Bio::DB::CacheServer::SeqDB - Caching DB object
Give standard usage here
Bio::DB::SeqI implmenting object which implements a cache via a bioperl-db database handle
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_Seq_by_id
Usage : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
Function: Gets a Bio::Seq object by its name
Returns : a Bio::Seq object
Args : the id (as a string) of a sequence
Throws : "id does not exist" exception
Title : get_Seq_by_acc
Usage : $seq = $db->get_Seq_by_acc('X77802');
Function: Gets a Bio::Seq object by accession number
Returns : A Bio::Seq object
Args : accession number (as a string)
Throws : "acc does not exist" exception
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
Title : get_all_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
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
Title : seq_adaptor Usage : $obj->seq_adaptor($newval) Function: Example : Returns : value of seq_adaptor Args : newvalue (optional)
Title : db_adaptor Usage : $obj->db_adaptor($newval) Function: Example : Returns : value of db_adaptor Args : newvalue (optional)
Title : dbid Usage : $obj->dbid($newval) Function: Example : Returns : value of dbid Args : newvalue (optional)
Title : read_db Usage : $obj->read_db($newval) Function: Example : Returns : value of read_db Args : newvalue (optional)
