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.examples	This package contains several examples that uses Paxtools to demonstrate basic functionality.
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.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.io.sif.level2
org.biopax.paxtools.io.sif.level3	This package contains the SIF rules for BioPAX Level 3.
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.pattern	Main package.
org.biopax.paxtools.pattern.constraint	Package for constraints.
org.biopax.paxtools.pattern.miner	Package for pattern miner utility.
org.biopax.paxtools.query	Graph-theoretic querying module in Paxtools is used for identifying paths between molecules or identifying other molecules that is reachable through some specific paths using the BioPAX data model.
org.biopax.paxtools.query.wrapperL3	This package contains TODO annotate!
org.biopax.paxtools.query.wrapperL3undirected	This package contains TODO annotate!
org.biopax.paxtools.search	Public interfaces and classes (API) for indexing and full-text searching BioPAX models.
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 void	AddCommand.redoAction(BioPAXElement bpe)
protected abstract void	AbstractAddRemoveCommand.redoAction(BioPAXElement bpe)
void	CommandManager.removeProperty(BioPAXElement bpe, PropertyEditor editor, Object value)
protected void	RemoveCommand.undoAction(BioPAXElement bpe)
protected void	AddCommand.undoAction(BioPAXElement bpe)
protected abstract void	AbstractAddRemoveCommand.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,?>	SimpleEditorMap.getEditorForProperty(String property, Class<D> javaClass)
<D extends BioPAXElement> PropertyEditor<? super D,?>	EditorMapImpl.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>>	SimpleEditorMap.getKnownSubClassesOf(Class<E> javaClass)
<E extends BioPAXElement> Set<? extends Class<E>>	EditorMapImpl.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,?>>	SimpleEditorMap.getSubclassEditorsForProperty(String property, Class<D> domain)
<D extends BioPAXElement> Set<PropertyEditor<? extends D,?>>	EditorMapImpl.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	Traverser.traverse(D element, Model model) Traverse and visit Visitor all properties of the element.
<D extends BioPAXElement> void	AbstractTraverser.traverse(D element, Model model)

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, Model model)
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.
static void	ModelUtils.fixDanglingInverseProperties(BioPAXElement bpe, Model model) Unlinks inverse properties of the BioPAX object from values the other 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) Gets all the child BioPAX elements of a given BioPAX element (using the "tuned" Fetcher) and adds them to a new model.
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>	SimpleEditorMap.getEditorsOf(BioPAXElement bpe)
Set<PropertyEditor>	EditorMapImpl.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>	SimpleEditorMap.getInverseEditorsOf(BioPAXElement bpe)
Set<ObjectPropertyEditor>	EditorMapImpl.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)
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 model, 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) 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, Model model)
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>	SimpleEditorMap.getEditorsOf(Class<? extends BioPAXElement> domain)
Set<PropertyEditor>	EditorMapImpl.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>	SimpleEditorMap.getInverseEditorsOf(Class<? extends BioPAXElement> domain)
Set<ObjectPropertyEditor>	EditorMapImpl.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> mergeObjPropOf)

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.examples

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

Modifier and Type	Method and Description
static Set<? extends BioPAXElement>	UseOfReflection.getObjectBiopaxPropertyValues(BioPAXElement bpe, String property) Example 1.

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

Modifier and Type	Method and Description
static Set	UseOfReflection.getBiopaxPropertyValues(BioPAXElement bpe, String property) Example 2.
static Set<? extends BioPAXElement>	UseOfReflection.getObjectBiopaxPropertyValues(BioPAXElement bpe, String property) Example 1.
void	PathwayGenesExtractor.visit(BioPAXElement domain1, Object range, Model model, 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	XrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	UnificationXrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	StoichiometryImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SmallMoleculeReferenceImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SimplePhysicalEntityImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SequenceSiteImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SequenceIntervalImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	SequenceEntityReferenceImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	RelationshipXrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	PublicationXrefImpl.semanticallyEquivalent(BioPAXElement other)
protected boolean	PhysicalEntityImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ModificationFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	KPrimeImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	FragmentFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	EvidenceImpl.semanticallyEquivalent(BioPAXElement element) Answers whether two Evidence objects are semantically equivalent.
protected boolean	EntityImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	EntityFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	DeltaGImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	CovalentBindingFeatureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ConversionImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ControlledVocabularyImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ComplexImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ChemicalStructureImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	ChemicalConstantImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	BioSourceImpl.semanticallyEquivalent(BioPAXElement element)
protected boolean	BindingFeatureImpl.semanticallyEquivalent(BioPAXElement element)

