Package org.biopax.paxtools.util

This package contains various collections and utilities that is used by the other packages and modules of paxtools.

See: Description

Interface Summary

Interface	Description
BPCollections.CollectionProvider	This interface is responsible for setting the class and initialize and load factor for all sets and maps used in all model objects for performance purposes.
Filter<T>	Generic interface for defining filter decorators.

Class Summary

Class	Description
AbstractFilterSet<F,E>	Base class for implementing various filter sets.
AccessibleSet<E>	This is a decorator set for capturing a set member that is equal to the given parameter.
BasicFilterFactory	Deprecated Hibernate ORM/Search will be removed in v5
BiopaxSafeSet<E extends BioPAXElement>	A thread-safe set of BioPAX objects that also prevents adding several elements having the same URI.
ClassFilterSet<E,F extends E>	A FilterSet that filters based on the class.
CompositeIterator<T>	A composite iterator that iterates over multiple iterators.
DataSourceFieldBridge	Deprecated Hibernate ORM/Search will be removed in v5
DataSourceFilterFactory	Deprecated Hibernate ORM/Search will be removed in v5
EquivalenceGrouper<T extends BioPAXElement>	Utility class for equivalence based comparison of a set of BioPAXElements.
OrganismFieldBridge	Deprecated Hibernate ORM/Search will be removed in v5
OrganismFilterFactory	Deprecated Hibernate ORM/Search will be removed in v5
ParentPathwayFieldBridge	Deprecated Hibernate ORM/Search will be removed in v5
SetEquivalenceChecker	This class performs set operations based on equivalence.
SetStringBridge	Deprecated Hibernate ORM/Search will be removed in v5
XrefFieldBridge	Deprecated Hibernate ORM/Search will be removed in v5

Enum Summary

Enum	Description
BPCollections

Exception Summary

Exception	Description
BioPaxIOException	This exception is thrown if a problem occurs during an input/output operation related to BioPAX Handlers.
IllegalBioPAXArgumentException	This exception is thrown typically when BioPAX domain or cardinality restrictions are violated.

Annotation Types Summary

Annotation Type	Description
AutoComplete	Interface for demarcating excise-able boundaries of the object graph.

Package org.biopax.paxtools.util Description

This package contains various collections and utilities that is used by the other packages and modules of paxtools. TODO describe which classes are public API and which not (or are SPI, legacy, etc. made public for some good reason)