Uses of Interface
org.biopax.paxtools.model.BioPAXElement

Packages that use BioPAXElement

Package	Description
org.biopax.paxtools.command	This package contains classes for implementing undoable editing the model.
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.impl.level3	This package contains the default implementation for BioPAX Level 3.
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.
org.biopax.paxtools.model.level2	This package contains the interfaces that maps to the BioPAX level 2 specification.
org.biopax.paxtools.model.level3	This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
org.biopax.paxtools.util	This package contains various collections and utilities that is used by the other packages and modules of paxtools.

Uses of BioPAXElement in org.biopax.paxtools.command

Classes in org.biopax.paxtools.command with type parameters of type BioPAXElement

Modifier and Type	Class and Description
class	AbstractPropertyCommand<D extends BioPAXElement,R>
class	PropertySetCommand<D extends BioPAXElement,R>

Methods in org.biopax.paxtools.command with parameters of type BioPAXElement

Modifier and Type	Method and Description
void	CommandManager.addProperty(BioPAXElement bpe, PropertyEditor editor, Object value)
protected void	RemoveCommand.redoAction(BioPAXElement bpe)
protected abstract void	AbstractAddRemoveCommand.redoAction(BioPAXElement bpe)
protected void	AddCommand.redoAction(BioPAXElement bpe)
void	CommandManager.removeProperty(BioPAXElement bpe, PropertyEditor editor, Object value)
protected void	RemoveCommand.undoAction(BioPAXElement bpe)
protected abstract void	AbstractAddRemoveCommand.undoAction(BioPAXElement bpe)
protected void	AddCommand.undoAction(BioPAXElement bpe)

Method parameters in org.biopax.paxtools.command with type arguments of type BioPAXElement

Modifier and Type	Method and Description
void	CommandManager.addObjects(Set<BioPAXElement> bpes)
void	CommandManager.removeObjects(Set<BioPAXElement> bpes)

Constructor parameters in org.biopax.paxtools.command with type arguments of type BioPAXElement

Constructor and Description
AbstractAddRemoveCommand(Model model, Set<BioPAXElement> bpes)
AddCommand(Model model, Set<BioPAXElement> bpes)
RemoveCommand(Model model, Set<BioPAXElement> bpes)

Uses of BioPAXElement in org.biopax.paxtools.controller

Classes in org.biopax.paxtools.controller with type parameters of type BioPAXElement

Modifier and Type	Class and Description
class	AbstractPropertyEditor<D extends BioPAXElement,R> This is the base class for all property editors.
interface	DataPropertyEditor<D extends BioPAXElement,R> Created by igor on 13/08/15.
class	DecoratingPropertyAccessor<D extends BioPAXElement,R>
class	EnumeratedPropertyEditor<D extends BioPAXElement,R extends Enum> Provides an ENUM class compatible editor by extending the PropertyEditor.
class	FilteredPropertyAccessor<D extends BioPAXElement,R> This class is a decorating property accessor that filters values with a given class.
class	ObjectPropertyEditor<D extends BioPAXElement,R extends BioPAXElement> Provides an editor for all object value types, e.g.
class	ObjectPropertyEditor<D extends BioPAXElement,R extends BioPAXElement> Provides an editor for all object value types, e.g.
class	PrimitivePropertyEditor<D extends BioPAXElement,R> Provides a primitive (int, float, double) class compatible editor by extending the PropertyEditor.
interface	PropertyAccessor<D extends BioPAXElement,R> Allows generic access to the properties or a path of properties from a bean.
class	PropertyAccessorAdapter<D extends BioPAXElement,R> Adapter class for all property accessors.
interface	PropertyEditor<D extends BioPAXElement,R>
class	SimplePropertyAccessor<D extends BioPAXElement,R>
class	StringPropertyEditor<D extends BioPAXElement> Provides an String class compatible editor by extending the PropertyEditor.
class	TransitivePropertyAccessor<R extends BioPAXElement,D extends R> This class is a transitive decorator for PropertyAccessors.
class	UnionPropertyAccessor<D extends BioPAXElement,R> In OWL a single property can have multiple domains.

Fields in org.biopax.paxtools.controller with type parameters of type BioPAXElement

Modifier and Type	Field and Description
protected Map<Class<? extends BioPAXElement>,Map<String,PropertyEditor>>	EditorMapImpl.classToEditorMap A map from classes to their registered editors.
protected Map<Class<? extends BioPAXElement>,Set<PropertyEditor>>	EditorMapImpl.classToEditorSet Another map to keep editors as a set rather than a map.
protected Map<Class<? extends BioPAXElement>,Set<ObjectPropertyEditor>>	EditorMapImpl.classToInverseEditorMap A map from classes to their registered inverse editors
protected Set<BioPAXElement>	AbstractTraverser.visited

