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

Packages that use Model

Package	Description
org.biopax.paxtools
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.io	This package contains classes that handle IO operations including reading and writing BioPAX from files and streams..
org.biopax.paxtools.io.gsea	This package contains a simple GSEA converter.
org.biopax.paxtools.io.jena	This package contains a Jena bases reader/writer for reading BioPAX files.
org.biopax.paxtools.io.sbgn	This package contains a BioPAX to SBGN-PD converter and associated classes.
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.pattern	Main package.
org.biopax.paxtools.pattern.example
org.biopax.paxtools.pattern.miner	Package for pattern miner utility.
org.biopax.paxtools.pattern.util	Package for several utility classes.
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.

Uses of Model in org.biopax.paxtools

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

Modifier and Type	Method and Description
static void	PaxtoolsMain.summarize(Model model, PrintStream out)

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) 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) Gets all the child BioPAX elements of a given BioPAX element (using the "tuned" Fetcher) and adds them to a new model.
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.addPathwayAnnotations(Model model, boolean directParentsOnly, Class<? extends BioPAXElement>... types) Given BioPAX model, for each BioPAX object of the listed classes and their sub-classes, such as e.g.
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)
<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.
static void	ModelUtils.copySimplePointers(Model model, Named source, Named target) Copies names and xrefs from source to target biopax object; it does not copy unification xrefs but instead adds relationship xrefs using the same db and id values as source's unification xrefs.
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.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.
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	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).
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.
static void	ModelUtils.mergeEquivalentInteractions(Model model) Merges equivalent interactions.
static void	ModelUtils.normalizeGenerics(Model model) Converts generic simple physical entities, i.e., physical entities except Complexes that have not empty memberPhysicalEntity property, into equivalent physical entities with generic entity references (which have members); this is a better and less error prone way to model generic molecules in BioPAX L3.
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.
static void	ModelUtils.resolveFeatures(Model model) TODO annotate or deprecate...
void	TraverserBilinked.traverse(BioPAXElement element, Model model)
<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)
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.
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.examples

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

Modifier and Type	Method and Description
static Model	Macros.open(String filename)

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

Modifier and Type	Method and Description
void	Tutorial.graphQuery(Model model, PhysicalEntity entity3, PhysicalEntity entity2, PhysicalEntity entity1)
static void	ProteinNameLister.listProteinUnificationXrefsPerPathway(Model model)
static void	ProteinNameLister.listUnificationXrefsPerPathway(Model model) Here is a more elegant way of doing the previous method!
static void	Tutorial.merge(EditorMap editorMap, Model srcModel2, Model srcModel1)
static void	SimpleIOExample.output(Model model)
static void	PathwayComponentLister.printPathwayComponents(Model model)
void	PathwayGenesExtractor.visit(BioPAXElement domain1, Object range, Model model, 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	BioPAXIOHandlerAdapter.convertFromMultipleOwlFiles(String... files) Deprecated. experimental and incomplete; e.g., files are to be ordered, i.e., a former file should not point to the latter. Use it at your own risk. Or, use #convertFromOWL to get independent models; then, try merging them...
Model	BioPAXIOHandler.convertFromMultipleOwlFiles(String... files) This method will read multiple OWL document and will merge them 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.
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.

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	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) This method will write the model to the output stream.
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.
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.
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 void	SimpleIOHandler.createAndBind(Model 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 BioPAXElement	BioPAXIOHandlerAdapter.L1ToL2Fixes(PropertyEditor editor, BioPAXElement bpe, Model model, String value) Deprecated. BioPAX Level 1 exports are extremely rare and obsolete.

Uses of Model in org.biopax.paxtools.io.gsea

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

Modifier and Type	Method and Description
Collection<org.biopax.paxtools.io.gsea.GSEAEntry>	GSEAConverter.convert(Model model) Creates GSEA entries from the pathways contained in the model.
void	GSEAConverter.writeToGSEA(Model model, OutputStream out) Converts model to GSEA (GMT) and writes to out.

Uses of Model in org.biopax.paxtools.io.jena

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

Modifier and Type	Method and Description
void	JenaIOHandler.convertToOWL(Model model, OutputStream outputStream) Writes a model in OWL format using the an output stream.
protected void	JenaIOHandler.createAndBind(Model model)

Uses of Model in org.biopax.paxtools.io.sbgn

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

Modifier and Type	Method and Description
org.sbgn.bindings.Sbgn	L3ToSBGNPDConverter.createSBGN(Model model) Creates an Sbgn object from the given model.
void	L3ToSBGNPDConverter.writeSBGN(Model model, OutputStream stream) Converts the given model to SBGN, and writes in the specified output stream.
void	L3ToSBGNPDConverter.writeSBGN(Model model, String file) Converts the given model to SBGN, and writes in the specified file.

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

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

Modifier and Type	Method and Description
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.
Set<SimpleInteraction>	SimpleInteractionConverter.inferInteractions(Model model) Deprecated. Infers simple interactions from the interactions found in the model for every interaction rule given; and returns this inferred simple interactions.
void	SimpleInteractionConverter.writeInteractionsInSIF(Model model, OutputStream out) Deprecated. Infers simple interactions from the model using SimpleInteractionConverter.inferInteractions(org.biopax.paxtools.model.Model) and wrties them to an output stream.
void	SimpleInteractionConverter.writeInteractionsInSIFNX(Model model, OutputStream edgeStream, OutputStream nodeStream, List<String> interactorPropertyPaths, List<String> mediatorPropertyPaths, boolean writeEntityTypes) Deprecated. This method outputs inferred interactions in SIF annotation extended format (Sifnx).

