/ 
BioPerl-DB-1.006900
River stage zero No dependents
/ Bio::DB::CacheServer::SeqDB

NAME

Bio::DB::CacheServer::SeqDB - Caching DB object

SYNOPSIS

Give standard usage here

DESCRIPTION

Bio::DB::SeqI implmenting object which implements a cache via a bioperl-db database handle

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@bio.perl.org

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:

http://redmine.open-bio.org/projects/bioperl/

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 _

Methods inherited from Bio::DB::RandomAccessI

get_Seq_by_id

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

get_Seq_by_acc

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

Methods [that were] specific for Bio::DB::SeqI

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_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    : accession number (as a string)
Throws  : "acc does not exist" exception

Get/Sets for attributes stored in this object

seq_adaptor

Title   : seq_adaptor
Usage   : $obj->seq_adaptor($newval)
Function: 
Example : 
Returns : value of seq_adaptor
Args    : newvalue (optional)

db_adaptor

Title   : db_adaptor
Usage   : $obj->db_adaptor($newval)
Function: 
Example : 
Returns : value of db_adaptor
Args    : newvalue (optional)

dbid

Title   : dbid
Usage   : $obj->dbid($newval)
Function: 
Example : 
Returns : value of dbid
Args    : newvalue (optional)

read_db

Title   : read_db
Usage   : $obj->read_db($newval)
Function: 
Example : 
Returns : value of read_db
Args    : newvalue (optional)