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

Modifier and Type	Method and Description
<T extends BioPAXElement> T	ShallowCopy.copy(Model model, T source, String newID) Creates a copy of the BioPAX object with all its properties are the same, and also adds it to a model.
<T extends BioPAXElement> T	ShallowCopy.copy(T source, String newID) Returns a copy of the BioPAX element (with all the property values are same)
static <R extends BioPAXElement,D extends R> TransitivePropertyAccessor<R,D>	TransitivePropertyAccessor.create(PropertyAccessor<D,R> pa)
static <D extends BioPAXElement,R> PropertyAccessor<D,R>	FilteredPropertyAccessor.create(PropertyAccessor<D,R> pa, Class filter) FactoryMethod that creates a filtered property accessor by decorating a given accessor with a class filter.
static <D extends BioPAXElement,R> PropertyEditor<D,R>	AbstractPropertyEditor.createPropertyEditor(Class<D> domain, String property) This method creates a property reflecting on the domain and property.
<T extends BioPAXElement> Set<T>	Fetcher.fetch(BioPAXElement element, Class<T> filterByType) Goes over object type biopax properties to collect nested objects (using only properties that pass all the filters set in Constructor, and taking #isSkipSubPathways into account) of the given biopax element, its children, etc.
<D extends BioPAXElement> PropertyEditor<? super D,?>	EditorMapImpl.getEditorForProperty(String property, Class<D> javaClass)
<D extends BioPAXElement> PropertyEditor<? super D,?>	SimpleEditorMap.getEditorForProperty(String property, Class<D> javaClass)
<D extends BioPAXElement> PropertyEditor<? super D,?>	EditorMap.getEditorForProperty(String property, Class<D> javaClass) This method returns the editor intended to handle property named property of a class (javaClass).
<E extends BioPAXElement> Set<? extends Class<E>>	EditorMapImpl.getKnownSubClassesOf(Class<E> javaClass)
<E extends BioPAXElement> Set<? extends Class<E>>	SimpleEditorMap.getKnownSubClassesOf(Class<E> javaClass)
<E extends BioPAXElement> Set<? extends Class<E>>	EditorMap.getKnownSubClassesOf(Class<E> javaClass) Returns a set of sub classes of a given class.
static <T extends BioPAXElement> T	ModelUtils.getObject(Model model, String uri, Class<T> clazz) A more strict, type-safe way to ask for a biopax object from the model, unlike Model.getByID(String).
static <T extends BioPAXElement> Set<T>	ModelUtils.getRootElements(Model model, Class<T> filterClass) Finds "root" BioPAX objects that belong to a particular class (incl.
<D extends BioPAXElement> Set<PropertyEditor<? extends D,?>>	EditorMapImpl.getSubclassEditorsForProperty(String property, Class<D> domain)
<D extends BioPAXElement> Set<PropertyEditor<? extends D,?>>	SimpleEditorMap.getSubclassEditorsForProperty(String property, Class<D> domain)
<D extends BioPAXElement> Set<PropertyEditor<? extends D,?>>	EditorMap.getSubclassEditorsForProperty(String property, Class<D> domain) This method returns the set of editors intended to handle property named property.
static <T extends BioPAXElement> Set<BioPAXElement>	ModelUtils.removeObjectsIfDangling(Model model, Class<T> clazz) Iteratively removes "dangling" elements of given type and its sub-types, e.g.
<D extends BioPAXElement> void	AbstractTraverser.traverse(D element, Model model)
<D extends BioPAXElement> void	Traverser.traverse(D element, Model model) Traverse and visit Visitor all properties of the element.

Methods in org.biopax.paxtools.controller that return types with arguments of type BioPAXElement

Modifier and Type	Method and Description
Set<BioPAXElement>	Completer.complete(Collection<BioPAXElement> elements)
Set<BioPAXElement>	Completer.complete(Collection<BioPAXElement> elements, Model model) Deprecated. use Completer.complete(Collection) instead (- model is never explicitly used there)
Set<BioPAXElement>	Fetcher.fetch(BioPAXElement element) Recursively finds and collects all child objects, while escaping possible infinite loops.
Set<BioPAXElement>	Fetcher.fetch(BioPAXElement bpe, int depth) Recursively collects unique child objects from BioPAX object type properties that pass all the filters (as set via Constructor).
static Map<Class<? extends BioPAXElement>,Integer>	ModelUtils.generateClassMetrics(Model model) Generates simple counts of different elements in the model.
HashSet<BioPAXElement>	Merger.getAddedElements() After a merge is accomplished, this set will contain the newly added elements.
static Set<BioPAXElement>	ModelUtils.getDirectChildrenAsSet(BioPAXElement bpe) Collects direct children of a given BioPAX element.
HashSet<BioPAXElement>	Merger.getMergedElements() After a merge is accomplished, this set will contain the merged elements.
Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>>	ObjectPropertyEditor.getRestrictedRanges()
Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>>	ObjectPropertyEditor.getRestrictedRanges()
Set<Class<? extends BioPAXElement>>	ObjectPropertyEditor.getRestrictedRangesFor(Class<? extends D> restrictedDomain)
static <T extends BioPAXElement> Set<BioPAXElement>	ModelUtils.removeObjectsIfDangling(Model model, Class<T> clazz) Iteratively removes "dangling" elements of given type and its sub-types, e.g.

