Package | Description |
---|---|
org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
org.biopax.paxtools.examples |
This package contains several examples that uses Paxtools to demonstrate basic functionality.
|
org.biopax.paxtools.impl.level3 |
This package contains the default implementation for BioPAX Level 3.
|
org.biopax.paxtools.io.sbgn |
This package contains a BioPAX to SBGN-PD converter and associated classes.
|
org.biopax.paxtools.io.sif.level3 |
This package contains the SIF rules for BioPAX Level 3.
|
org.biopax.paxtools.model.level3 |
This package contains the interfaces that maps classes defined in the BioPAX Level 3 specification.
|
org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
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!
|
Modifier and Type | Method and Description |
---|---|
static Set<EntityFeature> |
ModelUtils.findFeaturesAddedToSecond(PhysicalEntity first,
PhysicalEntity second,
boolean fix) |
static Set<EntityFeature> |
ModelUtils.getFeatureIntersection(PhysicalEntity first,
org.biopax.paxtools.controller.ModelUtils.FeatureType firstClass,
PhysicalEntity second,
org.biopax.paxtools.controller.ModelUtils.FeatureType secondClass) |
static Set<EntityFeature> |
ModelUtils.getFeatureSetByType(PhysicalEntity pe,
org.biopax.paxtools.controller.ModelUtils.FeatureType type) |
Modifier and Type | Method and Description |
---|---|
void |
Tutorial.graphQuery(Model model,
PhysicalEntity entity3,
PhysicalEntity entity2,
PhysicalEntity entity1) |
Modifier and Type | Class and Description |
---|---|
class |
ComplexImpl |
class |
DnaImpl |
class |
DnaRegionImpl |
class |
NucleicAcidImpl |
class |
PhysicalEntityImpl |
class |
ProteinImpl |
class |
RnaImpl |
class |
RnaRegionImpl |
class |
SimplePhysicalEntityImpl |
class |
SmallMoleculeImpl |
Modifier and Type | Method and Description |
---|---|
PhysicalEntity |
StoichiometryImpl.getPhysicalEntity() |
Modifier and Type | Method and Description |
---|---|
Set<PhysicalEntity> |
CatalysisImpl.getCofactor() |
Set<PhysicalEntity> |
ComplexImpl.getComponent() |
Set<PhysicalEntity> |
EntityFeatureImpl.getFeatureOf() |
Set<PhysicalEntity> |
ConversionImpl.getLeft() |
Set<PhysicalEntity> |
PhysicalEntityImpl.getMemberPhysicalEntity() |
Set<PhysicalEntity> |
PhysicalEntityImpl.getMemberPhysicalEntityOf() |
Class<? extends PhysicalEntity> |
SmallMoleculeImpl.getModelInterface() |
Class<? extends PhysicalEntity> |
PhysicalEntityImpl.getModelInterface() |
Set<PhysicalEntity> |
EntityFeatureImpl.getNotFeatureOf() |
protected Set<PhysicalEntity> |
ControlImpl.getPeController() |
Class<? extends PhysicalEntity> |
ComplexImpl.getPhysicalEntityClass() |
Set<PhysicalEntity> |
TemplateReactionImpl.getProduct() |
Set<PhysicalEntity> |
ConversionImpl.getRight() |
Modifier and Type | Method and Description |
---|---|
void |
CatalysisImpl.addCofactor(PhysicalEntity cofactor) |
void |
ComplexImpl.addComponent(PhysicalEntity component) |
void |
ConversionImpl.addLeft(PhysicalEntity left) |
void |
PhysicalEntityImpl.addMemberPhysicalEntity(PhysicalEntity newMember) |
void |
TemplateReactionImpl.addProduct(PhysicalEntity product) |
void |
ConversionImpl.addRight(PhysicalEntity right) |
protected void |
ComplexImpl.collectSimpleMembersRecursive(PhysicalEntity pe,
Set<SimplePhysicalEntity> set) |
boolean |