Uses of BioPAXElement in org.biopax.paxtools.io

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

Modifier and Type	Method and Description
protected BioPAXElement	BioPAXIOHandlerAdapter.L1ToL2Fixes(PropertyEditor editor, BioPAXElement bpe, Model model, String value) Deprecated. BioPAX Level 1 exports are extremely rare and obsolete.

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 BioPAXElement	BioPAXIOHandlerAdapter.L1ToL2Fixes(PropertyEditor editor, BioPAXElement bpe, Model model, String value) Deprecated. BioPAX Level 1 exports are extremely rare and obsolete.
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.io.jena

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

Modifier and Type	Method and Description
protected Class<? extends BioPAXElement>	JenaEditorMap.extractClass(com.hp.hpl.jena.rdf.model.Resource resource)

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

Methods in org.biopax.paxtools.io.sif that return BioPAXElement

Modifier and Type	Method and Description
BioPAXElement	SimpleInteraction.getSource() Gets source element.
BioPAXElement	SimpleInteraction.getTarget() Gets target element.

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

Modifier and Type	Method and Description
Set<BioPAXElement>	SimpleInteraction.getMediators() Gets other related elements of the interaction.

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

Modifier and Type	Method and Description
void	SimpleInteraction.addMediator(BioPAXElement element) Adds a mediator to the interaction.
String	SimpleInteraction.getANameForSIF(BioPAXElement element) This method is used when we want to use readable names in the simple SIF format instead of IDs.
void	InteractionRule.inferInteractions(InteractionSet set, BioPAXElement entity, Model model) This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
void	SimpleInteraction.setSource(BioPAXElement source) Sets source element.
void	SimpleInteraction.setTarget(BioPAXElement target) Sets target element.

Constructors in org.biopax.paxtools.io.sif with parameters of type BioPAXElement

Constructor and Description
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type) Constructor with parameters, without mediators.
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type, BioPAXElement... mediator) Constructor with parameters, with mediators.
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type, BioPAXElement... mediator) Constructor with parameters, with mediators.
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type, Collection<BioPAXElement> mediator) Constructor with parameters, with mediators.

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

Constructor and Description
SimpleInteraction(BioPAXElement source, BioPAXElement target, BinaryInteractionType type, Collection<BioPAXElement> mediator) Constructor with parameters, with mediators.

Uses of BioPAXElement in org.biopax.paxtools.io.sif.level2

Methods in org.biopax.paxtools.io.sif.level2 with parameters of type BioPAXElement

Modifier and Type	Method and Description
void	InteractionRuleL2Adaptor.inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Uses physicalEntity as source of the interaction.

Uses of BioPAXElement in org.biopax.paxtools.io.sif.level3

Classes in org.biopax.paxtools.io.sif.level3 that implement BioPAXElement

Modifier and Type	Class and Description
class	Group This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.