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

Modifier and Type	Method and Description
boolean	PathAccessor.applies(BioPAXElement bpe)
Set<BioPAXElement>	Fetcher.fetch(BioPAXElement element) Recursively finds and collects all child objects, while escaping possible infinite loops.
<T extends BioPAXElement> Set<T>	Fetcher.fetch(BioPAXElement element, Class<T> filterByType) Goes over object type biopax properties to collect nested objects (using only properties that pass all the filters set in Constructor, and taking #isSkipSubPathways into account) of the given biopax element, its children, etc.
Set<BioPAXElement>	Fetcher.fetch(BioPAXElement bpe, int depth) Recursively collects unique child objects from BioPAX object type properties that pass all the filters (as set via Constructor).
void	Fetcher.fetch(BioPAXElement element, Model model) Adds the element and all its children (found via traversing into object properties that pass all the filters defined in the Constructor, and also taking #isSkipSubPathways into account) to the target model.
Set<String>	IdFetcher.fetchID(BioPAXElement ele)
static void	ModelUtils.fixDanglingInverseProperties(BioPAXElement bpe, Model model) Unlinks inverse properties of the BioPAX object from values the model does not have.
static void	ModelUtils.fixDanglingObjectProperties(BioPAXElement bpe, Model model) Unlinks object properties of the BioPAX object from values the model does not have.
Object	ReusedPEPHelper.fixReusedPEP(physicalEntityParticipant pep, BioPAXElement bpe)
static Model	ModelUtils.getAllChildren(BioPAXElement bpe, Filter<PropertyEditor>... filters) Deprecated. use Fetcher.fetch(BioPAXElement, Model) instead (with Fetcher.nextStepFilter or without)
static Set<Provenance>	ModelUtils.getDatasources(BioPAXElement biopaxElement) Collects all Provenance objects associated with this one as follows: - if the element is Entity (has 'dataSource' property) or is Provenence itself, get the values and quit; - if the biopax element is PathwayStep or EntityReference, traverse into some of its object/inverse properties to collect dataSource values from associated entities.
static Model	ModelUtils.getDirectChildren(BioPAXElement bpe) Gets direct children of a given BioPAX element and adds them to a new model.
static Set<BioPAXElement>	ModelUtils.getDirectChildrenAsSet(BioPAXElement bpe) Collects direct children of a given BioPAX element.
Set<PropertyEditor>	EditorMapImpl.getEditorsOf(BioPAXElement bpe)
Set<PropertyEditor>	SimpleEditorMap.getEditorsOf(BioPAXElement bpe)
Set<PropertyEditor>	EditorMap.getEditorsOf(BioPAXElement bpe) This method returns the set of editors whose domain subsumes the class of given BioPAX element.
Set<ObjectPropertyEditor>	EditorMapImpl.getInverseEditorsOf(BioPAXElement bpe)
Set<ObjectPropertyEditor>	SimpleEditorMap.getInverseEditorsOf(BioPAXElement bpe)
Set<ObjectPropertyEditor>	EditorMap.getInverseEditorsOf(BioPAXElement bpe) Properties in BioPAX specification is unidirectional.
static Set<String>	ModelUtils.getKeywords(BioPAXElement biopaxElement, int depth, Filter<DataPropertyEditor>... dataPropertyFilters) Collects data type (not object) property values (can be then used for full-text indexing).
static Set<BioSource>	ModelUtils.getOrganisms(BioPAXElement biopaxElement) Collects BioSource objects from this or related elements (where it makes sense; though the biopax element might have no or empty 'organism' property at all.
static Set<Pathway>	ModelUtils.getParentPathways(BioPAXElement biopaxElement) Collects all parent Pathway objects recursively traversing the inverse object properties of the biopax element.
Set	PathAccessor.getValueFromBean(BioPAXElement bean)
void	SimpleMerger.merge(Model target, BioPAXElement source) Merges the source element (and its "downstream" dependents) into target model.
boolean	Fetcher.subgraphContains(BioPAXElement root, String uri, Class<? extends BioPAXElement> type) Iterates over child objects of the given biopax element, using BioPAX object-type properties, until the element with specified URI and class (including its sub-classes).
void	TraverserBilinked.traverse(BioPAXElement element, Model model)
protected void	Traverser.traverseElements(BioPAXElement element, Model model, PropertyEditor<?,?> editor, Set<?> valueSet)
static void	ModelUtils.updateUri(Model model, BioPAXElement el, String newUri) Replaces the URI of a BioPAX object in the Model using java reflection.
void	ShallowCopy.visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) An implementation of this method should perform a BioPAX element and editor dependent operation on the model.
void	Merger.visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor) Checks whether model contains bpe element, and if it does, then it updates the value of the equivalent element for bpe by using the specific editor.
void	Completer.visit(BioPAXElement domain, Object range, Model model, PropertyEditor editor)
void	Cloner.visit(BioPAXElement domain, Object range, Model targetModel, PropertyEditor editor)
void	Visitor.visit(BioPAXElement domain, Object range, Model model, PropertyEditor<?,?> editor) An implementation of this method should perform a BioPAX element and editor dependent operation on the model.
void	AbstractTraverser.visit(BioPAXElement domain, Object range, Model model, PropertyEditor<?,?> editor) Calls the protected abstract method visit that is to be implemented in subclasses of this abstract class.
protected abstract void	AbstractTraverser.visit(Object range, BioPAXElement domain, Model model, PropertyEditor<?,?> editor) This is to implement a real action here: do something, return or even to continue (traverse) into the child (range) element's properties if it's a BioPAX object.

