Uses of Class
org.biopax.paxtools.model.BioPAXFactory

Packages that use BioPAXFactory

Package	Description
org.biopax.paxtools.controller	This package contains various methods and algorithms for traversing and manipulating the model.
org.biopax.paxtools.converter	This package contains a tools for upgrading BioPAX L1 and L2 to L3.
org.biopax.paxtools.impl	This package contains the default BioPAX Model implementations.
org.biopax.paxtools.io	This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..
org.biopax.paxtools.model	This package contains the interfaces that maps to the OWL classes defined in the BioPAX specification.

Uses of BioPAXFactory in org.biopax.paxtools.controller

Constructors in org.biopax.paxtools.controller with parameters of type BioPAXFactory

Modifier	Constructor	Description
	Cloner(EditorMap map, BioPAXFactory factory)

Uses of BioPAXFactory in org.biopax.paxtools.converter

Constructors in org.biopax.paxtools.converter with parameters of type BioPAXFactory

Modifier	Constructor	Description
	LevelUpgrader(BioPAXFactory factory)	Constructor

Uses of BioPAXFactory in org.biopax.paxtools.impl

Subclasses of BioPAXFactory in org.biopax.paxtools.impl

Modifier and Type	Class	Description
class	MockFactory	This factory returns decorated objects for testing.

Methods in org.biopax.paxtools.impl with parameters of type BioPAXFactory

Modifier and Type	Method	Description
void	ModelImpl.setFactory(BioPAXFactory factory)

Constructors in org.biopax.paxtools.impl with parameters of type BioPAXFactory

Modifier	Constructor	Description
	ModelImpl(BioPAXFactory factory)

Uses of BioPAXFactory in org.biopax.paxtools.io

Fields in org.biopax.paxtools.io declared as BioPAXFactory

Modifier and Type	Field	Description
protected BioPAXFactory	BioPAXIOHandlerAdapter.factory

Methods in org.biopax.paxtools.io that return BioPAXFactory

Modifier and Type	Method	Description
BioPAXFactory	BioPAXIOHandler.getFactory()
BioPAXFactory	BioPAXIOHandlerAdapter.getFactory()

Methods in org.biopax.paxtools.io with parameters of type BioPAXFactory

Modifier and Type	Method	Description
protected final void	BioPAXIOHandlerAdapter.resetLevel(BioPAXLevel level, BioPAXFactory factory)	Updates the level and factory for this I/O (final - because used in the constructor)
void	BioPAXIOHandler.setFactory(BioPAXFactory factory)
void	BioPAXIOHandlerAdapter.setFactory(BioPAXFactory factory)

Constructors in org.biopax.paxtools.io with parameters of type BioPAXFactory

Modifier	Constructor	Description
	BioPAXIOHandlerAdapter(BioPAXFactory factory, BioPAXLevel level)
	SimpleIOHandler(BioPAXFactory factory, BioPAXLevel level)	Full constructor

Uses of BioPAXFactory in org.biopax.paxtools.model

Methods in org.biopax.paxtools.model that return BioPAXFactory

Modifier and Type	Method	Description
BioPAXFactory	BioPAXLevel.getDefaultFactory()	This method returns the default factory for this level

Methods in org.biopax.paxtools.model with parameters of type BioPAXFactory

Modifier and Type	Method	Description
void	Model.setFactory(BioPAXFactory factory)	This method sets the factory this model will use for creating BioPAX objects.