Methods in org.biopax.paxtools.io.sif.level3 that return BioPAXElement

Modifier and Type	Method and Description
protected BioPAXElement	GroupMap.getEntityReferenceOrGroup(BioPAXElement bpe)

Methods in org.biopax.paxtools.io.sif.level3 that return types with arguments of type BioPAXElement

Modifier and Type	Method and Description
protected Set<BioPAXElement>	InteractionRuleL3Adaptor.collectEntities(Set<PhysicalEntity> pes, InteractionSetL3 set)
Map<BioPAXElement,Group>	GroupMap.getMap()

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

Modifier and Type	Method and Description
protected void	InteractionRuleL3Adaptor.createAndAdd(BioPAXElement source, BioPAXElement target, InteractionSetL3 is3, BinaryInteractionType type, BioPAXElement... mediators) Creates the binary interaction and adds to the inferred interaction list.
protected void	InteractionRuleL3Adaptor.createAndAdd(BioPAXElement source, BioPAXElement target, InteractionSetL3 is3, BinaryInteractionType type, BioPAXElement... mediators) Creates the binary interaction and adds to the inferred interaction list.
protected void	InteractionRuleL3Adaptor.createClique(InteractionSetL3 interactionSet, List<BioPAXElement> components, BinaryInteractionType type, BioPAXElement... mediators) Creates an interactions between every ordered pair of components.
static boolean	Simplify.entityHasAChange(BioPAXElement target, Conversion conv, GroupMap groupMap, Set<PEStateChange> peStateChanges)
static boolean	Simplify.entityHasAChange(BioPAXElement element, Conversion conv, GroupMap map, Set<PEStateChange> changeSet, Map<Conversion,Set<EntityReference>> extendedControls)
protected BioPAXElement	GroupMap.getEntityReferenceOrGroup(BioPAXElement bpe)
void	InteractionRuleL3Adaptor.inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Selects only PhysicalEntity as seed.
boolean	Group.isEquivalent(BioPAXElement element)

Method parameters in org.biopax.paxtools.io.sif.level3 with type arguments of type BioPAXElement

Modifier and Type	Method and Description
protected void	InteractionRuleL3Adaptor.createClique(InteractionSetL3 interactionSet, List<BioPAXElement> components, BinaryInteractionType type, BioPAXElement... mediators) Creates an interactions between every ordered pair of components.

Constructors in org.biopax.paxtools.io.sif.level3 with parameters of type BioPAXElement

Constructor and Description
PEStateChange(SimplePhysicalEntity left, SimplePhysicalEntity right, PhysicalEntity leftRoot, PhysicalEntity rightRoot, BioPAXElement element, Conversion conv)

Constructor parameters in org.biopax.paxtools.io.sif.level3 with type arguments of type BioPAXElement

Constructor and Description
GroupMap(Map<BioPAXElement,Group> element2GroupMap)

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 add the given onject 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 Rationale: Unification xrefs are critically important for data integration.
interface	UtilityClass
interface	Xref

Uses of BioPAXElement in org.biopax.paxtools.pattern

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

Modifier and Type	Field and Description
protected Class<? extends BioPAXElement>	Pattern.startingClass Class of the first elements to match with this pattern.

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

Modifier and Type	Method and Description
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(BioPAXElement ele, Pattern pattern, int index, Class<T> c) Searches the given pattern starting from the given element, then collects the specified elements of the matches and returns.
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(Collection<? extends BioPAXElement> eles, Pattern pattern, int index, Class<T> c) Searches the given pattern starting from the given elements, then collects the specified elements of the matches and returns.
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(Model model, Pattern pattern, int index, Class<T> c) Searches a model for the given pattern, then collects the specified elements of the matches and returns.

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

Modifier and Type	Method and Description
BioPAXElement	Match.get(int index) Gets element at the index.
BioPAXElement	Match.get(String label, Pattern p) Gets element corresponding to the given label in the pattern.
BioPAXElement	Match.getFirst() Gets first element of the match
BioPAXElement	Match.getLast() Gets last element of the match.
BioPAXElement[]	Match.getVariables() Getter for the element array.

