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.io.jena |
This package contains a Jena bases reader/writer for reading BioPAX files.
|
org.biopax.paxtools.model |
This package contains the interfaces that maps to the OWL classes defined in the BioPAX specification.
|
Constructor and Description |
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Cloner(EditorMap map,
BioPAXFactory factory) |
Constructor and Description |
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LevelUpgrader(BioPAXFactory factory)
Constructor
|
Modifier and Type | Class and Description |
---|---|
class |
MockFactory
This factory returns decorated objects for testing.
|
Modifier and Type | Method and Description |
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void |
ModelImpl.setFactory(BioPAXFactory factory) |
Constructor and Description |
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ModelImpl(BioPAXFactory factory) |
Modifier and Type | Field and Description |
---|---|
protected BioPAXFactory |
BioPAXIOHandlerAdapter.factory |
Modifier and Type | Method and Description |
---|---|
BioPAXFactory |
BioPAXIOHandlerAdapter.getFactory() |
BioPAXFactory |
BioPAXIOHandler.getFactory() |
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)
|
void |
BioPAXIOHandlerAdapter.setFactory(BioPAXFactory factory) |
void |
BioPAXIOHandler.setFactory(BioPAXFactory factory) |
Constructor and Description |
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BioPAXIOHandlerAdapter(BioPAXFactory factory,
BioPAXLevel level) |
SimpleIOHandler(BioPAXFactory factory,
BioPAXLevel level)
Full constructor
|
Constructor and Description |
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JenaIOHandler(BioPAXFactory factory,
BioPAXLevel level) |
Modifier and Type | Method and Description |
---|---|
BioPAXFactory |
BioPAXLevel.getDefaultFactory()
This method returns the default factory for this level
|
Modifier and Type | Method and Description |
---|---|
void |
Model.setFactory(BioPAXFactory factory)
This method sets the factory this model will use for creating
BioPAX objects.
|
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