Bio::Index::AbstractSeq - base class for AbstractSeq

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

       Email birney@ebi.ac.uk

       Provides a common base class for multiple sequence files built using the Bio::Index::Abstract system, and
       provides a Bio::DB::SeqI interface.

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       Bio::Index::AbstractSeq - base class for AbstractSeq

       Bio::Index::Abstract, which provides dbm indexing for flat files of any type, containing sequence or not.
       Bio::Index::AbstractSeq inherits from Bio::Index::Abstract

   _file_format
        Title   : _file_format
        Usage   : $self->_file_format
        Function: Derived classes should override this
                  method (it throws an exception here)
                  to give the file format of the files used
        Example :
        Returns :
        Args    :

   fetch
         Title   : fetch
         Usage   : $index->fetch( $id )
         Function: Returns a Bio::Seq object from the index
         Example : $seq = $index->fetch( 'dJ67B12' )
         Returns : Bio::Seq object
         Args    : ID

   _get_SeqIO_object
         Title   : _get_SeqIO_object
         Usage   : $index->_get_SeqIO_object( $file )
         Function: Returns a Bio::SeqIO object for the file
         Example : $seq = $index->_get_SeqIO_object( 0 )
         Returns : Bio::SeqIO object
         Args    : File number (an integer)

   get_Seq_by_id
        Title   : get_Seq_by_id
        Usage   : $seq = $db->get_Seq_by_id()
        Function: retrieves a sequence object, identically to
                  ->fetch, but here behaving as a Bio::DB::BioSeqI
        Returns : new Bio::Seq object
        Args    : string represents the id

   get_Seq_by_acc
        Title   : get_Seq_by_acc
        Usage   : $seq = $db->get_Seq_by_acc()
        Function: retrieves a sequence object, identically to
                  ->fetch, but here behaving as a Bio::DB::BioSeqI
        Returns : new Bio::Seq object
        Args    : string represents the accession number

   get_PrimarySeq_stream
        Title   : get_PrimarySeq_stream
        Usage   : $stream = get_PrimarySeq_stream
        Function: Makes a Bio::DB::SeqStreamI compliant object
                  which provides a single method, next_primary_seq
        Returns : Bio::DB::SeqStreamI
        Args    : none

   get_all_primary_ids
        Title   : get_all_primary_ids
        Usage   : @ids = $seqdb->get_all_primary_ids()
        Function: gives an array of all the primary_ids of the
                  sequence objects in the database. These
                  maybe ids (display style) or accession numbers
                  or something else completely different - they
                  *are not* meaningful outside of this database
                  implementation.
        Example :
        Returns : an array of strings
        Args    : none

   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    : primary id (as a string)
        Throws  : "acc does not exist" exception

perl v5.32.1                                       2021-08-15                       Bio::Index::AbstractSeq(3pm)

         # Make a new sequence file indexing package

         package MyShinyNewIndexer;

         use base qw(Bio::Index::AbstractSeq);

         # Now provide the necessary methods...