Summary

Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI

Package variables

Included modules

Inherit

Bio::AnnotationCollectionI Bio::Root::Root

Synopsis

  # add synopsis here

Description

Bioperl implementation for Bio::AnnotationCollecitonI

Methods

Methods description

 Title   : new
 Usage   : $coll = Bio::Annotation::Collection->new()
 Function: Makes a new Annotation::Collection object. 
 Returns : Bio::Annotation::Collection
 Args    : none

 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_Annotations
 Usage   : my @annotations = $collection->get_Annotations('key')
 Function: Retrieves all the Bio::AnnotationI objects for a specific key
 Returns : list of Bio::AnnotationI - empty if no objects stored for a key
 Args    : string which is key for 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

 Title   : add_Annotation
 Usage   : $self->add_Annotation('reference',$object);
           $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI');
 Function: Adds an annotation for a specific 
 Returns : none
 Args    : annotation key ('disease', 'dblink', ...)
           object to store (must be Bio::AnnotationI compliant)
           [optional] object archytype to map future storage of object 
                      of these types to

 Title   : description
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : add_gene_name
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : each_gene_name
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : add_Reference
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : each_Reference
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : add_Comment
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : each_Comment
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : add_DBLink
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : each_DBLink
 Usage   :
 Function:
 Example :
 Returns : 
 Args    :

 Title   : _typemap
 Usage   : $obj->_typemap($newval)
 Function: 
 Example : 
 Returns : value of _typemap
 Args    : newvalue (optional)

Methods code

sub new {

   my ($class,@args) = @_;

   my $self = $class->SUPER::new(@args);

   $self->{'_annotation'} = {};
   $self->_typemap(Bio::Annotation::TypeManager->new());

   return $self;

}

sub get_all_annotation_keys {

   my ($self) = @_;
   return keys %{$self->{'_annotation'}};

}

sub get_Annotations {

   my ($self,$key) = @_;

   if( !defined $self->{'_annotation'}->{$key} ) {
       return ();
   } else {
       return @{$self->{'_annotation'}->{$key}};
   }

}

sub get_num_of_annotations {

   my ($self) = @_;
   my $count = 0;
   map { $count += scalar @$_ } values %{$self->{'_annotation'}};
   return $count;

}

sub add_Annotation {

   my ($self,$key,$object,$archytype) = @_;
   
   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 or ControledVocabTerm for simple text additions");
   }

   if( !$object->isa("Bio::AnnotationI") ) {
       $self->throw("object must be AnnotationI compliant, otherwise we wont add it!");
   }

   # ok, now we are ready! If we don't have an archytype, set it
   # from the type of the object

   if( !defined $archytype ) {
       $archytype = ref $object;
   }

   # check typemap, storing if needed.
   my $stored_map = $self->_typemap->type_for_key($key);

   if( defined $stored_map ) {
       # check validity, irregardless of archytype. 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 of the archytype method to allow registration to a more basic type");
       }
   } else {
       $self->_typemap->_add_type_map($key,$archytype);
   }

   # we are ok to store

   if( !defined $self->{'_annotation'}->{$key} ) {
       $self->{'_annotation'}->{$key} = [];
   }

   push(@{$self->{'_annotation'}->{$key}},$object);

   return 1;

}

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;

}

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 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 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);
   }

}

sub each_Reference {

   my ($self) = @_;

   $self->deprecated("each_Reference (old style Annotation) on new style Annotation::Collection");
   
   return $self->get_Annotations('reference');

}

sub add_Comment {

   my ($self,$value) = @_;

   $self->deprecated("add_Comment (old style Annotation) on new style Annotation::Collection");

   $self->add_Annotation('comment',$value);

}

sub each_Comment {

   my ($self) = @_;

   $self->deprecated("each_Comment (old style Annotation) on new style Annotation::Collection");
   
   return $self->get_Annotations('comment');

}

sub add_DBLink {

   my ($self,$value) = @_;

   $self->deprecated("add_DBLink (old style Annotation) on new style Annotation::Collection");

   $self->add_Annotation('dblink',$value);

}

sub each_DBLink {

   my ($self) = @_;

   $self->deprecated("each_DBLink (old style Annotation) on new style Annotation::Collection");
   
   return $self->get_Annotations('dblink');

}

sub _typemap {

   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'_typemap'} = $value;
    }
    return $self->{'_typemap'};

}

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
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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://bio.perl.org/bioperl-bugs/

Email birney@ebi.ac.uk
Describe contact details here

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

Functions put in for backward compatibility with old
Bio::Annotation.pm stuff