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

Packages that use Model

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.io	This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..
org.biopax.paxtools.model	This package contains the interfaces that maps to the OWL classes defined in the BioPAX specification.

Uses of Model in org.biopax.paxtools.command

Constructors in org.biopax.paxtools.command with parameters of type Model

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

Uses of Model in org.biopax.paxtools.controller

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

Modifier and Type	Method and Description
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.
Model	ModelFilter.filter(Model model)
static Model	ModelUtils.getAllChildren(BioPAXElement bpe, Filter<PropertyEditor>... filters) Deprecated. use Fetcher.fetch(BioPAXElement, Model) instead (with Fetcher.nextStepFilter or without)
static Model	ModelUtils.getDirectChildren(BioPAXElement bpe) Gets direct children of a given BioPAX element and adds them to a new model.
static Model	ModelUtils.writeRead(Model model) Cuts the BioPAX model off other models and BioPAX objects by essentially performing write/read to/from OWL.

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

Modifier and Type	Method and Description
static void	ModelUtils.addMissingEntityReference(Model model, SimplePhysicalEntity pe) For a non-generic simple physical entity (memberPhysicalEntity property is empty) that does not have entityReference property defined, this method generates and adds a new entity reference of proper type to both this entity and the model, and also copies names and xrefs from the source physical entity to the generated entity reference (UnificationXrefs are converted to RelationshipXref and then also deleted from the original entity.)
static void	ModelUtils.breakPathwayComponentCycle(Model model) Removes cyclic pathway inclusions, non-trivial infinite loops, in 'pathwayComponent' biopax property.
Model	Cloner.clone(Model source, Set<BioPAXElement> toBeCloned) Deprecated. use Cloner.clone(Set) instead ('source' model was not used in previous versions)
Set<BioPAXElement>	Completer.complete(Collection<BioPAXElement> elements, Model model) Deprecated. use Completer.complete(Collection) instead (- model is never explicitly used there)
<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.
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.
Model	ModelFilter.filter(Model model)
static void	ModelUtils.fixControlled(Model model, Control control) In Paxtools v6, controlled property won't accept multiple values (due to the OWL functional property restriction, which we so far forgot of); so, let's make sure every Control has at most one controlled process.
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.
static Map<Class<? extends BioPAXElement>,Integer>	ModelUtils.generateClassMetrics(Model model) Generates simple counts of different elements in the model.
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 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.
Set	PathAccessor.getValueFromModel(Model model) This method runs the path query on all the elements within the model.
void	SimpleMerger.merge(Model target, BioPAXElement source) Merges the source element (and its "downstream" dependents) into target model.
void	SimpleMerger.merge(Model target, Collection<? extends BioPAXElement> elements) Merges the elements and all their child biopax objects into the target model.
void	Merger.merge(Model target, Model... sources) Merges the source models into target model.
void	Merger.merge(Model target, Model... sources) Merges the source models into target model.
void	SimpleMerger.merge(Model target, Model... sources) Merges the source models into target model, one after another (in the order they are listed).
void	SimpleMerger.merge(Model target, Model... sources) Merges the source models into target model, one after another (in the order they are listed).
static void	ModelUtils.mergeEquivalentInteractions(Model model) Merges equivalent interactions (currently - Conversions only).
static void	ModelUtils.mergeEquivalentPhysicalEntities(Model model) Merges equivalent physical entities.
static void	ModelUtils.normalizeGeneric(Model model, PhysicalEntity generic) In all interactions and complexes, replace generic physical entities (having members) with their corresponding members; clone the parent object, if needed, for each member.
static void	ModelUtils.normalizeGenerics(Model model) Converts each generic simple (except a Complex) physical entity having memberPhysicalEntity property set into equivalent physical entity with a generic entity reference (have memberEntityReference values).
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.
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.replaceEquivalentFeatures(Model model) This method iterates over the features in a model and tries to find equivalent objects and merges them.
void	TraverserBilinked.traverse(BioPAXElement element, Model model)
<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.
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.
static Model	ModelUtils.writeRead(Model model) Cuts the BioPAX model off other models and BioPAX objects by essentially performing write/read to/from OWL.

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

Constructor and Description
Integrator(EditorMap editorMap, Model target, Model... sources)
Integrator(EditorMap editorMap, Model target, Model... sources)
ReusedPEPHelper(Model model)

Uses of Model in org.biopax.paxtools.converter

Methods in org.biopax.paxtools.converter that return Model

Modifier and Type	Method and Description
Model	LevelUpgrader.filter(Model model) Converts a BioPAX Model, Level 1 or 2, to the Level 3.

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

Modifier and Type	Method and Description
Model	LevelUpgrader.filter(Model model) Converts a BioPAX Model, Level 1 or 2, to the Level 3.
protected void	LevelUpgrader.preparePep2PEIDMap(Model model)
protected void	LevelUpgrader.visit(Object value, BioPAXElement parent, Model newModel, PropertyEditor editor)

Uses of Model in org.biopax.paxtools.impl

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

Modifier and Type	Class and Description
class	ModelImpl This is the default implementation of the Model.

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

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)
void	ModelImpl.merge(Model source) This is default implementation that uses the id-based merging (SimpleMerger.merge(Model, Model...)) NOTE: some applications, such as those dealing with persistence/transactions or advanced BioPAX alignment/comparison algorithms (like the Patch), may have to implement and use a more specific method instead.

Uses of Model in org.biopax.paxtools.io

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

Modifier and Type	Method and Description
Model	BioPAXIOHandler.convertFromOWL(InputStream in) This method will read the OWL document given by the input stream and will convert it into an in memory BioPAX model.
Model	BioPAXIOHandlerAdapter.convertFromOWL(InputStream in) Reads a BioPAX model from an OWL file input stream (in) and converts it to a model.

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

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.
static String	SimpleIOHandler.convertToOwl(Model model) Serializes a (not too large) BioPAX model to the RDF/XML (OWL) formatted string.
void	BioPAXIOHandler.convertToOWL(Model model, OutputStream outputStream) This method will write the model to the output stream.
void	SimpleIOHandler.convertToOWL(Model model, OutputStream outputStream) Converts a model into BioPAX (OWL) format, and writes it into the outputStream.
void	BioPAXIOHandler.convertToOWL(Model model, OutputStream outputStream, String... ids) This method will "excise" a new model from the given model that contains the objects with given ids and their dependents.
void	BioPAXIOHandlerAdapter.convertToOWL(Model model, OutputStream outputStream, String... ids) Similar to BioPAXIOHandler.convertToOWL(org.biopax.paxtools.model.Model, java.io.OutputStream) (org.biopax.paxtools.model.Model, Object)}, but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream.
protected void	BioPAXIOHandlerAdapter.createAndAdd(Model model, String id, String localName) This method is called by the reader for each OWL instance in the OWL model.
protected abstract void	BioPAXIOHandlerAdapter.createAndBind(Model model) This method provides a hook for the implementers of this abstract class to create objects themselves and bind the properties to the objects.
protected void	SimpleIOHandler.createAndBind(Model model)

Uses of Model in org.biopax.paxtools.model

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

Modifier and Type	Method and Description
Model	BioPAXFactory.createModel() Creates a new BioPAX model.

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

Modifier and Type	Method and Description
void	Model.merge(Model source) Merges the source model into this one.