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BioPerl-DB-1.006900
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/ Bio::DB::BioSQL::BiosequenceAdaptor

NAME

Bio::DB::BioSQL::BiosequenceAdaptor - 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 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 email or the web:


            

              
              
bioperl-bugs@bio.perl.org
http://bio.perl.org/bioperl-bugs/

AUTHOR - Hilmar Lapp

Email hlapp at gmx.net

Describe contact details here

APPENDIX

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

get_persistent_slots


            

              
              
Title   : get_persistent_slots
Usage   :
Function: Get the slots of the object that map to attributes in its respective
          entity in the datastore.
Example :
Returns : an array of method names constituting the serializable slots
Args    : the object about to be inserted or updated

get_persistent_slot_values


            

              
              
Title   : get_persistent_slot_values
Usage   :
Function: Obtain the values for the slots returned by get_persistent_slots(),
          in exactly that order.
Example :
Returns : A reference to an array of values for the persistent slots of this
          object. Individual values may be undef.
Args    : The object about to be serialized.
          A reference to an array of foreign key objects if not retrievable 
          from the object itself.

get_foreign_key_objects


            

              
              
Title   : get_foreign_key_objects
Usage   :
Function: Gets the objects referenced by this object, and which therefore need
          to be referenced as foreign keys in the datastore.
          A Bio::PrimarySeqI references a namespace with authority.
Example :
Returns : an array of Bio::DB::PersistentObjectI implementing objects
Args    : The object about to be inserted or updated, or undef if the call
          is for a SELECT query. In the latter case return class or interface
          names that are mapped to the foreign key tables.

instantiate_from_row


            

              
              
Title   : instantiate_from_row
Usage   :
Function: Instantiates the class this object is an adaptor for, and populates
          it with values from columns of the row.
          This implementation calls populate_from_row() to do the real job.
Example :
Returns : An object, or undef, if the row contains no values
Args    : A reference to an array of column values. The first column is the
          primary key, the other columns are expected to be in the order 
          returned by get_persistent_slots().
          Optionally, the object factory to be used for instantiating the
          proper class. The adaptor must be able to instantiate a default
          class if this value is undef.

populate_from_row


            

              
              
Title   : populate_from_row
Usage   :
Function: Instantiates the class this object is an adaptor for, and populates
          it with values from columns of the row.
          Usually a derived class will instantiate the proper class and pass
          it on to populate_from_row().
Example :
Returns : An object, or undef, if the row contains no values
Args    : The object to be populated, or the class to be instantiated.
          A reference to an array of column values. The first column is the
          primary key, the other columns are expected to be in the order 
          returned by get_persistent_slots().

get_unique_key_query


            

              
              
Title   : get_unique_key_query
Usage   :
Function: Obtain the suitable unique key slots and values as determined by the
          attribute values of the given object and the additional foreign
          key objects, in case foreign keys participate in a UK. 
          This method MUST be overridden by a derived class. Alternatively,
          a derived class may choose to override find_by_unique_key() instead,
          as that one calls this method.
Example :
Returns : One or more references to hash(es) where each hash
          represents one unique key, and the keys of each hash
          represent the names of the object's slots that are part of
          the particular unique key and their values are the values
          of those slots as suitable for the key.
Args    : The object with those attributes set that constitute the chosen
          unique key (note that the class of the object will be suitable for
          the adaptor).
          A reference to an array of foreign key objects if not retrievable 
          from the object itself.

attach_foreign_key_objects


            

              
              
Title   : attach_foreign_key_objects
Usage   :
Function: Attaches foreign key objects to the given object as far as
          necessary.
          This method is called after find_by_XXX() queries, not for INSERTs
          or UPDATEs.
Example :
Returns : TRUE on success, and FALSE otherwise.
Args    : The object to which to attach foreign key objects.
          A reference to an array of foreign key values, in the order of
          foreign keys returned by get_foreign_key_objects().

remove_children


            

              
              
Title   : remove_children
Usage   :
Function: This method is to cascade deletes in maintained objects.
          We just return TRUE here.
Example :
Returns : TRUE on success and FALSE otherwise
Args    : The persistent object that was just removed from the database.
          Additional (named) parameter, as passed to remove().

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 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).