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

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

Modifier and Type	Method and Description
void	InteractionRuleL2Adaptor.inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Uses physicalEntity as source of the interaction.
void	ParticipatesRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infer using given physicalEntity as source.
void	InteractionRuleL2.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity entity, Model model) This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
void	ControlsTogetherRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity A, Model model) Infers interactions using A as source.
void	ControlRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity A, Model model) When options map is null, then all rules are generated.
void	ConsecutiveCatalysisRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infers using the given physicalEntity as source.
void	ComponentRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity A, Model model) Infer starting from the given physicalEntity.
void	AffectsRule.inferInteractionsFromPE(InteractionSet interactionSet, physicalEntity pe, Model model) Infers interactions using the given physicalEntity as seed.

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

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

Modifier and Type	Method and Description
void	ActivityNetworkAnalyzer.analyzeStates(Model model) Deprecated. Given a model this method will analyze the states and populate the stateChangeMap and extendedControls maps.
static GroupMap	Grouper.inferGroups(Model model)
void	InteractionRuleL3Adaptor.inferInteractions(InteractionSet interactionSet, BioPAXElement entity, Model model) Selects only PhysicalEntity as seed.
void	ParticipatesRule.inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Infers interactions starting from the given PhysicalEntity.
void	InteractionRuleL3.inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) This method populates the interactionSet with simple interactions that can be derived from the model based on this rule.
void	ExpressionRule.inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Searches the transcriptional relations using the pattern, then decides the interaction type according to the type of the Control.
void	ControlsTogetherRule.inferInteractionsFromPE(InteractionSetL3 l3, PhysicalEntity pe, Model model)
void	ControlRule.inferInteractionsFromPE(InteractionSetL3 is3, PhysicalEntity pe, Model model) When options map is null, then all rules are generated.
void	ConsecutiveCatalysisRule.inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Infers interactions using the given PhysicalEntity as seed.
void	ComponentRule.inferInteractionsFromPE(InteractionSetL3 interactionSet, PhysicalEntity pe, Model model) Infer interactions where A = the given PhysicalEntity.

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

Constructor and Description
InteractionSetL3(Model model) Constructor with the 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.

Uses of Model in org.biopax.paxtools.pattern

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

Modifier and Type	Method and Description
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.
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.
static List<Match>	Searcher.searchPlain(Model model, Pattern pattern) Searches the pattern in a given model, but instead of a match map, returns all matches in a list.

Uses of Model in org.biopax.paxtools.pattern.example

Methods in org.biopax.paxtools.pattern.example with parameters of type Model

Modifier and Type	Method and Description
void	DeltaFeatureExtractor.mineAndCollect(Model model)

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

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

Modifier and Type	Method and Description
Blacklist	BlacklistGenerator.generateBlacklist(Model model) Generates the blacklist.
Set<SIFInteraction>	SIFSearcher.searchSIF(Model model) Searches the given model with the contained miners.
boolean	SIFSearcher.searchSIF(Model model, OutputStream out) Searches the given model with the contained miners.
boolean	SIFSearcher.searchSIF(Model model, OutputStream out, boolean withMediators) Searches the given model with the contained miners.
boolean	SIFSearcher.searchSIF(Model model, OutputStream out, SIFToText stt) Searches the given model with the contained miners.
AdjacencyMatrix	SIFSearcher.searchSIFGetMatrix(Model model) Searches the given model with the contained miners.

Uses of Model in org.biopax.paxtools.pattern.util

Constructors in org.biopax.paxtools.pattern.util with parameters of type Model

Constructor and Description
ChemicalNameNormalizer(Model model) Constructor that also infers all the mapping.

Uses of Model in org.biopax.paxtools.query

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

Modifier and Type	Method and Description
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.

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

Fields in org.biopax.paxtools.query.wrapperL3 declared as Model

Modifier and Type	Field and Description
protected Model	GraphL3.model The model to be wrapped.

Methods in org.biopax.paxtools.query.wrapperL3 that return Model

Modifier and Type	Method and Description
Model	GraphL3.getModel()

Constructors in org.biopax.paxtools.query.wrapperL3 with parameters of type Model

Constructor and Description
GraphL3(Model model, Filter... filters) Constructor with the model and the IDs of the ubiquitous molecules.

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

Fields in org.biopax.paxtools.query.wrapperL3undirected declared as Model

Modifier and Type	Field and Description
protected Model	GraphL3Undirected.model The model to be wrapped.

Methods in org.biopax.paxtools.query.wrapperL3undirected that return Model

Modifier and Type	Method and Description
Model	GraphL3Undirected.getModel()

Constructors in org.biopax.paxtools.query.wrapperL3undirected with parameters of type Model

Constructor and Description
GraphL3Undirected(Model model, Filter... filters) Constructor with the model and the IDs of the ubiquitous molecules.

Uses of Model in org.biopax.paxtools.search

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

Constructor and Description
SearchEngine(Model model, String indexLocation) Main Constructor.