# $Id: TagTree.pm 11693 2007-09-17 20:54:04Z cjfields $
#
# BioPerl module for Bio::Annotation::TagTree
#
# Cared for Chris Fields
#
# You may distribute this module under the same terms as perl itself.
# Refer to the Perl Artistic License (see the license accompanying this
# software package, or see http://www.perl.com/language/misc/Artistic.html)
# for the terms under which you may use, modify, and redistribute this module.
#
# THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
# WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF
# MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Annotation::TagTree - AnnotationI with tree-like hierarchal key-value
relationships ('structured tags') that can be represented as simple text.
=head1 SYNOPSIS
use Bio::Annotation::TagTree;
use Bio::Annotation::Collection;
my $col = Bio::Annotation::Collection->new();
# data structure can be an array reference with a data structure
# corresponding to that defined by Data::Stag:
my $sv = Bio::Annotation::TagTree->new(-tagname => 'mytag1',
-value => $data_structure);
$col->add_Annotation($sv);
# regular text passed is parsed based on the tagformat().
my $sv2 = Bio::Annotation::TagTree->new(-tagname => 'mytag2',
-tagformat => 'xml',
-value => $xmltext);
$col->add_Annotation($sv2);
=head1 DESCRIPTION
This takes tagged data values and stores them in a hierarchal structured
element-value hierarchy (complements of Chris Mungall's Data::Stag module). Data
can then be represented as text using a variety of output formats (indention,
itext, xml, spxr). Furthermore, the data structure can be queried using various
means. See L<Data::Stag> for details.
Data passed in using value() or the '-value' parameter upon instantiation
can either be:
1) an array reference corresponding to the data structure for Data::Stag;
2) a text string in 'xml', 'itext', 'spxr', or 'indent' format. The default
format is 'xml'; this can be changed using tagformat() prior to using value() or
by passing in the proper format using '-tagformat' upon instantiation;
3) another Bio::Annotation::TagTree or Data::Stag node instance. In both cases
a deep copy (duplicate) of the instance is generated.
Beyond checking for an array reference no format guessing occurs (so, for
roundtrip tests ensure that the IO formats correspond). For now, we recommend
when using text input to set tagformat() to one of these formats prior to data
loading to ensure the proper Data::Stag parser is selected. After data loading,
the tagformat() can be changed to change the text string format returned by
value(). (this may be rectified in the future)
This Annotation type is fully BioSQL compatible and could be considered a
temporary replacement for nested Bio::Annotation::Collections, at least until
BioSQL and bioperl-db can support nested annotation collections.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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
or the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Chris Fields
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Annotation::TagTree;
use strict;
# Object preamble - inherits from Bio::Root::Root
use base qw(Bio::Annotation::SimpleValue);
use Data::Stag;
=head2 new
Title : new
Usage : my $sv = Bio::Annotation::TagTree->new();
Function: Instantiate a new TagTree object
Returns : Bio::Annotation::TagTree object
Args : -value => $value to initialize the object data field [optional]
-tagname => $tag to initialize the tagname [optional]
-tagformat => format for output [optional]
(types 'xml', 'itext', 'sxpr', 'indent', default = 'itext')
-node => Data::Stag node or Bio::Annotation::TagTree instance
=cut
sub new {
my ( $class, @args ) = @_;
my $self = $class->SUPER::new();
my ( $node, $value, $tag, $format, $verbose ) = $self->_rearrange(
[
qw(
NODE
VALUE
TAGNAME
TAGFORMAT
VERBOSE)
],
@args
);
$self->throw("Cant use both node and value; mutually exclusive")
if defined $node && defined $value;
defined $tag && $self->tagname($tag);
$format ||= 'itext';
$self->tagformat($format);
defined $value && $self->value($value);
defined $node && $self->node($node);
defined $verbose && $self->verbose($verbose);
return $self;
}
=head1 AnnotationI implementing functions
=cut
=head2 as_text
Title : as_text
Usage : my $text = $obj->as_text
Function: return the string "Value: $v" where $v is the value
Returns : string
Args : none
=cut
sub as_text {
my ($self) = @_;
return "TagTree: " . $self->value;
}
=head2 display_text
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 the 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
=cut
{
my $DEFAULT_CB = sub { $_[0]->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);
}
}
=head2 hash_tree
Title : hash_tree
Usage : my $hashtree = $value->hash_tree
Function: For supporting the AnnotationI interface just returns the value
as a hashref with the key 'value' pointing to the value
Maybe reimplement using Data::Stag::hash()?
Returns : hashrf
Args : none
=cut
sub hash_tree {
my ($self) = @_;
my $h = {};
$h->{'value'} = $self->value;
}
=head2 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)
=cut
sub tagname {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->{'tagname'} = $value;
}
return $self->{'tagname'};
}
=head1 Specific accessors for TagTree
=cut
=head2 value
Title : value
Usage : $obj->value($newval)
Function: Get/set the value for this annotation.
