Bio::Annotation
Collection
Toolbar
Summary
Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI
Package variables
No package variables defined.
Included modules
Inherit
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();
}
}
Description
Bioperl implementation for Bio::AnnotationCollecitonI
Methods
Methods description
Title : _typemap
Usage : $obj->_typemap($newval)
Function:
Example :
Returns : value of _typemap
Args : newvalue (optional) |
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 |
Title : add_Comment
Usage :
Function:
Example :
Returns :
Args : |
Title : add_DBLink
Usage :
Function:
Example :
Returns :
Args : |
Title : add_Reference
Usage :
Function:
Example :
Returns :
Args : |
Title : add_gene_name
Usage :
Function:
Example :
Returns :
Args : |
Title : as_text
Usage :
Function: See Bio::AnnotationI
Example :
Returns : a string
Args : none |
Title : description
Usage :
Function:
Example :
Returns :
Args : |
Title : each_Comment
Usage :
Function:
Example :
Returns :
Args : |
Title : each_DBLink
Usage :
Function:
Example :
Returns :
Args : |
Title : each_Reference
Usage :
Function:
Example :
Returns :
Args : |
Title : each_gene_name
Usage :
Function:
Example :
Returns :
Args : |
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 |
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) |
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 Bio::AnnotationI compliant objects
Args : keys (list of strings) for annotations (optional) |
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 |
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 |
Title : hash_tree
Usage :
Function: See Bio::AnnotationI
Example :
Returns : a hash reference
Args : none |
Title : new
Usage : $coll = Bio::Annotation::Collection->new()
Function: Makes a new Annotation::Collection object.
Returns : Bio::Annotation::Collection
Args : none |
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) |
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) |
Methods code
sub _typemap
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'_typemap'} = $value;
}
return $self->{'_typemap'};
}
1;} | sub add_Annotation
{ my ($self,$key,$object,$archetype) = @_;
if(ref($key) && $key->isa("Bio::AnnotationI") &&
(! ($object && ref($object)))) {
$archetype = $object if $object;
$object = $key;
$key = $object->tagname();
$key = $key->name() if $key && ref($key);
$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 wont add it!");
}
if( !defined $archetype ) {
$archetype = ref $object;
}
my $stored_map = $self->_typemap->type_for_key($key);
if( defined $stored_map ) {
if( !$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 of the archetype method to allow registration to a more basic type");
}
} else {
$self->_typemap->_add_type_map($key,$archetype);
}
if( !defined $self->{'_annotation'}->{$key} ) {
$self->{'_annotation'}->{$key} = [];
}
push(@{$self->{'_annotation'}->{$key}},$object);
return 1; } | sub add_Comment
{ my ($self,$value) = @_;
$self->deprecated("add_Comment (old style Annotation) on new style Annotation::Collection");
$self->add_Annotation('comment',$value);} | sub add_DBLink
{ my ($self,$value) = @_;
$self->deprecated("add_DBLink (old style Annotation) on new style Annotation::Collection");
$self->add_Annotation('dblink',$value);} | sub add_Reference
{ my ($self, @values) = @_;
$self->deprecated("add_Reference (old style Annotation) on new style Annotation::Collection");
foreach my $value (@values) {
$self->add_Annotation('reference',$value);
}} | 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);} | 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 $txt;} | sub description
{ my ($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');
return $desc ? $desc->value : undef;} | sub each_Comment
{ my ($self) = @_;
$self->deprecated("each_Comment (old style Annotation) on new style Annotation::Collection");
return $self->get_Annotations('comment');} | sub each_DBLink
{ my ($self) = @_;
$self->deprecated("each_DBLink (old style Annotation) on new style Annotation::Collection - use get_Annotations('dblink')");
return $self->get_Annotations('dblink');} | sub each_Reference
{ my ($self) = @_;
$self->deprecated("each_Reference (old style Annotation) on new style Annotation::Collection");
return $self->get_Annotations('reference');} | sub each_gene_name
{ my ($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;} | 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;} | 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'}->{$key}});
}
}
return @anns;} | sub get_all_Annotations
{ my ($self,@keys) = @_;
return map {
$_->isa("Bio::AnnotationCollectionI") ?
$_->get_all_Annotations() : $_;
} $self->get_Annotations(@keys);} | sub get_all_annotation_keys
{ my ($self) = @_;
return keys %{$self->{'_annotation'}};} | sub get_num_of_annotations
{ my ($self) = @_;
my $count = 0;
map { $count += scalar @$_ } values %{$self->{'_annotation'}};
return $count;} | sub hash_tree
{ my $self = shift;
my $tree = {};
foreach my $key ($self->get_all_annotation_keys()) {
$tree->{$key} = [$self->get_Annotations($key)];
}
return $tree;} | sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_annotation'} = {};
$self->_typemap(Bio::Annotation::TypeManager->new());
return $self;} | sub remove_Annotations
{ my ($self, @keys) = @_;
@keys = $self->get_all_annotation_keys() unless @keys;
my @anns = $self->get_Annotations(@keys);
foreach (@keys) {
delete $self->{'_annotation'}->{$_};
}
return @anns;} | sub tagname
{ my $self = shift;
return $self->{'tagname'} = shift if @_;
return $self->{'tagname'};} | 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://bio.perl.org/MailList.html - About the mailing lists
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
| Implementation specific functions - mainly for adding | Top |
| Bio::AnnotationI methods implementations | Top |
This is to allow nested annotation: you can a collection as an
annotation object to an annotation collection.
| Backward compatible functions | Top |
Functions put in for backward compatibility with old
Bio::Annotation.pm stuff
| Implementation management functions | Top |