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#
# BioPerl module for Bio::Annotation::Collection.pm
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Annotation::Collection - Default Perl implementation of
AnnotationCollectionI
=head1 SYNOPSIS
# get an AnnotationCollectionI somehow, eg
$ac = $seq->annotation();
foreach $key ( $ac->get_all_annotation_keys() ) {
@values = $ac->get_Annotations($key);
foreach $value ( @values ) {
# value is an Bio::AnnotationI, and defines a "as_text" method
print "Annotation ",$key," stringified value ",$value->as_text,"\n";
# also defined hash_tree method, which allows data orientated
# access into this object
$hash = $value->hash_tree();
}
}
=head1 DESCRIPTION
Bioperl implementation for Bio::AnnotationCollectionI
=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
the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=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::Collection;
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Annotation::TypeManager;
use Bio::Annotation::SimpleValue;
use base qw(Bio::Root::Root Bio::AnnotationCollectionI Bio::AnnotationI);
=head2 new
Title : new
Usage : $coll = Bio::Annotation::Collection->new()
Function: Makes a new Annotation::Collection object.
Returns : Bio::Annotation::Collection
Args : none
=cut
sub new{
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_annotation'} = {};
$self->_typemap(Bio::Annotation::TypeManager->new());
return $self;
}
=head1 L<Bio::AnnotationCollectionI> implementing methods
=cut
=head2 get_all_annotation_keys
Title : get_all_annotation_keys
Usage : $ac->get_all_annotation_keys()
Function: gives back a list of annotation keys, which are simple text strings
Returns : list of strings
Args : none
=cut
sub get_all_annotation_keys{
my ($self) = @_;
return keys %{$self->{'_annotation'}};
}
=head2 get_Annotations
Title : get_Annotations
Usage : my @annotations = $collection->get_Annotations('key')
Function: Retrieves all the Bio::AnnotationI objects for one or more
specific key(s).
If no key is given, returns all annotation objects.
The returned objects will have their tagname() attribute set to
the key under which they were attached, unless the tagname was
already set.
Returns : list of Bio::AnnotationI - empty if no objects stored for a key
Args : keys (list of strings) for annotations (optional)
=cut
sub get_Annotations{
my ($self,@keys) = @_;
my @anns = ();
@keys = $self->get_all_annotation_keys() unless @keys;
foreach my $key (@keys) {
if(exists($self->{'_annotation'}->{$key})) {
push(@anns,
map {
$_->tagname($key) if ! $_->tagname(); $_;
} @{$self->{'_annotation'}->{$key}});
}
}
return @anns;
}
=head2 get_nested_Annotations
Title : get_nested_Annotations
Usage : my @annotations = $collection->get_nested_Annotations(
'-key' => \@keys,
'-recursive => 1);
Function: Retrieves all the Bio::AnnotationI objects for one or more
specific key(s). If -recursive is set to true, traverses the nested
annotation collections recursively and returns all annotations
matching the key(s).
If no key is given, returns all annotation objects.
The returned objects will have their tagname() attribute set to
the key under which they were attached, unless the tagname was
already set.
Returns : list of Bio::AnnotationI - empty if no objects stored for a key
Args : -keys => arrayref of keys to search for (optional)
-recursive => boolean, whether or not to recursively traverse the
nested annotations and return annotations with matching keys.
=cut
sub get_nested_Annotations {
my ($self, @args) = @_;
my ($keys, $recursive) = $self->_rearrange([qw(KEYS RECURSIVE)], @args);
$self->verbose(1);
my @anns = ();
# if not recursive behave exactly like get_Annotations()
if (!$recursive) {
my @keys = $keys? @$keys : $self->get_all_annotation_keys();
foreach my $key (@keys) {
if(exists($self->{'_annotation'}->{$key})) {
push(@anns,
map {
$_->tagname($key) if ! $_->tagname(); $_;
} @{$self->{'_annotation'}->{$key}});
}
}
}
# if recursive search for keys recursively
else {
my @allkeys = $self->get_all_annotation_keys();
foreach my $key (@allkeys) {
my $keymatch = 0;
foreach my $searchkey (@$keys) {
if ($key eq $searchkey) { $keymatch = 1;}
}
if ($keymatch) {
if(exists($self->{'_annotation'}->{$key})) {
push(@anns,
map {
$_->tagname($key) if ! $_->tagname(); $_;
} @{$self->{'_annotation'}->{$key}});
}
}
else {
my @annotations = @{$self->{'_annotation'}->{$key}};
foreach (@annotations) {
if ($_->isa("Bio::AnnotationCollectionI")) {
push (@anns,
$_->get_nested_Annotations('-keys' => $keys, '-recursive' => 1)
);
}
}
}
}
}
return @anns;
}
=head2 get_all_Annotations
Title : get_all_Annotations
Usage :
Function: Similar to get_Annotations, but traverses and flattens nested
annotation collections. This means that collections in the
tree will be replaced by their components.
Keys will not be passed on to nested collections. I.e., if the
tag name of a nested collection matches the key, it will be
flattened in its entirety.
Hence, for un-nested annotation collections this will be identical
to get_Annotations.
