- AUTHOR - Hilmar Lapp
- Methods specific to this adaptor
Bio::DB::BioSQL::PathAdaptor - DESCRIPTION of Object
Give standard usage here
Bio::Ontology::PathI DB adaptor
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AUTHOR - Hilmar Lapp
Email hlapp at gmx.net
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : get_persistent_slots Usage : Function: Get the slots of the object that map to attributes in its respective entity in the datastore. Slots should be methods callable without an argument. Example : Returns : an array of method names constituting the serializable slots Args : the object about to be inserted or updated
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.
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 call populate_from_row() to do the real job. We override this here in order to create a Bio::Ontology::Path object by default. 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.
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. Example : Returns : An object, or undef, if the row contains no values Args : The object to be populated. 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().
Methods specific to this adaptor
Title : compute_transitive_closure Usage : Function: Compute the transitive closure over a given ontology and populate the respective path table in the relational schema. There are options that allow one to create certain necessary relationships between predicates on-the-fly. Read below. Example : Returns : TRUE on success, and FALSE otherwise Args : The ontology over which to create the transitive closure (a Bio::Ontology::OntologyI compliant object). In addition, named parameters. Currently, the following are recognized. -truncate If assigned a true value, will cause an existing transitive closure for the ontology be deleted from the path table. Usually, this option should be enabled. -predicate_superclass A Bio::Ontology::TermI compliant object that specifies a common ancestor predicate for all predicates in the ontology. If this is specified, the method will create and serialize relationships between all predicates in the ontology and the ancestor predicate, where the ancestor predicate is the object, the predicate is either the one given by -subclass_predicate or the term 'implies', and the ontology is the ontology referenced by the ancestor predicate. If this is not provided, the aforementioned relationships should be present in an ontology in the database already, unless the ontology over which to compute the transitive closure has only one predicate, or if paths over mixed predicates are void. Otherwise the transitive closure will not be complete for mixed predicate paths. -subclass_predicate A Bio::Ontology::TermI compliant object that represents the predicate for the relationship between predicate A and predicate B if predicate A can be considered to subclass, or imply, predicate B. -identity_predicate A Bio::Ontology::TermI compliant object that represents the predicate for the identity of a predicate with itself. If provided, the method will create relationships for all predicates in the ontology, where subject and object are the predicate of the ontology, the predicate is the supplied identity predicate, and the ontology is the ontology referenced by the supplied term object. If this is not provided, the aforementioned relationships should be present in an ontology in the database already. Otherwise the transitive closure will be incomplete. The predicate will also be used for indicating identity between a term and itself for the paths of distance zero between a term and itself. If undef the zero distance paths will not be created.