PhysicalEntityImpl.hasEquivalentCellularLocation(PhysicalEntity that) |
boolean |
PhysicalEntityImpl.hasEquivalentFeatures(PhysicalEntity that) |
void |
CatalysisImpl.removeCofactor(PhysicalEntity cofactor) |
void |
ComplexImpl.removeComponent(PhysicalEntity component) |
void |
ConversionImpl.removeLeft(PhysicalEntity left) |
void |
PhysicalEntityImpl.removeMemberPhysicalEntity(PhysicalEntity oldMember) |
void |
TemplateReactionImpl.removeProduct(PhysicalEntity product) |
void |
ConversionImpl.removeRight(PhysicalEntity right) |
void |
StoichiometryImpl.setPhysicalEntity(PhysicalEntity PhysicalEntity) |
Modifier and Type | Method and Description |
---|---|
protected void |
CatalysisImpl.setCofactor(Set<PhysicalEntity> cofactor) |
protected void |
ComplexImpl.setComponent(Set<PhysicalEntity> component) |
protected void |
EntityFeatureImpl.setFeatureOf(Set<PhysicalEntity> featureOf) |
protected void |
ConversionImpl.setLeft(Set<PhysicalEntity> left) |
protected void |
PhysicalEntityImpl.setMemberPhysicalEntity(Set<PhysicalEntity> memberPhysicalEntity) |
protected void |
PhysicalEntityImpl.setMemberPhysicalEntityOf(Set<PhysicalEntity> memberPhysicalEntityOf) |
protected void |
EntityFeatureImpl.setNotFeatureOf(Set<PhysicalEntity> notFeatureOf) |
protected void |
ControlImpl.setPeController(Set<PhysicalEntity> peController) |
protected void |
TemplateReactionImpl.setProduct(Set<PhysicalEntity> product) |
protected void |
ConversionImpl.setRight(Set<PhysicalEntity> right) |
Modifier and Type | Method and Description |
---|---|
boolean |
UbiqueDetector.isUbique(PhysicalEntity pe)
Checks if the PhysicalEntity is a ubiquitous molecule.
|
boolean |
ListUbiqueDetector.isUbique(PhysicalEntity pe)
Checks if the ID of the PhysicalEntity is in the set.
|
Modifier and Type | Method and Description |
---|---|
PhysicalEntity |
PEStateChange.getLeftRoot() |
PhysicalEntity |
PEStateChange.getRightRoot() |
Modifier and Type | Method and Description |
---|---|
static Map<EntityFeature,ChangeType> |
ChangeType.getDeltaFeatures(PhysicalEntity left,
PhysicalEntity right,
PhysicalEntity leftRoot,
PhysicalEntity rightRoot)
This method returns the features that are "changed" between the left and right physical entities.
|
static void |
Simplify.getSimpleMembers(PhysicalEntity root,
Set<SimplePhysicalEntity> value) |
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.
|
Modifier and Type | Method and Description |
---|---|
protected Set<BioPAXElement> |
InteractionRuleL3Adaptor.collectEntities(Set<PhysicalEntity> pes,
InteractionSetL3 set) |
Constructor and Description |
---|
PEStateChange(SimplePhysicalEntity left,
SimplePhysicalEntity right,
PhysicalEntity leftRoot,
PhysicalEntity rightRoot,
BioPAXElement element,
Conversion conv) |
Modifier and Type | Interface and Description |
---|---|
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 |
Dna
Definition: A physical entity consisting of a sequence of deoxyribonucleotide monophosphates; a deoxyribonucleic
acid.
|
interface |
DnaRegion
Definition: A region on a DNA molecule.
|
interface |
NucleicAcid
Tagger interface for DNA and RNA
|
interface |
Protein |
interface |
Rna |
interface |
RnaRegion
Definition: A region on a RNA molecule.
|
interface |
SequenceEntity
Tagger interface for macromolecules that are related to a genetic sequence: DNA, RNA, Protein.
