[Bioperl-l] Automatic typing in Annotation::Collection

[Charles Tilford]

Hmm, just investigated TypeManager. It looks like it would make more 
sense to first modify that module:

modified method in TypeManager:

sub _add_type_map{
   my ($self,$key,$type) = @_;
   $self->{'_type'}->{$key} = $type;
    # Add this line to get the reciprocal hash:
   $self->{'_key'}->{$type} = $key;
}

new methods in TypeManager:

sub key_for_object {
   my ($self,$object) = @_;
   return $self->{'_key'}->{ref($object)};
}

sub key_for_type {
   my ($self,$type) = @_;
   return $self->{'_key'}->{$type};
}

Modification within Bio::Annotation::Collection->add_Annotation

if ( !defined $object ) {
    # Check to see if the user passed a single object of known type:
    my $tm = Bio::Annotation::TypeManager->new();
    if (my $keycheck = $tm->key_for_object($key)) {
    ($key, $object) = ($keycheck, $key);
    }
    $self->throw("Must have at least key and object in add_Annotation")
    if( !defined $object );
}

-Charles

> Charles Tilford wrote:
>
> Any objections to modifying Bio::Annotation::Collection so that the 
> "common" annotation types can be passed on their own, and the code 
> figure out the key value from them? Aside from allowing the user to be 
> a little lazier, I think it would also help guarantee standardization 
> of the hash keys in Collection - that is, if Collection.pm knew that 
> DBLink objects should be put under the "dblink" key, I would not have 
> to worry about such entries accidentally going to "DBlink" or 
> "db_link" keys.
>
> The modification I was thinking of would look something like this:
>
> sub add_Annotation{
>   my ($self,$key,$object,$archytype) = @_;
>  
>   if( !defined $object ) {
>       # Check to see if the user passed a single object of known type:
>       if (my $ref = ref($key)) {
>       $object = $key;
>       if ($ref eq "Bio::Annotation::Comment") {
>           $key = "comment";
>       } elsif ($ref eq "Bio::Annotation::DBLink") {
>           $key = "dblink";
>       } elsif ($ref eq "Bio::Annotation::Reference") {
>           $key = "reference";
>       } else {
>           $object = undef;
>           $self->throw("Must have at least key and object in 
> add_Annotation - I was unsure how to classify the '$ref' object you 
> provided.")
>       }
>       }
>       $self->throw("Must have at least key and object in add_Annotation")
>       if( !defined $object );
>   }
>
> -Charles
>
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