Example :
Returns : an array of L<Bio::AnnotationI> compliant objects
Args : keys (list of strings) for annotations (optional)
=cut
sub get_all_Annotations{
my ($self,@keys) = @_;
return map {
$_->isa("Bio::AnnotationCollectionI") ?
$_->get_all_Annotations() : $_;
} $self->get_Annotations(@keys);
}
=head2 get_num_of_annotations
Title : get_num_of_annotations
Usage : my $count = $collection->get_num_of_annotations()
Function: Returns the count of all annotations stored in this collection
Returns : integer
Args : none
=cut
sub get_num_of_annotations{
my ($self) = @_;
my $count = 0;
map { $count += scalar @$_ } values %{$self->{'_annotation'}};
return $count;
}
=head1 Implementation specific functions - mainly for adding
=cut
=head2 add_Annotation
Title : add_Annotation
Usage : $self->add_Annotation('reference',$object);
$self->add_Annotation($object,'Bio::MyInterface::DiseaseI');
$self->add_Annotation($object);
$self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI');
Function: Adds an annotation for a specific key.
If the key is omitted, the object to be added must provide a value
via its tagname().
If the archetype is provided, this and future objects added under
that tag have to comply with the archetype and will be rejected
otherwise.
Returns : none
Args : annotation key ('disease', 'dblink', ...)
object to store (must be Bio::AnnotationI compliant)
[optional] object archetype to map future storage of object
of these types to
=cut
sub add_Annotation{
my ($self,$key,$object,$archetype) = @_;
# if there's no key we use the tagname() as key
if(ref($key) && $key->isa("Bio::AnnotationI") && (!ref($object))) {
$archetype = $object if defined($object);
$object = $key;
$key = $object->tagname();
$key = $key->name() if ref($key); # OntologyTermI
$self->throw("Annotation object must have a tagname if key omitted")
unless $key;
}
if( !defined $object ) {
$self->throw("Must have at least key and object in add_Annotation");
}
if( !ref $object ) {
$self->throw("Must add an object. Use Bio::Annotation::{Comment,SimpleValue,OntologyTerm} for simple text additions");
}
if( !$object->isa("Bio::AnnotationI") ) {
$self->throw("object must be AnnotationI compliant, otherwise we won't add it!");
}
# ok, now we are ready! If we don't have an archetype, set it
# from the type of the object
if( !defined $archetype ) {
$archetype = ref $object;
}
# check typemap, storing if needed.
my $stored_map = $self->_typemap->type_for_key($key);
if( defined $stored_map ) {
# check validity, irregardless of archetype. A little cheeky
# this means isa stuff is executed correctly
if( !$self->_typemap()->is_valid($key,$object) ) {
$self->throw("Object $object was not valid with key $key. ".
"If you were adding new keys in, perhaps you want to make use\n".
"of the archetype method to allow registration to a more basic type");
}
} else {
$self->_typemap->_add_type_map($key,$archetype);
}
# we are ok to store
if( !defined $self->{'_annotation'}->{$key} ) {
$self->{'_annotation'}->{$key} = [];
}
push(@{$self->{'_annotation'}->{$key}},$object);
return 1;
}
=head2 remove_Annotations
Title : remove_Annotations
Usage :
Function: Remove the annotations for the specified key from this collection.
Example :
Returns : an array Bio::AnnotationI compliant objects which were stored
under the given key(s)
Args : the key(s) (tag name(s), one or more strings) for which to
remove annotations (optional; if none given, flushes all
annotations)
=cut
sub remove_Annotations{
my ($self, @keys) = @_;
@keys = $self->get_all_annotation_keys() unless @keys;
my @anns = $self->get_Annotations(@keys);
# flush
foreach my $key (@keys) {
delete $self->{'_annotation'}->{$key};
delete $self->{'_typemap'}->{'_type'}->{$key};
}
return @anns;
}
=head2 flatten_Annotations
Title : flatten_Annotations
Usage :
Function: Flattens part or all of the annotations in this collection.
This is a convenience method for getting the flattened
annotation for the given keys, removing the annotation for
those keys, and adding back the flattened array.
This should not change anything for un-nested collections.
Example :
Returns : an array Bio::AnnotationI compliant objects which were stored
under the given key(s)
Args : list of keys (strings) the annotation for which to flatten,
defaults to all keys if not given
=cut
sub flatten_Annotations{
my ($self,@keys) = @_;
my @anns = $self->get_all_Annotations(@keys);
my @origanns = $self->remove_Annotations(@keys);
foreach (@anns) {
$self->add_Annotation($_);
}
return @origanns;
}
=head1 Bio::AnnotationI methods implementations
This is to allow nested annotation: you can use a collection as an
annotation object for an annotation collection.