Method parameters in org.biopax.paxtools.controller with type arguments of type BioPAXElement

Modifier and Type	Method and Description
void	ObjectPropertyEditor.addRangeRestriction(Class<? extends BioPAXElement> domain, Set<Class<? extends BioPAXElement>> ranges) This method adds a range restriction to the property editor.
void	ObjectPropertyEditor.addRangeRestriction(Class<? extends BioPAXElement> domain, Set<Class<? extends BioPAXElement>> ranges) This method adds a range restriction to the property editor.
Model	Cloner.clone(Model source, Set<BioPAXElement> toBeCloned) Deprecated. use Cloner.clone(Set) instead ('source' model was not used in previous versions)
Model	Cloner.clone(Set<BioPAXElement> toBeCloned) For each element from the 'toBeCloned' list, it creates a copy in the new model, setting all the data properties; however, object property values that refer to BioPAX elements not in 'toBeCloned' list are ignored.
Set<BioPAXElement>	Completer.complete(Collection<BioPAXElement> elements)
Set<BioPAXElement>	Completer.complete(Collection<BioPAXElement> elements, Model model) Deprecated. use Completer.complete(Collection) instead (- model is never explicitly used there)
protected PropertyEditor	EditorMapImpl.createAndRegisterBeanEditor(String pName, Class domain, Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>> rRestrictions)
protected PropertyEditor	EditorMapImpl.createAndRegisterBeanEditor(String pName, Class domain, Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>> rRestrictions)
Set<PropertyEditor>	EditorMapImpl.getEditorsOf(Class<? extends BioPAXElement> domain)
Set<PropertyEditor>	SimpleEditorMap.getEditorsOf(Class<? extends BioPAXElement> domain)
Set<PropertyEditor>	EditorMap.getEditorsOf(Class<? extends BioPAXElement> domain) This method returns the set of editors whose domain subsumes the given class
Set<ObjectPropertyEditor>	EditorMapImpl.getInverseEditorsOf(Class<? extends BioPAXElement> domain)
Set<ObjectPropertyEditor>	SimpleEditorMap.getInverseEditorsOf(Class<? extends BioPAXElement> domain)
Set<ObjectPropertyEditor>	EditorMap.getInverseEditorsOf(Class<? extends BioPAXElement> domain) Properties in BioPAX specification is unidirectional.
Set	PathAccessor.getValueFromBeans(Collection<? extends BioPAXElement> beans)
protected boolean	AbstractPropertyEditor.isInstanceOfAtLeastOne(Set<Class<? extends BioPAXElement>> classes, Object value) Checks if value is an instance of one of the classes given in a set.
void	SimpleMerger.merge(Model target, Collection<? extends BioPAXElement> elements) Merges the elements and all their child biopax objects into the target model.
protected void	EditorMapImpl.registerEditorsWithSubClasses(PropertyEditor editor, Class<? extends BioPAXElement> domain) This method registers an editor with sub classes - i.e.
static void	ModelUtils.replace(Model model, Map<? extends BioPAXElement,? extends BioPAXElement> subs) Replaces BioPAX elements in the model with ones from the map, updates corresponding BioPAX object references.
static void	ModelUtils.replace(Model model, Map<? extends BioPAXElement,? extends BioPAXElement> subs) Replaces BioPAX elements in the model with ones from the map, updates corresponding BioPAX object references.
void	ObjectPropertyEditor.setRangeRestriction(Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>> restrictedRanges) This method sets all range restrictions.
void	ObjectPropertyEditor.setRangeRestriction(Map<Class<? extends BioPAXElement>,Set<Class<? extends BioPAXElement>>> restrictedRanges) This method sets all range restrictions.
boolean	Fetcher.subgraphContains(BioPAXElement root, String uri, Class<? extends BioPAXElement> type) Iterates over child objects of the given biopax element, using BioPAX object-type properties, until the element with specified URI and class (including its sub-classes).

Constructor parameters in org.biopax.paxtools.controller with type arguments of type BioPAXElement

Constructor and Description
PathAccessor(List<PropertyAccessor<? extends BioPAXElement,?>> objectAccessors, BioPAXLevel level) Constructor for defining the access path with a list of accessors.
SimpleMerger(EditorMap map, Filter<BioPAXElement> mergePropOf)

Uses of BioPAXElement in org.biopax.paxtools.converter

Methods in org.biopax.paxtools.converter with parameters of type BioPAXElement

Modifier and Type	Method and Description
static String	LevelUpgrader.getLocalId(BioPAXElement bpe) Gets the local part of the BioPAX element ID.
protected void	LevelUpgrader.visit(Object value, BioPAXElement parent, Model newModel, PropertyEditor editor)

