Christopher Fields
and 1 contributors

NAME

Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver - DESCRIPTION of Object

SYNOPSIS

Give standard usage here

DESCRIPTION

Describe the object here

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via email or the web:

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

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

APPENDIX

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

insert_object

 Title   : insert_object
 Usage   :
 Function: We override this here in order to omit the insert if there are
           no values. This is because this entity basically represents a
           derived class, and we may simply be dealing with the base class.

 Example :
 Returns : The primary key of the newly inserted record.
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($key, $sth),
            dbcontext(), and get_persistent_slots()).
           The object to be inserted.
           A reference to an array of foreign key objects; if any of those
           foreign key values is NULL (some foreign keys may be nullable),
           then give the class name.

update_object

 Title   : update_object
 Usage   :
 Function: See parent class. We need to override this here because there is
           no Biosequence object separate from PrimarySeq that would hold a
           primary key. Hence, store()s cannot recognize when the Biosequence
           for a Bioentry already exists and needs to be updated, or when it
           needs to be created. The way the code is currently wired, the
           presence of the primary key (stemming from the bioentry) will always
           trigger an update.

           So, what we need to do here is check whether the entry already
           exists and if not delegate to insert_object().
 Example :
 Returns : The number of updated rows
 Args    : A Bio::DB::BioSQL::BasePersistenceAdaptor derived object
           (basically, it needs to implement dbh(), sth($key, $sth),
            dbcontext(), and get_persistent_slots()).
           The object to be updated.
           A reference to an array of foreign key objects; if any of those
           foreign key values is NULL (some foreign keys may be nullable),
           then give the class name.

get_biosequence

 Title   : get_biosequence
 Usage   :
 Function: Returns the actual sequence for a bioentry, or a substring of it.
 Example :
 Returns : A string (the sequence or subsequence)
 Args    : The calling persistence adaptor.
           The primary key of the bioentry for which to obtain the sequence.
           Optionally, start and end position if only a subsequence is to be
           returned (for long sequences, obtaining the subsequence from the
           database may be much faster than obtaining it from the complete
           in-memory string, because the latter has to be retrieved first).