Provided by: libbio-perl-perl_1.7.2-3_all bug

NAME

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

SYNOPSIS

         # Make a new sequence file indexing package

         package MyShinyNewIndexer;

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

         # Now provide the necessary methods...

DESCRIPTION

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

FEEDBACK

   Mailing Lists
       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://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHOR - Ewan Birney

       Email birney@ebi.ac.uk

APPENDIX

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

SEE ALSO

       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