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

Modifier and Type	Method and Description
Collection<BioPAXElement>	MappedConst.generate(Match match, int... outer) Calls generate method of the constraint with index translation.
Collection<BioPAXElement>	Constraint.generate(Match match, int... ind) Generates candidate values for the variable to be generated.
List<BioPAXElement>	Match.get(String[] label, Pattern p) Gets elements corresponding to the given labels in the pattern.
Class<? extends BioPAXElement>	Pattern.getStartingClass() Gets the type of the initial element.
static Map<BioPAXElement,List<Match>>	Searcher.search(Collection<? extends BioPAXElement> eles, Pattern pattern) Searches the given pattern starting from the given elements.
static Map<BioPAXElement,List<Match>>	Searcher.search(Model model, Pattern pattern) Searches the given pattern in the given model.
static Map<BioPAXElement,List<Match>>	Searcher.search(Model model, Pattern pattern, ProgressWatcher prg) Searches the given pattern in the given model.

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

Modifier and Type	Method and Description
String	Match.getAName(BioPAXElement ele) Finds a name for the variable.
boolean	Searcher.hasSolution(Pattern p, BioPAXElement... ele) Checks if there is any match for the given pattern if search starts from the given element.
static List<Match>	Searcher.search(BioPAXElement ele, Pattern pattern) Searches the pattern starting from the given element.
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(BioPAXElement ele, Pattern pattern, int index, Class<T> c) Searches the given pattern starting from the given element, then collects the specified elements of the matches and returns.
void	Match.set(BioPAXElement ele, int index) Sets the given element to the given index.

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

Modifier and Type	Method and Description
static Map<BioPAXElement,List<Match>>	Searcher.search(Collection<? extends BioPAXElement> eles, Pattern pattern) Searches the given pattern starting from the given elements.
static <T extends BioPAXElement> Set<T>	Searcher.searchAndCollect(Collection<? extends BioPAXElement> eles, Pattern pattern, int index, Class<T> c) Searches the given pattern starting from the given elements, then collects the specified elements of the matches and returns.
static List<Match>	Searcher.searchPlain(Collection<? extends BioPAXElement> eles, Pattern pattern) Searches the pattern starting from given elements, but instead of a match map, returns all matches in a list.

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

Constructor and Description
Pattern(Class<? extends BioPAXElement> startingClass, Constraint firstConstraint, String... label) Constructor with the first constraint and labels it uses.
Pattern(Class<? extends BioPAXElement> startingClass, String label) Constructor with a label for the element at index 0.

Uses of BioPAXElement in org.biopax.paxtools.pattern.constraint

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

Modifier and Type	Method and Description
protected Collection<BioPAXElement>	InterToPartER.generate(Conversion conv, InterToPartER.Direction direction, Set<Entity> taboo) Gets the related entity references of the given interaction,
protected Collection<BioPAXElement>	InterToPartER.generate(Interaction inter, Set<Entity> taboo) Gets the related entity references of the given interaction.
Collection<BioPAXElement>	XOR.generate(Match match, int... ind) Gets xor of the generated elements by the member constraints.
Collection<BioPAXElement>	SelfOrThis.generate(Match match, int... ind) Gets the first mapped element along with the generated elements of wrapped constraint.
Collection<BioPAXElement>	RelatedControl.generate(Match match, int... ind) According to the relation between PhysicalEntity and the Conversion, checks of the Control is relevant.
Collection<BioPAXElement>	PathConstraint.generate(Match match, int... ind) Uses the encapsulated PAthAccessor to generate satisfying elements.
Collection<BioPAXElement>	ParticipatingPE.generate(Match match, int... ind) Deprecated. First evaluates the direction that the Control is affecting the Conversion, then gets the related participants.
Collection<BioPAXElement>	ParticipatesInConv.generate(Match match, int... ind) Identifies the conversion direction and gets the related participants.
Collection<BioPAXElement>	Participant.generate(Match match, int... ind) Identifies the conversion direction and gets the related participants.
Collection<BioPAXElement>	OtherSide.generate(Match match, int... ind) Deprecated. Checks which side is the first PhysicalEntity, and gathers participants on the other side.
Collection<BioPAXElement>	OR.generate(Match match, int... ind) Gets the intersection of the generated values of wrapped constraints.
Collection<BioPAXElement>	LinkedPE.generate(Match match, int... ind) Gets to the linked PhysicalEntity.
Collection<BioPAXElement>	InterToPartER.generate(Match match, int... ind) Iterated over non-taboo participants and collectes related ER.
Collection<BioPAXElement>	ConversionSide.generate(Match match, int... ind) Checks which side is the first PhysicalEntity, and gathers participants on either the other side or the same side.
Collection<BioPAXElement>	ConstraintChain.generate(Match match, int... ind) Chains the member constraints and returns the output of the last constraint.
Collection<BioPAXElement>	ConstraintAdapter.generate(Match match, int... ind) This method has to be overridden by generative constraints.
Collection<BioPAXElement>	AND.generate(Match match, int... ind) Gets intersection of the generated elements by the member constraints.
Set<BioPAXElement>	LinkedPE.getLinkedElements(PhysicalEntity pe)