Uses of BioPAXElement in org.biopax.paxtools.impl

Classes in org.biopax.paxtools.impl that implement BioPAXElement

Modifier and Type	Class and Description
class	BioPAXElementImpl

Fields in org.biopax.paxtools.impl with type parameters of type BioPAXElement

Modifier and Type	Field and Description
protected Map<String,BioPAXElement>	ModelImpl.idMap

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

Modifier and Type	Method and Description
<T extends BioPAXElement> T	ModelImpl.addNew(Class<T> c, String id)
<T extends BioPAXElement> T	MockFactory.create(Class<T> aClass, String uri)
<T extends BioPAXElement> T[]	MockFactory.create(Model model, Class<T> biopaxClass, int number)
<T extends BioPAXElement> T[]	MockFactory.create(Model model, Class<T> biopaxClass, int number, String pre)
<T extends BioPAXElement> Set<T>	ModelImpl.getObjects(Class<T> filterBy)

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

Modifier and Type	Method and Description
<T extends BioPAXElement> T[]	MockFactory.create(Model model, Class<T> biopaxClass, int number)
<T extends BioPAXElement> T[]	MockFactory.create(Model model, Class<T> biopaxClass, int number, String pre)
BioPAXElement	MockFactory.create(String localName, String uri)
BioPAXElement	ModelImpl.getByID(String id)

Methods in org.biopax.paxtools.impl that return types with arguments of type BioPAXElement

Modifier and Type	Method and Description
Set<BioPAXElement>	ModelImpl.getObjects()

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

Modifier and Type	Method and Description
void	ModelImpl.add(BioPAXElement aBioPAXElement)
void	MockFactory.bindArrays(ObjectPropertyEditor editor, BioPAXElement[] beans, BioPAXElement[] values)
void	MockFactory.bindArrays(ObjectPropertyEditor editor, BioPAXElement[] beans, BioPAXElement[] values)
void	MockFactory.bindArrays(String editor, BioPAXElement[] beans, BioPAXElement[] values)
void	MockFactory.bindArrays(String editor, BioPAXElement[] beans, BioPAXElement[] values)
void	MockFactory.bindInPairs(ObjectPropertyEditor editor, BioPAXElement... pairs)
void	MockFactory.bindInPairs(String editor, BioPAXElement... pairs)
boolean	ModelImpl.contains(BioPAXElement aBioPAXElement) This method returns true if given element is the same object ("==") as the object stored in the model usually (for self-consistent models) but not necessarily under the element's ID.
boolean	BioPAXElementImpl.isEquivalent(BioPAXElement element)
void	ModelImpl.remove(BioPAXElement aBioPAXElement)
void	ModelImpl.replace(BioPAXElement existing, BioPAXElement replacement) It does not automatically replace or clean up the old element's object properties, therefore, some child elements may become "dangling" if they were used by the replaced element only.
protected boolean	BioPAXElementImpl.semanticallyEquivalent(BioPAXElement element)

Method parameters in org.biopax.paxtools.impl with type arguments of type BioPAXElement

Modifier and Type	Method and Description
ObjectPropertyEditor	MockFactory.editor(String property, Class<? extends BioPAXElement> clazz)
String	MockFactory.mapClassName(Class<? extends BioPAXElement> aClass)

Uses of BioPAXElement in org.biopax.paxtools.impl.level3

Classes in org.biopax.paxtools.impl.level3 that implement BioPAXElement

Modifier and Type	Class and Description
class	BindingFeatureImpl
class	BiochemicalPathwayStepImpl
class	BiochemicalReactionImpl
class	BioSourceImpl
class	CatalysisImpl
class	CellularLocationVocabularyImpl
class	CellVocabularyImpl
class	ChemicalConstantImpl
class	ChemicalStructureImpl
class	ComplexAssemblyImpl
class	ComplexImpl
class	ControlImpl
class	ControlledVocabularyImpl
class	ConversionImpl
class	CovalentBindingFeatureImpl
class	DegradationImpl
class	DeltaGImpl
class	DnaImpl
class	DnaReferenceImpl
class	DnaRegionImpl
class	DnaRegionReferenceImpl
class	EntityFeatureImpl
class	EntityImpl
class	EntityReferenceImpl
class	EntityReferenceTypeVocabularyImpl
class	EvidenceCodeVocabularyImpl
class	EvidenceImpl
class	ExperimentalFormImpl
class	ExperimentalFormVocabularyImpl
class	FragmentFeatureImpl
class	GeneImpl
class	GeneticInteractionImpl
class	InteractionImpl
class	InteractionVocabularyImpl
class	KPrimeImpl
class	L3ElementImpl Base BioPAX Level3 element.
class	ModificationFeatureImpl
class	ModulationImpl
class	MolecularInteractionImpl
class	NamedImpl
class	NucleicAcidImpl
class	NucleicAcidReferenceImpl
class	NucleicAcidRegionReferenceImpl
class	PathwayImpl
class	PathwayStepImpl
class	PhenotypeVocabularyImpl
class	PhysicalEntityImpl
class	ProcessImpl
class	ProteinImpl
class	ProteinReferenceImpl
class	ProvenanceImpl
class	PublicationXrefImpl
class	RelationshipTypeVocabularyImpl
class	RelationshipXrefImpl
class	RnaImpl
class	RnaReferenceImpl
class	RnaRegionImpl
class	RnaRegionReferenceImpl
class	ScoreImpl
class	SequenceEntityReferenceImpl
class	SequenceIntervalImpl
class	SequenceLocationImpl
class	SequenceModificationVocabularyImpl
class	SequenceRegionVocabularyImpl
class	SequenceSiteImpl
class	SimplePhysicalEntityImpl
class	SmallMoleculeImpl
class	SmallMoleculeReferenceImpl
class	StoichiometryImpl
class	TemplateReactionImpl
class	TemplateReactionRegulationImpl
class	TissueVocabularyImpl
class	TransportImpl
class	TransportWithBiochemicalReactionImpl
class	UnificationXrefImpl
class	XReferrableImpl This class helps with managing the bidirectional xref links.
class	XrefImpl

