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

Packages that use Model

org.biopax.paxtools.command
org.biopax.paxtools.controller
org.biopax.paxtools.fixer
org.biopax.paxtools.impl
org.biopax.paxtools.io
org.biopax.paxtools.model

Uses of Model in org.biopax.paxtools.command

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

AbstractAddRemoveCommand(Model model, java.util.Set<BioPAXElement> bpes)

AddCommand(Model model, java.util.Set<BioPAXElement> bpes)

CommandManager(Model model)

RemoveCommand(Model model, java.util.Set<BioPAXElement> bpes)

Uses of Model in org.biopax.paxtools.controller

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

Model	Cloner.clone(Model source, java.util.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)
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.
Model	ModelUtils.getDirectChildren(BioPAXElement bpe) Gets direct children of a given BioPAX element and adds them to a new model.
Model	ModelUtils.getModel()
Model	ModelUtils.writeRead() 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

Model	Cloner.clone(Model source, java.util.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.
java.util.Set<BioPAXElement>	Completer.complete(java.util.Collection<BioPAXElement> elements, Model model)
<T extends BioPAXElement> T	ShallowCopy.copy(Model model, T source, java.lang.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 to the model.
Model	ModelFilter.filter(Model model)
void	SimpleMerger.merge(Model target, BioPAXElement source) Merges the source element (and its "downstream" dependents) into target model if its RDFId is not yet there.
void	SimpleMerger.merge(Model target, java.util.Collection<? extends BioPAXElement> elements) Merges the elements into target model.
void	SimpleMerger.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.
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	TraverserBilinked.traverse(BioPAXElement element, Model model)
void	Traverser.traverse(BioPAXElement element, Model model) Traverse and visit Visitor all properties of the element.
void	PropertyReasoner.traverse(BioPAXElement bpe, Model model) This traverse method, first, takes care about the PropertyReasoner.propertyName we are interested in, then proceeds- as the basic Traverser.traverse(BioPAXElement, Model) would normally do (i.e., - delivering to the method PropertyReasoner.visit(Object, BioPAXElement, Model, PropertyEditor) for all properties without any predefined order).
void	Visitor.visit(BioPAXElement domain, java.lang.Object range, Model model, PropertyEditor editor) An implementation of this method should perform a BioPAX element and editor dependent operation on the model.
void	ShallowCopy.visit(BioPAXElement domain, java.lang.Object range, Model model, PropertyEditor editor)
void	Merger.visit(BioPAXElement domain, java.lang.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, java.lang.Object range, Model model, PropertyEditor editor)
void	Cloner.visit(BioPAXElement domain, java.lang.Object range, Model model, PropertyEditor editor)
void	AbstractTraverser.visit(BioPAXElement domain, java.lang.Object range, Model model, PropertyEditor editor) Saves/restores the current "path" of the value in the model and calls the protected abstract method visitValue that is to be implemented in subclasses of this abstract class.
protected void	PropertyReasoner.visit(java.lang.Object range, BioPAXElement bpe, Model model, PropertyEditor editor) Simply, calls PropertyReasoner.traverse(BioPAXElement, Model) and goes deeper when the propertyName's range/valueStack is a BioPAX object.
protected void	Fetcher.visit(java.lang.Object range, BioPAXElement domain, Model model, PropertyEditor editor) Adds the BioPAX element into the model and traverses the element for its dependent elements.
protected abstract void	AbstractTraverser.visit(java.lang.Object range, BioPAXElement domain, Model model, PropertyEditor editor) This is to implement a real action here: do something, return or continue (traverse) into properties.

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

Integrator(EditorMap editorMap, Model target, Model... sources)

Integrator(EditorMap editorMap, Model target, Model... sources)

ModelUtils(Model model)
Constructor.

ReusedPEPHelper(Model model)

Uses of Model in org.biopax.paxtools.fixer

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

void	FeatureResolver.resolveFeatures(Model model)

Uses of Model in org.biopax.paxtools.impl

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

class

ModelImpl This is the default implementation of the Model.

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

Model

BioPAXFactoryAdaptor.createModel()

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

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

Model	BioPAXIOHandlerAdapter.convertFromMultipleOwlFiles(java.lang.String... files) This is experimental and is not not complete.
Model	BioPAXIOHandler.convertFromMultipleOwlFiles(java.lang.String... files) This method will read multiple OWL document and will merge them into an in memory BioPAX model.
Model	BioPAXIOHandlerAdapter.convertFromOWL(java.io.InputStream in) Reads a BioPAX model from an OWL file input stream (in) and converts it to a model.
Model	BioPAXIOHandler.convertFromOWL(java.io.InputStream in) This method will read the OWL document given by the input stream and will convert it into an in memory BioPAX model.

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

protected void	BioPAXIOHandlerAdapter.bindValue(java.lang.String valueString, PropertyEditor editor, BioPAXElement bpe, Model model)
void	SimpleIOHandler.convertToOWL(Model model, java.io.OutputStream outputStream) Converts a model into BioPAX (OWL) format, and writes it into the outputStream.
void	BioPAXIOHandler.convertToOWL(Model model, java.io.OutputStream outputStream) This method will write the model to the output stream.
void	BioPAXIOHandlerAdapter.convertToOWL(Model model, java.io.OutputStream outputStream, java.lang.String... ids) Similar to BioPAXIOHandler#convertToOWL(org.biopax.paxtools .model.Model, Object), but extracts a sub-model, converts it into BioPAX (OWL) format, and writes it into the outputStream.
void	BioPAXIOHandler.convertToOWL(Model model, java.io.OutputStream outputStream, java.lang.String... ids) This method will "excise" a new model from the given model that contains the objects with given ids and their dependents.
protected void	BioPAXIOHandlerAdapter.createAndAdd(Model model, java.lang.String id, java.lang.String localName)
protected void	SimpleIOHandler.createAndBind(Model model)
protected abstract void	BioPAXIOHandlerAdapter.createAndBind(Model model)
protected BioPAXElement	BioPAXIOHandlerAdapter.literalFixes(PropertyEditor editor, BioPAXElement bpe, Model model, java.lang.String value)

Uses of Model in org.biopax.paxtools.model

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

abstract Model

BioPAXFactory.createModel()

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

void	Model.merge(Model source) Merges the source model into this one.