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

Modifier and Type	Method and Description
protected Set	LinkedPE.access(PathAccessor pa, Set<BioPAXElement> seed, Set<BioPAXElement> all) Uses the given PathAccessor to access fields of the seed and return only new elements that is not in the given element set (all).
protected Set	LinkedPE.access(PathAccessor pa, Set<BioPAXElement> seed, Set<BioPAXElement> all) Uses the given PathAccessor to access fields of the seed and return only new elements that is not in the given element set (all).
protected void	LinkedPE.enrichWithCM(Set<BioPAXElement> seed, Set<BioPAXElement> all) Gets parent complexes or complex members recursively according to the type of the linkage.
protected void	LinkedPE.enrichWithCM(Set<BioPAXElement> seed, Set<BioPAXElement> all) Gets parent complexes or complex members recursively according to the type of the linkage.
protected void	LinkedPE.enrichWithGenerics(Set<BioPAXElement> seed, Set<BioPAXElement> all) Gets the linked homologies and then switches to complex-relationship mode.
protected void	LinkedPE.enrichWithGenerics(Set<BioPAXElement> seed, Set<BioPAXElement> all) Gets the linked homologies and then switches to complex-relationship mode.
static Constraint	ConBox.type(Class<? extends BioPAXElement> clazz) Creates an element type constraint.

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

Constructor and Description
HasAnID(IDFetcher fetcher, Map<BioPAXElement,Set<String>> idMap) Constructor with the ID fetcher.
Type(Class<? extends BioPAXElement> clazz) Constructor with the desired class.

Uses of BioPAXElement in org.biopax.paxtools.pattern.miner

Fields in org.biopax.paxtools.pattern.miner with type parameters of type BioPAXElement

Modifier and Type	Field and Description
protected Map<BioPAXElement,Set<String>>	MinerAdapter.idMap Memory for object IDs.
Set<BioPAXElement>	SIFInteraction.mediators
Set<BioPAXElement>	SIFInteraction.sourceERs
Set<BioPAXElement>	SIFInteraction.sourcePEs
Set<BioPAXElement>	SIFInteraction.targetERs
Set<BioPAXElement>	SIFInteraction.targetPEs

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

Modifier and Type	Method and Description
Map<BioPAXElement,Set<String>>	MinerAdapter.getIdMap()

Methods in org.biopax.paxtools.pattern.miner with parameters of type BioPAXElement

Modifier and Type	Method and Description
Set<String>	IDFetcher.fetchID(BioPAXElement ele) Finds a String ID for the given element.
Set<String>	CommonIDFetcher.fetchID(BioPAXElement ele)
protected Set<String>	MinerAdapter.fetchIDs(BioPAXElement ele, IDFetcher fetcher)

