Package Bio :: Package config :: Module DBRegistry :: Class BioSQLDB
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Class BioSQLDB

RegisterableObject --+    
                     |    
              DBObject --+
                         |
                        BioSQLDB


Represent a BioSQL-style database to retrieve SeqRecord objects.

This returns a SeqRecord-like object from _get() instead of a handle (since BioSQL is not going to give you a handle).
Method Summary
  __init__(self, name, doc, db_host, db_port, db_user, db_passwd, sql_db, namespace_db, db_type)
Intialize with information for connecting to the BioSQL db.
  _convert_to(self, data, to_io)
S._convert_to(data, to_io) -> another data type
  _get(self, key)
S._get(key) -> data
  _get_db_module(self, db_type)
Retrieve the appropriate module to use for connecting to a database
  _make_pickleable(self, item)
  _unmake_pickleable(self, item)
    Inherited from DBObject
  __getitem__(self, key)
  get(self, key, default)
S.get(key[, default]) -> data
  get_as(self, key, to_io, default)
S.get_as(key[, to_io][, default]) -> object
  set(self, key, data)
  _set(self, key, data)
S._set(key, data)

Method Details

__init__(self, name, doc='', db_host='localhost', db_port='', db_user='root', db_passwd='', sql_db='', namespace_db='', db_type='mysql')
(Constructor)

Intialize with information for connecting to the BioSQL db.
Overrides:
Bio.config.DBRegistry.DBObject.__init__

_convert_to(self, data, to_io)

S._convert_to(data, to_io) -> another data type
Overrides:
Bio.config.DBRegistry.DBObject._convert_to (inherited documentation)

_get(self, key)

S._get(key) -> data
Overrides:
Bio.config.DBRegistry.DBObject._get (inherited documentation)

_get_db_module(self, db_type)

Retrieve the appropriate module to use for connecting to a database

This parses a description of the database and tries to determine which module is appropriate for that database type.

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