=cut
=head2 as_text
Title : as_text
Usage :
Function: See L<Bio::AnnotationI>
Example :
Returns : a string
Args : none
=cut
sub as_text{
my $self = shift;
my $txt = "Collection consisting of ";
my @texts = ();
foreach my $ann ($self->get_Annotations()) {
push(@texts, $ann->as_text());
}
if(@texts) {
$txt .= join(", ", map { '['.$_.']'; } @texts);
} else {
$txt .= "no elements";
}
return $txt;
}
=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 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
=cut
{
# this just calls the default display_text output for
# any AnnotationI
my $DEFAULT_CB = sub {
my $obj = shift;
my $txt;
foreach my $ann ($obj->get_Annotations()) {
$txt .= $ann->display_text()."\n";
}
return $txt;
};
sub display_text {
my ($self, $cb) = @_;
$cb ||= $DEFAULT_CB;
$self->throw("") if ref $cb ne 'CODE';
return $cb->($self);
}
}
=head2 hash_tree
Title : hash_tree
Usage :
Function: See L<Bio::AnnotationI>
Example :
Returns : a hash reference
Args : none
=cut
sub hash_tree{
my $self = shift;
my $tree = {};
foreach my $key ($self->get_all_annotation_keys()) {
# all contained objects will support hash_tree()
# (they are AnnotationIs)
$tree->{$key} = [$self->get_Annotations($key)];
}
return $tree;
}
=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 Bio::AnnotationCollectionI when adding
this object. When obtaining an AnnotationI object from the
collection, the collection will set the value to the tag
under which it was stored unless the object has a tag
stored already.
Example :
Returns : value of tagname (a scalar)
Args : new value (a scalar, optional)
=cut
sub tagname{
my $self = shift;
return $self->{'tagname'} = shift if @_;
return $self->{'tagname'};
}
=head1 Backward compatible functions
Functions put in for backward compatibility with old
Bio::Annotation.pm stuff
=cut
=head2 description
Title : description
Usage :
Function:
Example :
Returns :
Args :
=cut
sub description{
my ($self,$value) = @_;
$self->deprecated("Using old style annotation call on new Annotation::Collection object");
if( defined $value ) {
my $val = Bio::Annotation::SimpleValue->new();
$val->value($value);
$self->add_Annotation('description',$val);
}
my ($desc) = $self->get_Annotations('description');
# If no description tag exists, do not attempt to call value on undef:
return $desc ? $desc->value : undef;
}
=head2 add_gene_name
Title : add_gene_name
Usage :
Function:
Example :
Returns :
Args :
=cut
sub add_gene_name{
my ($self,$value) = @_;
$self->deprecated("Old style add_gene_name called on new style Annotation::Collection");
my $val = Bio::Annotation::SimpleValue->new();
$val->value($value);
$self->add_Annotation('gene_name',$val);
}
=head2 each_gene_name
Title : each_gene_name
Usage :
Function:
Example :
Returns :
Args :
=cut
sub each_gene_name{
my ($self) = @_;
$self->deprecated("Old style each_gene_name called on new style Annotation::Collection");
my @out;
my @gene = $self->get_Annotations('gene_name');
foreach my $g ( @gene ) {
push(@out,$g->value);
}
return @out;
}
=head2 add_Reference
Title : add_Reference
Usage :
Function:
Example :
Returns :
Args :
=cut
sub add_Reference{
my ($self, @values) = @_;
$self->deprecated("add_Reference (old style Annotation) on new style Annotation::Collection");
# Allow multiple (or no) references to be passed, as per old method
foreach my $value (@values) {
$self->add_Annotation('reference',$value);
}
}
=head2 each_Reference
Title : each_Reference
Usage :
Function:
Example :
Returns :
Args :
=cut
sub each_Reference{
my ($self) = @_;
$self->deprecated("each_Reference (old style Annotation) on new style Annotation::Collection");
return $self->get_Annotations('reference');
}
=head2 add_Comment
Title : add_Comment
Usage :
Function:
Example :
Returns :
Args :
=cut
sub add_Comment{
my ($self,$value) = @_;
$self->deprecated("add_Comment (old style Annotation) on new style Annotation::Collection");
$self->add_Annotation('comment',$value);
}
=head2 each_Comment
Title : each_Comment
Usage :
Function:
Example :
Returns :
Args :
=cut
sub each_Comment{
my ($self) = @_;
$self->deprecated("each_Comment (old style Annotation) on new style Annotation::Collection");
return $self->get_Annotations('comment');
}
=head2 add_DBLink
Title : add_DBLink
Usage :
Function:
Example :
Returns :
Args :
=cut
sub add_DBLink{
my ($self,$value) = @_;
$self->deprecated("add_DBLink (old style Annotation) on new style Annotation::Collection");
$self->add_Annotation('dblink',$value);
}
=head2 each_DBLink
Title : each_DBLink
Usage :
Function:
Example :
Returns :
Args :
=cut
sub each_DBLink{
my ($self) = @_;
$self->deprecated("each_DBLink (old style Annotation) on new style Annotation::Collection - use get_Annotations('dblink')");
return $self->get_Annotations('dblink');
}
=head1 Implementation management functions
=cut
=head2 _typemap
Title : _typemap
Usage : $obj->_typemap($newval)
Function:
Example :
Returns : value of _typemap
Args : newvalue (optional)
=cut
sub _typemap{
my ($self,$value) = @_;
if( defined $value) {
$self->{'_typemap'} = $value;
}
return $self->{'_typemap'};
}
1;