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

Packages that use BioPAXLevel

Package	Description
org.biopax.paxtools.controller	This package contains various methods and algorithms for traversing and manipulating the model.
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.io.jena	This package contains a Jena bases reader/writer for reading BioPAX files.
org.biopax.paxtools.io.sif	This package contains methods and algorithms for reducing BioPAX to Simple Interaction Format.
org.biopax.paxtools.model	This package contains the interfaces that maps to the OWL classes defined in the BioPAX specification.

Uses of BioPAXLevel in org.biopax.paxtools.controller

Fields in org.biopax.paxtools.controller declared as BioPAXLevel

Modifier and Type	Field and Description
protected BioPAXLevel	EditorMapImpl.level

Methods in org.biopax.paxtools.controller that return BioPAXLevel

Modifier and Type	Method and Description
BioPAXLevel	SimpleEditorMap.getLevel()
BioPAXLevel	EditorMapImpl.getLevel()
BioPAXLevel	EditorMap.getLevel() Returns the BioPAX level for which editor map is created.

Methods in org.biopax.paxtools.controller with parameters of type BioPAXLevel

Modifier and Type	Method and Description
static EditorMap	SimpleEditorMap.buildCustomEditorMap(BioPAXLevel level, InputStream stream)
static SimpleEditorMap	SimpleEditorMap.get(BioPAXLevel level) To obtain a copy of the editor map for the corresponding level, use the

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

Constructor and Description
EditorMapImpl(BioPAXLevel level)
PathAccessor(List<PropertyAccessor<? extends BioPAXElement,?>> objectAccessors, BioPAXLevel level) Constructor for defining the access path with a list of accessors.
PathAccessor(String path, BioPAXLevel level) Constructor for defining the access path via a XPath like string.
ShallowCopy(BioPAXLevel level) BioPAXLevel based constructor

Uses of BioPAXLevel in org.biopax.paxtools.impl

Methods in org.biopax.paxtools.impl that return BioPAXLevel

Modifier and Type	Method and Description
BioPAXLevel	ModelImpl.getLevel()
BioPAXLevel	MockFactory.getLevel()

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

Constructor and Description
MockFactory(BioPAXLevel level)
ModelImpl(BioPAXLevel level)

Uses of BioPAXLevel in org.biopax.paxtools.io

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

Modifier and Type	Field and Description
protected BioPAXLevel	BioPAXIOHandlerAdapter.level

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

Modifier and Type	Method and Description
BioPAXLevel	BioPAXIOHandlerAdapter.getLevel()
BioPAXLevel	BioPAXIOHandler.getLevel()

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

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

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

Constructor and Description
BioPAXIOHandlerAdapter(BioPAXFactory factory, BioPAXLevel level)
BioPAXIOHandlerAdapter(BioPAXLevel level)
SimpleIOHandler(BioPAXFactory factory, BioPAXLevel level) Full constructor
SimpleIOHandler(BioPAXLevel level) Basic constructor, defaults to level.defaultFactory

Uses of BioPAXLevel in org.biopax.paxtools.io.jena

Methods in org.biopax.paxtools.io.jena that return BioPAXLevel

Modifier and Type	Method and Description
BioPAXLevel	JenaEditorMap.getLevel()

Constructors in org.biopax.paxtools.io.jena with parameters of type BioPAXLevel

Constructor and Description
JenaEditorMap(BioPAXLevel level)
JenaIOHandler(BioPAXFactory factory, BioPAXLevel level)
JenaIOHandler(BioPAXLevel level)

Uses of BioPAXLevel in org.biopax.paxtools.io.sif

Methods in org.biopax.paxtools.io.sif with parameters of type BioPAXLevel

Modifier and Type	Method and Description
static List<InteractionRule>	SimpleInteractionConverter.getRules(BioPAXLevel level) Deprecated. Gets all available interaction rules for the given level.

Uses of BioPAXLevel in org.biopax.paxtools.model

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

Modifier and Type	Method and Description
BioPAXLevel	Model.getLevel() This method returns the level of the objects that are contained within this model.
abstract BioPAXLevel	BioPAXFactory.getLevel() Gets the level.
static BioPAXLevel	BioPAXLevel.getLevelFromNameSpace(String namespace)
static BioPAXLevel	BioPAXLevel.valueOf(String name) Returns the enum constant of this type with the specified name.
static BioPAXLevel[]	BioPAXLevel.values() Returns an array containing the constants of this enum type, in the order they are declared.