Bio::Index::AbstractSeq - Base class for AbstractSeq s # Make a new sequence file indexing package package MyShinyNewIndexer; use Bio::Index::AbstractSeq; @ISA = ('Bio::Index::AbstractSeq'); # Now provide the necessary methods... Provides a common base class for multiple sequence files built using the Bio::Index::Abstract system, and provides a Bio::DB::SeqI interface.

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/MailList.shtml - About the mailing lists

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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email birney@ebi.ac.uk Describe contact details here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 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