Methods in org.biopax.paxtools.impl.level3 with parameters of type BioPAXElement

Modifier and Type	Method and Description
protected boolean	SequenceIntervalImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	BioSourceImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ChemicalConstantImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ConversionImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	PublicationXrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	DeltaGImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	EvidenceImpl.semanticallyEquivalent(BioPAXElement element) Answers whether two Evidence objects are semantically equivalent.
protected boolean	BindingFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	FragmentFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ModificationFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	KPrimeImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SequenceSiteImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	EntityImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	RelationshipXrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	PhysicalEntityImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ChemicalStructureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SimplePhysicalEntityImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SmallMoleculeReferenceImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	EntityFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	XrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	ComplexImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	UnificationXrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	ControlledVocabularyImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	StoichiometryImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SequenceEntityReferenceImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	CovalentBindingFeatureImpl.semanticallyEquivalent(BioPAXElement element)

Uses of BioPAXElement in org.biopax.paxtools.io

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

Modifier and Type	Method and Description
protected void	BioPAXIOHandlerAdapter.bindValue(String valueString, PropertyEditor editor, BioPAXElement bpe, Model model) This method binds the value to the bpe.
protected StringPropertyEditor	BioPAXIOHandlerAdapter.getRDFCommentEditor(BioPAXElement bpe) Paxtools maps BioPAX:comment (L3) and BioPAX:COMMENT (L2) to rdf:comment.
protected Object	BioPAXIOHandlerAdapter.resourceFixes(BioPAXElement bpe, Object value) This method currently only fixes reusedPEPs if the option is set.
void	SimpleIOHandler.writeObject(Writer out, BioPAXElement bean) Writes the XML representation of individual BioPAX element that is BioPAX-like but only for display or debug purpose (incomplete).

Uses of BioPAXElement in org.biopax.paxtools.model

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

Modifier and Type	Method and Description
<T extends BioPAXElement> T	Model.addNew(Class<T> aClass, String id) This method creates a new object using the model's factory, adds it to the model and returns it.
<T extends BioPAXElement> T	BioPAXFactory.create(Class<T> aClass, String uri) Universal method that creates a new BioPAX object.
<T extends BioPAXElement> Class<T>	BioPAXFactory.getImplClass(Class<T> aModelInterfaceClass) Get a concrete or abstract BioPAX type (not interface), from org.biopax.paxtools.impl..*, i.e., one that has persistence/search annotations, etc.
<T extends BioPAXElement> Set<T>	Model.getObjects(Class<T> filterBy) This method returns a set of objects in the model of the given class.

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

Modifier and Type	Method and Description
BioPAXElement	BioPAXFactory.create(String localName, String uri)
BioPAXElement	Model.getByID(String id) This method returns the biopax element with the given id, returns null if the object with the given id does not exist in this model.

Methods in org.biopax.paxtools.model that return types with arguments of type BioPAXElement

Modifier and Type	Method and Description
Class<? extends BioPAXElement>	BioPAXLevel.getInterfaceForName(String localName) Gets the BioPAX type (java interface) by name.
Class<? extends BioPAXElement>	BioPAXElement.getModelInterface() This method returns the actual model interface that a class implements.
Set<BioPAXElement>	Model.getObjects() This method returns a set of objects in the model.

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

Modifier and Type	Method and Description
void	Model.add(BioPAXElement aBioPAXElement) This method adds the given object to this model.
boolean	Model.contains(BioPAXElement aBioPAXElement) This method returns true if the parameter is contained within this model.
boolean	BioPAXLevel.hasElement(BioPAXElement element)
boolean	BioPAXElement.isEquivalent(BioPAXElement element) This method compares the given element for equivalency.
void	Model.remove(BioPAXElement aBioPAXElement) This method removes the given BioPAX Element from the model.
void	Model.replace(BioPAXElement existing, BioPAXElement replacement) Replaces existing BioPAX element with another one, of the same or possibly equivalent type, and updates all the affected references to it (object properties).

