) if defined($value) && (@args == 0); # no, get mode
# determine joins and brackets
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, $brackets); # if there's only brackets at the start and end, remove them
if((@{$self->{'values'}} == 1) && (length($brackets->[0]) == 1) && (length($brackets->[1]) == 1)) { my $re = '\\'.$brackets->[0]. '([^\\'.$brackets->[1].']*)\\'.$brackets->[1]; $txt =~ s/^$re$/$1/; } return $txt;
}
_to_textdescriptionprevnextTop
sub _to_text {
    my ($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;
}
get_valuesdescriptionprevnextTop
sub get_values {
    my $self = shift;

    return @{$self->{'values'}};
}
get_all_valuesdescriptionprevnextTop
sub get_all_values {
    my ($self) = @_;
    # we code lazy here and just take advantage of value()
my $txt = $self->value(-joins => ['@!@'], -brackets => ['','']); return split(/\@!\@/, $txt);
}
add_valuedescriptionprevnextTop
sub add_value {
    my ($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
FEEDBACKTop
Mailing ListsTop
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
SupportTop
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 BugsTop
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/
AUTHOR - Hilmar LappTop
Email hlapp-at-gmx.net
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
AnnotationI implementing functionsTop
Specific accessors for StructuredValueTop