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

Modifier and Type	Method and Description
void	MinerAdapter.setIdMap(Map<BioPAXElement,Set<String>> idMap)
void	UbiquitousIDMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
void	RelatedGenesOfInteractionsMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the IDs of interaction, then gene symbols of related proteins in a line.
void	Miner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the text output to the given stream.
void	DirectedRelationMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.
void	ControlsStateChangeDetailedMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the result as "A modifications-of-A B gains-of-B loss-of-B", where A and B are gene symbols, and whitespace is tab.
void	AbstractSIFMiner.writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the result as "A used-for-production-of B", where A and B are small molecule names, and whitespace is tab.
void	MinerAdapter.writeResultAsSIF(Map<BioPAXElement,List<Match>> matches, OutputStream out, boolean directed, String label1, String label2) This method writes the output as pairs of gene symbols of the given two ProteinReference.
void	MinerAdapter.writeResultDetailed(Map<BioPAXElement,List<Match>> matches, OutputStream out, int columns) Writes the result as a tab delimited format, where the column values are customized.
void	MinerAdapter.writeSIFsUsingSIFFramework(Map<BioPAXElement,List<Match>> matches, OutputStream out) This method writes the output as pairs of gene symbols of the given two ProteinReference.

Constructors in org.biopax.paxtools.pattern.miner with parameters of type BioPAXElement

Constructor and Description
SIFInteraction(String sourceID, String targetID, BioPAXElement sourceER, BioPAXElement targetER, SIFType type, Set<BioPAXElement> mediators, Set<BioPAXElement> sourcePEs, Set<BioPAXElement> targetPEs)

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

Constructor and Description
SIFInteraction(String sourceID, String targetID, BioPAXElement sourceER, BioPAXElement targetER, SIFType type, Set<BioPAXElement> mediators, Set<BioPAXElement> sourcePEs, Set<BioPAXElement> targetPEs)
SIFInteraction(String sourceID, String targetID, BioPAXElement sourceER, BioPAXElement targetER, SIFType type, Set<BioPAXElement> mediators, Set<BioPAXElement> sourcePEs, Set<BioPAXElement> targetPEs)
SIFInteraction(String sourceID, String targetID, BioPAXElement sourceER, BioPAXElement targetER, SIFType type, Set<BioPAXElement> mediators, Set<BioPAXElement> sourcePEs, Set<BioPAXElement> targetPEs)

Uses of BioPAXElement in org.biopax.paxtools.query

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

Modifier and Type	Method and Description
static Map<BioPAXElement,Set<PhysicalEntity>>	QueryExecuter.getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements) Maps each BioPAXElement to its related PhysicalEntity objects.
static Set<BioPAXElement>	QueryExecuter.runCommonStream(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters) Gets the elements in the common upstream or downstream of the seed
static Set<BioPAXElement>	QueryExecuter.runCommonStreamWithPOI(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters) First finds the common stream, then completes it with the paths between seed and common stream.
static Set<BioPAXElement>	QueryExecuter.runGOI(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters) Deprecated. Use runPathsBetween instead
static Set<BioPAXElement>	QueryExecuter.runNeighborhood(Set<BioPAXElement> sourceSet, Model model, int limit, Direction direction, Filter... filters) Gets neighborhood of the source set.
static Set<BioPAXElement>	QueryExecuter.runPathsBetween(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters) Gets the graph constructed by the paths between the given seed nodes.
static Set<BioPAXElement>	QueryExecuter.runPathsFromTo(Set<BioPAXElement> sourceSet, Set<BioPAXElement> targetSet, Model model, LimitType limitType, int limit, Filter... filters) Gets paths the graph composed of the paths from a source node, and ends at a target node.

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

Modifier and Type	Method and Description
static Set<PhysicalEntity>	QueryExecuter.getRelatedPhysicalEntities(BioPAXElement element, Set<PhysicalEntity> pes) Gets the related PhysicalEntity objects of the given BioPAXElement, in level 3 models.