Returns : value of value
Args : newvalue (optional)
=cut
sub value {
my ( $self, $value ) = @_;
# set mode? This resets the entire tagged database
my $format = $self->tagformat;
if ($value) {
if ( ref $value ) {
if ( ref $value eq 'ARRAY' ) {
# note the tagname() is not used here; it is only used for
# storing this AnnotationI in the annotation collection
eval { $self->{db} = Data::Stag->nodify($value) };
}
else {
# assuming this is blessed; passing on to node() and copy
$self->node( $value, 'copy' );
}
}
else {
# not trying to guess here for now; we go by the tagformat() setting
my $h = Data::Stag->getformathandler($format);
eval { $self->{db} = Data::Stag->from( $format . 'str', $value ) };
}
$self->throw("Data::Stag error:\n$@") if $@;
}
# get mode?
# How do we return a data structure?
# for now, we use the output (if there is a Data::Stag node present)
# may need to run an eval {} to catch Data::Stag output errors
$self->node->$format;
}
=head2 tagformat
Title : tagformat
Usage : $obj->tagformat($newval)
Function: Get/set the output tag format for this annotation.
Returns : value of tagformat
Args : newvalue (optional) - format for the data passed into value
must be of values 'xml', 'indent', 'sxpr', 'itext', 'perl'
=cut
my %IS_VALID_FORMAT = map { $_ => 1 } qw(xml indent sxpr itext);
sub tagformat {
my ( $self, $value ) = @_;
if ( defined $value ) {
$self->throw( "$value is not a valid format; valid format types:\n"
. join( ',', map { "'$_'" } keys %IS_VALID_FORMAT ) )
if !exists $IS_VALID_FORMAT{$value};
$self->{'tagformat'} = $value;
}
return $self->{'tagformat'};
}
=head2 node
Title : node
Usage : $obj->node()
Function: Get/set the topmost Data::Stag node used for this annotation.
Returns : Data::Stag node implementation
(default is Data::Stag::StagImpl)
Args : (optional) Data::Stag node implementation
(optional)'copy' => flag to create a copy of the node
=cut
sub node {
my ( $self, $value, $copy ) = @_;
if ( defined $value && ref $value ) {
$self->{'db'} =
$value->isa('Data::Stag::StagI')
? ( $copy && $copy eq 'copy' ? $value->duplicate : $value )
: $value->isa('Bio::Annotation::TagTree') ? ( $copy
&& $copy eq 'copy' ? $value->node->duplicate : $value->node )
: $self->throw(
'Object must be Data::Stag::StagI or Bio::Annotation::TagTree');
}
# lazily create Data::Stag instance if not present
if (!$self->{'db'}) {
$self->{'db'} = Data::Stag->new();
}
return $self->{'db'};
}
=head2 Data::Stag convenience methods
Because Data::Stag uses blessed arrays and the core Bioperl class uses blessed
hashes, TagTree uses an internal instance of a Data::Stag node for data storage.
Therefore the following methods actually delegate to the Data:::Stag internal
instance.
For consistency (since one could recursively check child nodes), methods retain
the same names as Data::Stag. Also, no 'magic' (AUTOLOAD'ed) methods are
employed, simply b/c full-fledged Data::Stag functionality can be attained by
grabbing the Data::Stag instance using node().
=head2 element
Title : element
Usage :
Function: Returns the element name (key name) for this node
Example :
Returns : scalar
Args : none
=cut
sub element {
my $self = shift;
return $self->node->element;
}
=head2 data
Title : data
Usage :
Function: Returns the data structure (array ref) for this node
Example :
Returns : array ref
Args : none
=cut
sub data {
my $self = shift;
return $self->node->data;
}
=head2 children
Title : children
Usage :
Function: Get the top-level array of Data::Stag nodes or (if the top level is
a terminal node) a scalar value.
This is similar to StructuredValue's get_values() method, with the
key difference being instead of array refs and scalars you get either
Data::Stag nodes or the value for this particular node.
For consistency (since one could recursively check nodes),
we use the same method name as Data::Stag children().
