Bio::Index::AbstractSeq(3)

NAME
Bio::Index::AbstractSeq - Base class for AbstractSeq s

SYNOPSIS
  # Make a new sequence file indexing package

  package MyShinyNewIndexer;
  use Bio::Index::AbstractSeq;

  @ISA = ('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.

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AUTHOR - Ewan Birney
Email birney@ebi.ac.uk

Describe contact details here

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

SEE ALSO
Bio::Index::Abstract - Module which Bio::Index::AbstractSeq inherits off, which provides dbm indexing for flat files (which are not necessarily sequence files).

  _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