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lib/Bio/DB/BioSQL/BasePersistenceAdaptor.pm  view on Meta::CPAN

    $self->finish();
    $self->SUPER::DESTROY();
}

=head1 Abstract Methods

    Almost all of the following methods MUST be overridden by a
    derived class.  For some methods there is an implementation here
    that assumes "no action" is the right thing, but for many adaptors
    this won't be right. There is no way this base implementation can
    make any meaningful guesses at the correct values for those.

=cut

=head2 get_persistent_slots

 Title   : get_persistent_slots
 Usage   :
 Function: Get the slots of the object that map to attributes in its
           respective entity in the datastore.

lib/Bio/DB/CacheServer/SeqDB.pm  view on Meta::CPAN

   return $self->read_db->get_all_primary_ids;
}


=head2 get_Seq_by_primary_id

 Title   : get_Seq_by_primary_id
 Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
 Function: Gets a Bio::Seq object by the primary id. The primary
           id in these cases has to come from $db->get_all_primary_ids.
           There is no other way to get (or guess) the primary_ids
           in a database.

           The other possibility is to get Bio::PrimarySeqI objects
           via the get_PrimarySeq_stream and the primary_id field
           on these objects are specified as the ids to use here.
 Returns : A Bio::Seq object
 Args    : accession number (as a string)
 Throws  : "acc does not exist" exception

t/lib/Test/Builder.pm  view on Meta::CPAN

    my $todo_reason = $Test->todo;
    my $todo_reason = $Test->todo($pack);

todo() looks for a $TODO variable in your tests.  If set, all tests
will be considered 'todo' (see Test::More and Test::Harness for
details).  Returns the reason (ie. the value of $TODO) if running as
todo tests, false otherwise.

todo() is about finding the right package to look for $TODO in.  It
uses the exported_to() package to find it.  If that's not set, it's
pretty good at guessing the right package to look at based on $Level.

Sometimes there is some confusion about where todo() should be looking
for the $TODO variable.  If you want to be sure, tell it explicitly
what $pack to use.

=cut

sub todo {
    my($self, $pack) = @_;