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.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 |
Main package.
|
org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
ModelUtils.checkERFeatureSet(EntityReference er,
boolean fix)
Finds and adds all (missing) entity features
to given entity reference from all its owner
simple physical entities ('feature' and 'notFeature'
properties).
|
Modifier and Type | Class and Description |
---|---|
class |
DnaReferenceImpl |
class |
DnaRegionReferenceImpl |
class |
EntityReferenceImpl |
class |
NucleicAcidReferenceImpl |
class |
NucleicAcidRegionReferenceImpl |
class |
ProteinReferenceImpl |
class |
RnaReferenceImpl |
class |
RnaRegionReferenceImpl |
class |
SequenceEntityReferenceImpl |
class |
SmallMoleculeReferenceImpl |
Modifier and Type | Method and Description |
---|---|
EntityReference |
EntityFeatureImpl.getEntityFeatureOf() |
EntityReference |
SimplePhysicalEntityImpl.getEntityReference() |
EntityReference |
SimplePhysicalEntityImpl.getEntityReferenceX() |
Modifier and Type | Method and Description |
---|---|
Set<EntityReference> |
SimplePhysicalEntityImpl.getGenericEntityReferences() |
Set<EntityReference> |
EntityReferenceImpl.getMemberEntityReference() |
Set<EntityReference> |
EntityReferenceImpl.getMemberEntityReferenceOf() |
Set<EntityReference> |
ComplexImpl.getMemberReferences() |
Class<? extends EntityReference> |
EntityReferenceImpl.getModelInterface() |
Modifier and Type | Method and Description |
---|---|
void |
EntityReferenceImpl.addMemberEntityReference(EntityReference memberEntity) |
void |
EntityReferenceImpl.removeMemberEntityReference(EntityReference memberEntity) |
void |
EntityFeatureImpl.setEntityFeatureOf(EntityReference entityReference) |
void |
SimplePhysicalEntityImpl.setEntityReference(EntityReference entityReference) |
void |
SimplePhysicalEntityImpl.setEntityReferenceX(EntityReference entityReference) |
Modifier and Type | Method and Description |
---|---|
protected void |
EntityReferenceImpl.setMemberEntity(Set<EntityReference> memberEntity) |
void |
EntityReferenceImpl.setMemberEntityReference(Set<EntityReference> memberEntity) |
protected void |
EntityReferenceImpl.setMemberEntityReferenceOf(Set<EntityReference> newOwnerEntityReferenceSet) |
Modifier and Type | Class and Description |
---|---|
class |
Group
This class represents a grouping of EntityReferences strictly used by SIF rules for handling generics and complexes.
|
Modifier and Type | Method and Description |
---|---|
Set<EntityReference> |
Group.getAllSimpleMembers() |
Modifier and Type | Method and Description |
---|---|
void |
Group.addMember(EntityReference member) |
Set<PEStateChange> |
ActivityNetworkAnalyzer.getAllStates(EntityReference er)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
Simplify.entityHasAChange(BioPAXElement element,
Conversion conv,
GroupMap map,
Set<PEStateChange> changeSet,
Map<Conversion,Set<EntityReference>> extendedControls) |
Modifier and Type | Interface and Description |
---|---|
interface |
DnaReference
A DNA reference is a grouping of several DNA entities that are common in
sequence and genomic position.
|
interface |
DnaRegionReference
Definition: A DNARegionReference is a grouping of several DNARegion entities that are common in sequence and
genomic position.
|
interface |
NucleicAcidReference
Role interface for NucleicAcidReferences, namely DNA and RNA.
|
interface |
NucleicAcidRegionReference |
interface |
ProteinReference
Description: A protein reference is a grouping of several protein entities that are encoded by the same
genetic sequence.
|
interface |
RnaReference |
interface |
RnaRegionReference
A RNA region reference
|
interface |
SequenceEntityReference
Tagger interface for protein, dna and rna entities
|
interface |
SmallMoleculeReference |
Modifier and Type | Method and Description |
---|---|
EntityReference |
EntityFeature.getEntityFeatureOf()
Inverse of
getEntityFeature() |
EntityReference |
SimplePhysicalEntity.getEntityReference()
Reference entity for this physical entity.
|
Modifier and Type | Method and Description |
---|---|
Set<EntityReference> |
SimplePhysicalEntity.getGenericEntityReferences()
This method returns:
The entity reference of this PhysicalEntity plus
If this PhysicalEntity has member PhysicalEntities their generic EntityReferences iteratively plus
If the EntityReference of this PhysicalEntity has member EntityReferences their members iteratively
|
Set<EntityReference> |
EntityReference.getMemberEntityReference() |
Set<EntityReference> |
EntityReference.getMemberEntityReferenceOf()
Reverse of
getMemberEntityReference() |
Set<EntityReference> |
Complex.getMemberReferences()
Gets the
EntityReference s of the member simple physical entities. |
Modifier and Type | Method and Description |
---|---|
void |
EntityReference.addMemberEntityReference(EntityReference entityReference)
Adds the given entityReference to the member list
|
void |
EntityReference.removeMemberEntityReference(EntityReference entityReference)
Removes the given entityReference from the member list
|
void |
SimplePhysicalEntity.setEntityReference(EntityReference entityReference)
Reference entity for this physical entity.
|
Modifier and Type | Method and Description |
---|---|
static Pattern |
PatternBox.actChange(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Pattern for the activity of an EntityReference is changed through a Conversion.
|
static Pattern |
PatternBox.actChange(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Pattern for the activity of an EntityReference is changed through a Conversion.
|
Modifier and Type | Method and Description |
---|---|
protected Map<EntityReference,Set<String>> |
ActivityModificationChangeConstraint.extractModifNames(Map mfMap)
Extracts the modification terms from the moficiation features.
|
Constructor and Description |
---|
ActivityModificationChangeConstraint(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Constructor with the desired change and maps to activating and inactivating features,
|
ActivityModificationChangeConstraint(boolean activating,
Map<EntityReference,Set<ModificationFeature>> activityFeat,
Map<EntityReference,Set<ModificationFeature>> inactivityFeat)
Constructor with the desired change and maps to activating and inactivating features,
|
Copyright © 2015 BioPAX. All rights reserved.