Package | Description |
---|---|
org.biopax.paxtools.pattern.constraint |
Package for constraints.
|
org.biopax.paxtools.pattern.util |
Package for several utility classes.
|
Modifier and Type | Method and Description |
---|---|
protected Set<PhysicalEntity> |
ConstraintAdapter.getConvParticipants(Conversion conv,
RelType type)
Gets input ot output participants of the Conversion.
|
static Constraint |
ConBox.simplePEToConv(RelType type)
From simple PhysicalEntity to related Conversion.
|
Constructor and Description |
---|
ConversionSide(ConversionSide.Type type,
Blacklist blacklist,
RelType relType)
Constructor.
|
Participant(RelType type)
Constructor with parameters.
|
Participant(RelType type,
Blacklist blacklist)
Constructor with parameters.
|
Participant(RelType type,
Blacklist blacklist,
boolean considerControl)
Constructor with parameters.
|
Participant(RelType type,
Blacklist blacklist,
boolean considerControl,
boolean considerPathway)
Constructor with parameters.
|
Participant(RelType type,
boolean considerControl)
Constructor with parameters.
|
Participant(RelType type,
boolean considerControl,
boolean considerPathway)
Constructor with parameters.
|
ParticipatesInConv(RelType type)
Constructor with parameters.
|
ParticipatesInConv(RelType type,
Blacklist blacklist)
Constructor with parameters.
|
ParticipatingPE(RelType type)
Deprecated.
Constructor with parameters.
|
ParticipatingPE(RelType type,
Blacklist blacklist)
Deprecated.
Constructor with parameters.
|
RelatedControl(RelType peType)
Constructor with the relation type between PhysicalEntity and Conversion.
|
RelatedControl(RelType peType,
Blacklist blacklist)
Constructor with the relation type between PhysicalEntity and Conversion, and the blacklist.
|
Modifier and Type | Method and Description |
---|---|
RelType |
Blacklist.getContext(String id)
Gets the context of the ubiquity of the ID.
|
static RelType |
RelType.valueOf(String name)
Returns the enum constant of this type with the specified name.
|
static RelType[] |
RelType.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
void |
Blacklist.addEntry(String id,
int score,
RelType context)
Adds a new blacklisted ID.
|
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.
|
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.
|
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