Example :
Returns : an array
Args : none
=cut
sub children {
my $self = shift;
return $self->node->children;
}
=head2 subnodes
Title : subnodes
Usage :
Function: Get the top-level array of Data::Stag nodes. Unlike children(),
this only returns an array of nodes (if this is a terminal node,
no value is returned)
Example :
Returns : an array of nodes
Args : none
=cut
sub subnodes {
my $self = shift;
return $self->node->subnodes;
}
=head2 get
Title : get
Usage :
Function: Returns the nodes or value for the named element or path
Example :
Returns : returns array of nodes or a scalar (if node is terminal)
dependent on wantarray
Args : none
=cut
sub get {
my ( $self, @vals ) = @_;
return $self->node->get(@vals);
}
=head2 find
Title : find
Usage :
Function: Recursively searches for and returns the nodes or values for the
named element or path
Example :
Returns : returns array of nodes or scalars (for terminal nodes)
Args : none
=cut
sub find {
my ( $self, @vals ) = @_;
return $self->node->find(@vals);
}
=head2 findnode
Title : findnode
Usage :
Function: Recursively searches for and returns a list of nodes
of the given element path
Example :
Returns : returns array of nodes
Args : none
=cut
sub findnode {
my ( $self, @vals ) = @_;
return $self->node->findnode(@vals);
}
=head2 findval
Title : findval
Usage :
Function:
Example :
Returns : returns array of nodes or values
Args : none
=cut
sub findval {
my ( $self, @vals ) = @_;
return $self->node->findval(@vals);
}
=head2 addchild
Title : addchild
Usage : $struct->addchild(['name' => [['foo'=> 'bar1']]]);
Function: add new child node to the current node. One can pass in a node, TagTree,
or data structure; for instance, in the above, this would translate
to (in XML):
<name>
<foo>bar1</foo>
</name>
Returns : node
Args : first arg = element name
all other args are added as tag-value pairs
=cut
sub addchild {
my ( $self, @vals ) = @_;
# check for element tag first (if no element, must be empty Data::Stag node)
if ( !$self->element ) {
# try to do the right thing; if more than one element, wrap in array ref
@vals > 1 ? $self->value( \@vals ) : $self->value( $vals[0] );
return $self->{db};
}
elsif ( !$self->node->ntnodes ) {
# if this is a terminal node, can't add to it (use set?)
$self->throw("Can't add child to node; only terminal node is present!");
}
else {
return $self->node->addchild(@vals);
}
}
=head2 add
Title : add
Usage : $struct->add('foo', 'bar1', 'bar2', 'bar3');
Function: add tag-value nodes to the current node. In the above, this would
translate to (in XML):
<foo>bar1</foo>
<foo>bar2</foo>
<foo>bar3</foo>
Returns :
Args : first arg = element name
all other args are added as tag-value pairs
=cut
sub add {
my ( $self, @vals ) = @_;
# check for empty object and die for now
if ( !$self->node->element ) {
$self->throw("Can't add to terminal element!");
}
return $self->node->add(@vals);
}
=head2 set
Title : set
Usage : $struct->set('foo','bar');
Function: sets a single tag-value pair in the current node. Note this
differs from add() in that this replaces any data already present
Returns : node
Args : first arg = element name
all other args are added as tag-value pairs
=cut
sub set {
my ( $self, @vals ) = @_;
# check for empty object
if ( !$self->node->element ) {
$self->throw("Can't add to tree; empty tree!");
}
return $self->node->set(@vals);
}
=head2 unset
Title : unset
Usage : $struct->unset('foo');
Function: unsets all key-value pairs of the passed element from the
current node
Returns : node
Args : element name
=cut
sub unset {
my ( $self, @vals ) = @_;
return $self->node->unset(@vals);
}
=head2 free
Title : free
Usage : $struct->free
Function: removes all data from the current node
Returns :
Args :
=cut
sub free {
my ($self) = @_;
return $self->node->free;
}
=head2 hash
Title : hash
Usage : $struct->hash;
Function: turns the tag-value tree into a hash, all data values are array refs
Returns : hash
Args : first arg = element name
all other args are added as tag-value pairs
=cut
sub hash {
my ($self) = @_;
return $self->node->hash;
}
=head2 pairs
Title : pairs
Usage : $struct->pairs;
Function: turns the tag-value tree into a hash, all data values are scalar
Returns : hash
Args : first arg = element name
all other args are added as tag-value pairs, note that duplicates
will be lost
=cut
sub pairs {
my ($self) = @_;
return $self->node->pairs;
}
=head2 qmatch
Title : qmatch
Usage : @persons = $s->qmatch('person', ('name'=>'fred'));
Function : returns all elements in the node tree which match the
element name and the key-value pair
Returns : Array of nodes
Args : return-element str, match-element str, match-value str
=cut
sub qmatch {
my ( $self, @vals ) = @_;
return $self->node->qmatch(@vals);
}
=head2 tnodes
Title : tnodes
Usage : @termini = $s->tnodes;
Function : returns all terminal nodes below this node
Returns : Array of nodes
Args : return-element str, match-element str, match-value str
=cut
sub tnodes {
my ($self) = @_;
return $self->node->tnodes;
}
=head2 ntnodes
Title : ntnodes
Usage : @termini = $s->ntnodes;
Function : returns all nonterminal nodes below this node
Returns : Array of nodes
Args : return-element str, match-element str, match-value str
=cut
sub ntnodes {
my ($self) = @_;
return $self->node->ntnodes;
}
=head2 StructureValue-like methods
=cut
=head2 get_all_values
Title : get_all_values
Usage : @termini = $s->get_all_values;
Function : returns all terminal node values
Returns : Array of values
Args : return-element str, match-element str, match-value str
This is meant to emulate the values one would get from StructureValue's
get_all_values() method. Note, however, using this method dissociates the
tag-value relationship (i.e. you only get the value list, no elements)
=cut
sub get_all_values {
my $self = shift;
my @kids = $self->children;
my @vals;
while ( my $val = shift @kids ) {
( ref $val ) ? push @kids, $val->children : push @vals, $val;
}
return @vals;
}
1;