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

Modifier and Type	Method and Description
static Map<BioPAXElement,Set<PhysicalEntity>>	QueryExecuter.getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements) Maps each BioPAXElement to its related PhysicalEntity objects.
static Set<Node>	QueryExecuter.getSeedInteractions(Collection<BioPAXElement> elements, Graph graph) Extracts the querible interactions from the elements.
static Set<Node>	QueryExecuter.prepareSingleNodeSet(Set<BioPAXElement> elements, Graph graph) Gets the related wrappers of the given elements in a set.
protected static void	QueryExecuter.replaceXrefsWithRelatedER(Collection<BioPAXElement> elements) Replaces Xref objects with the related EntityReference objects.
static Set<BioPAXElement>	QueryExecuter.runCommonStream(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters) Gets the elements in the common upstream or downstream of the seed
static Set<BioPAXElement>	QueryExecuter.runCommonStreamWithPOI(Set<BioPAXElement> sourceSet, Model model, Direction direction, int limit, Filter... filters) First finds the common stream, then completes it with the paths between seed and common stream.
static Set<BioPAXElement>	QueryExecuter.runGOI(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters) Deprecated. Use runPathsBetween instead
static Set<BioPAXElement>	QueryExecuter.runNeighborhood(Set<BioPAXElement> sourceSet, Model model, int limit, Direction direction, Filter... filters) Gets neighborhood of the source set.
static Set<BioPAXElement>	QueryExecuter.runPathsBetween(Set<BioPAXElement> sourceSet, Model model, int limit, Filter... filters) Gets the graph constructed by the paths between the given seed nodes.
static Set<BioPAXElement>	QueryExecuter.runPathsFromTo(Set<BioPAXElement> sourceSet, Set<BioPAXElement> targetSet, Model model, LimitType limitType, int limit, Filter... filters) Gets paths the graph composed of the paths from a source node, and ends at a target node.
static Set<BioPAXElement>	QueryExecuter.runPathsFromTo(Set<BioPAXElement> sourceSet, Set<BioPAXElement> targetSet, Model model, LimitType limitType, int limit, Filter... filters) Gets paths the graph composed of the paths from a source node, and ends at a target node.

Uses of BioPAXElement in org.biopax.paxtools.query.wrapperL3

Methods in org.biopax.paxtools.query.wrapperL3 with parameters of type BioPAXElement

Modifier and Type	Method and Description
protected void	TemplateReactionWrapper.addToUpstream(BioPAXElement ele, Graph graph) Binds the given element to the upstream.
protected void	EventWrapper.addToUpstream(BioPAXElement ele, Graph graph) Bind the wrapper of the given element to the upstream.

Method parameters in org.biopax.paxtools.query.wrapperL3 with type arguments of type BioPAXElement

Modifier and Type	Method and Description
protected void	StringFieldFilter.addAccessor(PathAccessor acc, Class<? extends BioPAXElement> clazz) Adds the given PathAccessor to the list of accessors to use to get field values of objects and their related objects.

Uses of BioPAXElement in org.biopax.paxtools.query.wrapperL3undirected

Methods in org.biopax.paxtools.query.wrapperL3undirected with parameters of type BioPAXElement

Modifier and Type	Method and Description
protected void	InteractionWrapper.addToDownstream(BioPAXElement pe, Graph graph) Binds the given PhysicalEntity to the downstream.
protected void	InteractionWrapper.addToUpstream(BioPAXElement ele, Graph graph) Binds the given element to the upstream.
protected void	EventWrapper.addToUpstream(BioPAXElement ele, Graph graph) Bind the wrapper of the given element to the upstream.

Uses of BioPAXElement in org.biopax.paxtools.search

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

Modifier and Type	Method and Description
List<BioPAXElement>	SearchResult.getHits()

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

Modifier and Type	Method and Description
SearchResult	Searcher.search(String query, int page, Class<? extends BioPAXElement> filterByType, String[] datasources, String[] organisms) Full-text search for BioPAX elements.
SearchResult	SearchEngine.search(String query, int page, Class<? extends BioPAXElement> filterByType, String[] datasources, String[] organisms)
void	SearchResult.setHits(List<BioPAXElement> hits)

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)