Method parameters in org.biopax.paxtools.model with type arguments of type BioPAXElement

Modifier and Type	Method and Description
boolean	BioPAXFactory.canInstantiate(Class<? extends BioPAXElement> aClass) Checks whether objects of a BioPAX model interface can be created (some types are not official BioPAX types, abstract classes).
abstract String	BioPAXFactory.mapClassName(Class<? extends BioPAXElement> aClass) Maps a BioPAX type (model interface) to the full-qualified class name of an implementing class.

Uses of BioPAXElement in org.biopax.paxtools.model.level2

Subinterfaces of BioPAXElement in org.biopax.paxtools.model.level2

Modifier and Type	Interface and Description
interface	biochemicalReaction A conversion interaction in which one or more entities (substrates) undergo ovalent changes to become one or more other entities (products).
interface	bioSource The biological source of an entity (e.g.
interface	catalysis A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
interface	chemicalStructure Describes a small molecule structure.
interface	complex A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
interface	complexAssembly A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
interface	confidence Confidence that the containing instance actually occurs or exists in vivo, usually a statistical measure.
interface	control
interface	conversion
interface	dataSource XREF Should be only unification and publication xrefs
interface	deltaGprimeO
interface	dna
interface	entity This class represents a discrete biological unit used when describing pathways.
interface	evidence
interface	experimentalForm
interface	externalReferenceUtilityClass
interface	interaction
interface	InteractionParticipant marker interface for entities and PEPs
interface	kPrime
interface	Level2Element Created by IntelliJ IDEA.
interface	modulation get controlled should be catalysis
interface	openControlledVocabulary
interface	pathway
interface	pathwayComponent Interface for pathway steps and processes
interface	pathwayStep This represents a set of pathway events.
interface	physicalEntity
interface	physicalEntityParticipant
interface	physicalInteraction
interface	process Tagging interface for entities that needs evidence and can be targeted by a control : Pathway and Interaction
interface	protein
interface	publicationXref
interface	relationshipXref
interface	rna
interface	sequenceEntity User: root Date: Aug 7, 2006 Time: 4:51:19 PM_DOT
interface	sequenceFeature
interface	sequenceInterval
interface	sequenceLocation
interface	sequenceParticipant
interface	sequenceSite
interface	smallMolecule
interface	transport
interface	transportWithBiochemicalReaction
interface	unificationXref
interface	utilityClass
interface	xref
interface	XReferrable

