Package | Description |
---|---|
org.biopax.paxtools.controller |
This package contains various methods and algorithms for traversing and manipulating the model.
|
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.
|
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 | Class and Description |
---|---|
class |
BindingFeatureImpl |
class |
CovalentBindingFeatureImpl |
class |
EntityFeatureImpl |
class |
FragmentFeatureImpl |
class |
ModificationFeatureImpl |
Modifier and Type | Method and Description |
---|---|
Set<EntityFeature> |
EntityReferenceImpl.getEntityFeature()
The contents of this set should NOT be modified.
|
Set<EntityFeature> |
ExperimentalFormImpl.getExperimentalFeature() |
Set<EntityFeature> |
PhysicalEntityImpl.getFeature() |
Set<EntityFeature> |
EntityFeatureImpl.getMemberFeature() |
Set<EntityFeature> |
EntityFeatureImpl.getMemberFeatureOf() |
Class<? extends EntityFeature> |
EntityFeatureImpl.getModelInterface() |
Set<EntityFeature> |
PhysicalEntityImpl.getNotFeature() |
Modifier and Type | Method and Description |
---|---|
void |
EntityReferenceImpl.addEntityFeature(EntityFeature entityFeature) |
void |
ExperimentalFormImpl.addExperimentalFeature(EntityFeature experimentalFeature) |
void |
SmallMoleculeImpl.addFeature(EntityFeature feature) |
void |
PhysicalEntityImpl.addFeature(EntityFeature feature) |
void |
EntityFeatureImpl.addMemberFeature(EntityFeature feature) |
void |
SmallMoleculeImpl.addNotFeature(EntityFeature feature) |
void |
PhysicalEntityImpl.addNotFeature(EntityFeature feature) |
boolean |
EntityFeatureImpl.atEquivalentLocation(EntityFeature that) |
void |
EntityReferenceImpl.removeEntityFeature(EntityFeature entityFeature) |
void |
ExperimentalFormImpl.removeExperimentalFeature(EntityFeature experimentalFeature) |
void |
PhysicalEntityImpl.removeFeature(EntityFeature feature) |
void |
EntityFeatureImpl.removeMemberFeature(EntityFeature feature) |
void |
PhysicalEntityImpl.removeNotFeature(EntityFeature feature) |
Modifier and Type | Method and Description |
---|---|
protected void |
EntityReferenceImpl.setEntityFeature(Set<EntityFeature> entityFeature) |
void |
ExperimentalFormImpl.setExperimentalFeature(Set<EntityFeature> experimentalFeature) |
protected void |
PhysicalEntityImpl.setFeature(Set<EntityFeature> feature) |
protected void |
EntityFeatureImpl.setMemberFeature(Set<EntityFeature> memberFeature) |
protected void |
EntityFeatureImpl.setMemberFeatureOf(Set<EntityFeature> memberFeatureOf) |
protected void |
PhysicalEntityImpl.setNotFeature(Set<EntityFeature> featureSet) |
Modifier and Type | Method and Description |
---|---|
org.sbgn.bindings.Glyph.State |
FeatureDecorator.createStateVar(EntityFeature ef,
org.sbgn.bindings.ObjectFactory factory)
Creates the State for the given EntityFeature.
|
org.sbgn.bindings.Glyph.State |
CommonFeatureStringGenerator.createStateVar(EntityFeature ef,
org.sbgn.bindings.ObjectFactory factory)
Creates State to represent the entity feature.
|
Modifier and Type | Field and Description |
---|---|
static EntityFeature |
ChangeType.EXISTENCE
Special static entity feature used for representing changes that effect existence of protein -i.e.
|
Modifier and Type | Method and Description |
---|---|
Map<EntityFeature,ChangeType> |
PEStateChange.getDeltaFeatures() |
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.
|
Modifier and Type | Interface and Description |
---|---|
interface |
BindingFeature |
interface |
CovalentBindingFeature
Definition: An entity feature that represent the covalently bound state of a physical entity.
|
interface |
FragmentFeature
Definition: An entity feature that represents the resulting physical entity subsequent to a cleavage or
degradation event.
|
interface |
ModificationFeature
Definition: A covalently modified feature on a sequence, relevant to an interaction,
such as a post-translational modification.
|
Modifier and Type | Method and Description |
---|---|
Set<EntityFeature> |
EntityReference.getEntityFeature()
Variable features that are observed for the entities of this entityReference - such as known PTM
or methylation sites and non-covalent bonds.
|
Set<EntityFeature> |
ExperimentalForm.getExperimentalFeature()
Contents of this set should not be modified.
|
Set<EntityFeature> |
PhysicalEntity.getFeature() |
Set<EntityFeature> |
EntityFeature.getMemberFeature()
An entity feature that belongs to this homology grouping.
|
Set<EntityFeature> |
EntityFeature.getMemberFeatureOf()
Reverse of
getMemberFeature() |
Set<EntityFeature> |
PhysicalEntity.getNotFeature() |
Modifier and Type | Method and Description |
---|---|
void |
EntityReference.addEntityFeature(EntityFeature feature)
Variable features that are observed for the entities of this entityReference - such as known PTM
or methylation sites and non-covalent bonds.
|
void |
ExperimentalForm.addExperimentalFeature(EntityFeature experimentalFeature)
This method adds an experimental feature
|
void |
PhysicalEntity.addFeature(EntityFeature feature) |
void |
EntityFeature.addMemberFeature(EntityFeature entityFeature)
An entity feature that belongs to this homology grouping.
|
void |
PhysicalEntity.addNotFeature(EntityFeature feature) |
boolean |
EntityFeature.atEquivalentLocation(EntityFeature that) |
void |
EntityReference.removeEntityFeature(EntityFeature feature)
Variable features that are observed for the entities of this entityReference - such as known PTM
or methylation sites and non-covalent bonds.
|
void |
ExperimentalForm.removeExperimentalFeature(EntityFeature experimentalFeature)
This method removes an experimental feature
|
void |
PhysicalEntity.removeFeature(EntityFeature feature) |
void |
EntityFeature.removeMemberFeature(EntityFeature entityFeature)
An entity feature that belongs to this homology grouping.
|
void |
PhysicalEntity.removeNotFeature(EntityFeature feature) |
Copyright © 2015 BioPAX. All rights reserved.