|
interface |
SimplePhysicalEntity
Tagger interface for non-complex physical entities
|
interface |
SmallMolecule |
Modifier and Type | Method and Description |
---|---|
PhysicalEntity |
Stoichiometry.getPhysicalEntity() |
Modifier and Type | Method and Description |
---|---|
Set<PhysicalEntity> |
Catalysis.getCofactor()
Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
|
Set<PhysicalEntity> |
Complex.getComponent()
Defines the PhysicalEntity subunits of this complex.
|
Set<PhysicalEntity> |
EntityFeature.getFeatureOf()
Inverse of
getFeature()
Contents of this set is generated automatically and should not be modified. |
Set<PhysicalEntity> |
Conversion.getLeft()
The participants on the left side of the conversion interaction.
|
Set<PhysicalEntity> |
PhysicalEntity.getMemberPhysicalEntity()
Please avoid using this property in your BioPAX L3 models
unless absolutely sure/required, for there is an alternative way
(using PhysicalEntity/entityReference/memberEntityReference), and
this will probably be deprecated in the future BioPAX releases.
|
Set<PhysicalEntity> |
PhysicalEntity.getMemberPhysicalEntityOf() |
Class<? extends PhysicalEntity> |
PhysicalEntity.getModelInterface()
Overridden to provide better downcasting
|
Set<PhysicalEntity> |
EntityFeature.getNotFeatureOf()
Inverse of
getNotFeature()
Contents of this set is generated automatically and should not be modified. |
Set<PhysicalEntity> |
TemplateReaction.getProduct() |
Set<PhysicalEntity> |
Conversion.getRight()
The participants on the right side of the conversion interaction.
|
Modifier and Type | Method and Description |
---|---|
void |
Catalysis.addCofactor(PhysicalEntity cofactor)
Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
|
void |
Complex.addComponent(PhysicalEntity component)
Defines the PhysicalEntity subunits of this complex.
|
void |
Conversion.addLeft(PhysicalEntity left)
Adds a participant to the left side of the conversion interaction.
|
void |
PhysicalEntity.addMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity) |
void |
TemplateReaction.addProduct(PhysicalEntity product) |
void |
Conversion.addRight(PhysicalEntity right)
Adds a participant to the right side of the conversion interaction.
|
boolean |
PhysicalEntity.hasEquivalentCellularLocation(PhysicalEntity that) |
boolean |
PhysicalEntity.hasEquivalentFeatures(PhysicalEntity that) |
void |
Catalysis.removeCofactor(PhysicalEntity cofactor)
Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
|
void |
Complex.removeComponent(PhysicalEntity component)
Defines the PhysicalEntity subunits of this complex.
|
void |
Conversion.removeLeft(PhysicalEntity left)
Removes a participant from the left side of the conversion interaction.
|
void |
PhysicalEntity.removeMemberPhysicalEntity(PhysicalEntity memberPhysicalEntity) |
void |
TemplateReaction.removeProduct(PhysicalEntity product) |
void |
Conversion.removeRight(PhysicalEntity right)
Removes a participant from the right side of the conversion interaction.
|
void |
Stoichiometry.setPhysicalEntity(PhysicalEntity physicalEntity) |
Modifier and Type | Method and Description |
---|---|
protected Set<PhysicalEntity> |
ConstraintAdapter.getConvParticipants(Conversion conv,
RelType type)
Gets input ot output participants of the Conversion.
|
Modifier and Type | Method and Description |
---|---|
Set<BioPAXElement> |
LinkedPE.getLinkedElements(PhysicalEntity pe) |
Modifier and Type | Field and Description |
---|---|
PhysicalEntity[] |
PhysicalEntityChain.pes
Array that links two ends of the chain.
|
Modifier and Type | Method and Description |
---|---|
protected PhysicalEntity[] |
PhysicalEntityChain.fillArray(PhysicalEntity parent,
PhysicalEntity target,
int depth,
int dir)
Creates the chain that links the given endpoints.