Uses of BioPAXElement in org.biopax.paxtools.model.level3

Subinterfaces of BioPAXElement in org.biopax.paxtools.model.level3

Modifier and Type	Interface and Description
interface	BindingFeature
interface	BiochemicalPathwayStep Definition: Imposes ordering on a step in a biochemical pathway.
interface	BiochemicalReaction Definition: A conversion interaction in which one or more entities (substrates) undergo covalent changes to become one or more other entities (products).
interface	BioSource Definition: The biological source of an entity (e.g.
interface	Catalysis Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy.
interface	CellularLocationVocabulary Definition: A reference to the Gene Ontology Cellular Component (GO CC) ontology.
interface	CellVocabulary Definition: A reference to the Cell Type Ontology (CL).
interface	ChemicalConstant
interface	ChemicalStructure Definition: The chemical structure of a small molecule.
interface	Complex Definition: A physical entity whose structure is comprised of other physical entities bound to each other non-covalently, at least one of which is a macromolecule (e.g.
interface	ComplexAssembly Definition: A conversion interaction in which a set of physical entities, at least one being a macromolecule (e.g.
interface	Control Definition: An interaction in which one entity regulates, modifies, or otherwise influences a continuant entity, i.e.
interface	ControlledVocabulary Definition: This class represents a term from an external controlled vocabulary (CV).
interface	Controller This is a role interface for pathway elements that can control processes, namely Pathway and PhysicalEntity.
interface	Conversion Definition: An interaction in which molecules of one or more PhysicalEntity pools are physically transformed and become a member of one or more other PhysicalEntity pools.
interface	CovalentBindingFeature Definition: An entity feature that represent the covalently bound state of a physical entity.
interface	Degradation Definition: A conversion in which a pool of macromolecules are degraded into their elementary units.
interface	DeltaG Standard transformed Gibbs energy change for a reaction written in terms of biochemical reactants (sums of species), delta-G'o.
interface	Dna Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic acid.
interface	DnaReference A DNA reference is a grouping of several DNA entities that are common in sequence and genomic position.
interface	DnaRegion Definition: A region on a DNA molecule.
interface	DnaRegionReference Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and genomic position.
interface	Entity This class represents a discrete biological unit used when describing pathways.
interface	EntityFeature Description: A characteristic of a physical entity that can change while the entity still retains its biological identity.
interface	EntityReference Definition: An entity reference is a grouping of several physical entities across different contexts and molecular states, that share common physical properties and often named and treated as a single entity with multiple states by biologists.
interface	EntityReferenceTypeVocabulary Definiiton: A reference to a term from an entity reference group ontology.
interface	Evidence Definition: The support for a particular assertion, such as the existence of an interaction or pathway.
interface	EvidenceCodeVocabulary Definition: A reference to the PSI Molecular Interaction ontology experimental method types, including "interaction detection method", "participant identification method", "feature detection method".
interface	ExperimentalForm Definition: The form of a physical entity in a particular experiment, as it may be modified for purposes of experimental design.
interface	ExperimentalFormVocabulary Definition: A term that describes the form of the physical entity in the context of the experiment.
interface	FragmentFeature Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or degradation event.
interface	Gene Definition: A continuant that encodes information that can be inherited through replication.
interface	GeneticInteraction Definition : Genetic interactions between genes occur when two genetic perturbations (e.g.
interface	Interaction Definition: A biological relationship between two or more entities.
interface	InteractionVocabulary A reference to the PSI Molecular Interaction ontology (MI) interaction type.
interface	KPrime The apparent equilibrium constant, K', and associated values.
interface	Level3Element A Level 3 specific element.
interface	ModificationFeature Definition: A covalently modified feature on a sequence, relevant to an interaction, such as a post-translational modification.
interface	Modulation Definition: An interaction in which one entity regulates, modifies, or otherwise influences another.
interface	MolecularInteraction Definition: An interaction in which at least one participant is a physical entity, e.g.
interface	Named Interface for all classes that can have names in BioPAX.
interface	NucleicAcid Tagger interface for DNA and RNA
interface	NucleicAcidReference Role interface for NucleicAcidReferences, namely DNA and RNA.
interface	NucleicAcidRegionReference
interface	Observable User: demir Date: Aug 17, 2007 Time: 5:47:27 PM
interface	Pathway
interface	PathwayStep This represents a set of pathway events.
interface	PhenotypeVocabulary
interface	PhysicalEntity
interface	Process Tagging interface for entities that can participate in a pathway and can be targeted by a control : Pathway and Interaction
interface	Protein
interface	ProteinReference Description: A protein reference is a grouping of several protein entities that are encoded by the same genetic sequence.
interface	Provenance Definition: The direct source of a pathway data or score.
interface	PublicationXref
interface	RelationshipTypeVocabulary Vocabulary for defining relationship Xref types.
interface	RelationshipXref Definition: An xref that defines a reference to an entity in an external resource that does not have the same biological identity as the referring entity.
interface	Rna
interface	RnaReference
interface	RnaRegion Definition: A region on a RNA molecule.
interface	RnaRegionReference A RNA region reference
interface	Score Definition: A score associated with a publication reference describing how the score was determined, the name of the method and a comment briefly describing the method.
interface	SequenceEntity Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
interface	SequenceEntityReference Tagger interface for protein, dna and rna entities
interface	SequenceInterval
interface	SequenceLocation Definition: A location on a nucleotide or amino acid sequence.
interface	SequenceModificationVocabulary Definition: A term that describes the covalent modifications to an amino acid or nucleic acid chain.
interface	SequenceRegionVocabulary Definition: A reference to a controlled vocabulary of sequence regions, such as InterPro or Sequence Ontology (SO) Homepage at http://www.sequenceontology.org.
interface	SequenceSite
interface	SimplePhysicalEntity Tagger interface for non-complex physical entities
interface	SmallMolecule
interface	SmallMoleculeReference
interface	Stoichiometry Stoichiometric coefficient of a physical entity in the context of a conversion or complex.
interface	TemplateReaction
interface	TemplateReactionRegulation
interface	TissueVocabulary Definition: A reference to the BRENDA
interface	Transport
interface	TransportWithBiochemicalReaction
interface	UnificationXref Definition: A unification xref defines a reference to an entity in an external resource that has the same biological identity as the referring entity.
interface	UtilityClass
interface	Xref

Uses of BioPAXElement in org.biopax.paxtools.util

Classes in org.biopax.paxtools.util with type parameters of type BioPAXElement

Modifier and Type	Class and Description
class	BiopaxSafeSet<E extends BioPAXElement> A thread-safe set of BioPAX objects that also prevents adding several elements having the same URI.
class	EquivalenceGrouper<T extends BioPAXElement> Utility class for equivalence based comparison of a set of BioPAXElements.

Methods in org.biopax.paxtools.util with type parameters of type BioPAXElement

Modifier and Type	Method and Description
<R extends BioPAXElement> Set<R>	BPCollections.createSafeSet()
static <T extends BioPAXElement> Set<T>	SetEquivalenceChecker.findEquivalentIntersection(Set<? extends T> set1, Set<? extends T> set2)
static <T extends BioPAXElement> boolean	SetEquivalenceChecker.hasEquivalentIntersection(Set<? extends T> set1, Set<? extends T> set2)
static <T extends BioPAXElement> boolean	SetEquivalenceChecker.isEquivalent(Set<? extends T> set1, Set<? extends T> set2)

Methods in org.biopax.paxtools.util with parameters of type BioPAXElement

Modifier and Type	Method and Description
static boolean	SetEquivalenceChecker.containsEquivalent(Set<? extends BioPAXElement> set, BioPAXElement query)

Method parameters in org.biopax.paxtools.util with type arguments of type BioPAXElement

Modifier and Type	Method and Description
static boolean	SetEquivalenceChecker.containsEquivalent(Set<? extends BioPAXElement> set, BioPAXElement query)