|
Modifier and Type | Method and Description |
---|---|
Set<PhysicalEntity> |
Blacklist.getNonUbiques(Set<PhysicalEntity> entities,
RelType ctx)
Gets the non-ubiquitous physical entities in the given set and in the given context.
|
Modifier and Type | Method and Description |
---|---|
static Set<String> |
DifferentialModificationUtil.collectChangedPhosphorylationSites(PhysicalEntity before,
PhysicalEntity after,
boolean gained) |
protected PhysicalEntity[] |
PhysicalEntityChain.fillArray(PhysicalEntity parent,
PhysicalEntity target,
int depth,
int dir)
Creates the chain that links the given endpoints.
|
static Set<ModificationFeature>[] |
DifferentialModificationUtil.getChangedModifications(PhysicalEntity before,
PhysicalEntity after)
Gets the differential features.
|
boolean |
Blacklist.isUbique(PhysicalEntity pe)
Checks if the given entity is blacklisted in at least one context.
|
boolean |
Blacklist.isUbique(PhysicalEntity pe,
Conversion conv,
ConversionDirectionType dir,
RelType context)
Checks if the given entity is blacklisted for the given Conversion assuming the Conversion
flows towards the given direction, and the entity is in given context.
|
boolean |
Blacklist.isUbiqueInBothContexts(PhysicalEntity pe)
Checks if the given entity is blacklisted in both context together.
|
Modifier and Type | Method and Description |
---|---|
Set<PhysicalEntity> |
Blacklist.getNonUbiques(Set<PhysicalEntity> entities,
RelType ctx)
Gets the non-ubiquitous physical entities in the given set and in the given context.
|
Collection<SmallMolecule> |
Blacklist.getUbiques(Set<PhysicalEntity> entities,
RelType context)
Gets the ubiquitous small molecules among the given set and in the given context.
|
Constructor and Description |
---|
PhysicalEntityChain(PhysicalEntity small,
PhysicalEntity big)
Constructor with endpoints.
|
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.
|
static Map<BioPAXElement,Set<PhysicalEntity>> |
QueryExecuter.getRelatedPhysicalEntityMap(Collection<BioPAXElement> elements)
Maps each BioPAXElement to its related PhysicalEntity objects.
|
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.
|
Modifier and Type | Field and Description |
---|---|
protected PhysicalEntity |
PhysicalEntityWrapper.pe
Wrapped PhysicalEntity.
|
Modifier and Type | Method and Description |
---|---|
PhysicalEntity |
PhysicalEntityWrapper.getPhysicalEntity() |
Modifier and Type | Method and Description |
---|---|
protected void |
TemplateReactionWrapper.addToDownstream(PhysicalEntity pe,
Graph graph)
Binds the given PhysicalEntity to the downstream.
|
protected void |
EventWrapper.addToDownstream(PhysicalEntity pe,
Graph graph)
Bind the wrapper of the given PhysicalEntity to the downstream.
|
Constructor and Description |
---|
PhysicalEntityWrapper(PhysicalEntity pe,
GraphL3 graph)
Constructor with the wrapped PhysicalEntity and the owner graph.
|
Modifier and Type | Field and Description |
---|---|
protected PhysicalEntity |
PhysicalEntityWrapper.pe
Wrapped PhysicalEntity.
|
Modifier and Type | Method and Description |
---|---|
PhysicalEntity |
PhysicalEntityWrapper.getPhysicalEntity() |
Modifier and Type | Method and Description |
---|---|
protected void |
EventWrapper.addToDownstream(PhysicalEntity pe,
Graph graph)
Bind the wrapper of the given PhysicalEntity to the downstream.
|
Constructor and Description |
---|
PhysicalEntityWrapper(PhysicalEntity pe,
GraphL3Undirected graph)
Constructor with the wrapped PhysicalEntity and the owner graph.
|
Copyright © 2015 BioPAX. All rights reserved.