Uses of Interface
org.biopax.paxtools.pattern.Constraint

Packages that use Constraint

Package	Description
org.biopax.paxtools.pattern	Main package.
org.biopax.paxtools.pattern.constraint	Package for constraints.

Uses of Constraint in org.biopax.paxtools.pattern

Classes in org.biopax.paxtools.pattern that implement Constraint

Modifier and Type	Class	Description
class	MappedConst	This is a mapping from a constraint to the elements in a match.

Methods in org.biopax.paxtools.pattern that return Constraint

Modifier and Type	Method	Description
Constraint	MappedConst.getConstr()	Getter for the constraint.

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

Modifier and Type	Method	Description
void	Pattern.add(Constraint constr, String... label)	Creates a mapped constraint with the given generative constraint and the indexes it applies.
void	Pattern.insertPointConstraint(Constraint con, int... ind)	A point constraint deals with only one element in a match, checks its validity.

Constructors in org.biopax.paxtools.pattern with parameters of type Constraint

Modifier	Constructor	Description
	MappedConst(Constraint constr, int... inds)	Constructor with the constraint and the index mapping.
	Pattern(Class<? extends BioPAXElement> startingClass, Constraint firstConstraint, String... label)	Constructor with the first constraint and labels it uses.

Uses of Constraint in org.biopax.paxtools.pattern.constraint

Classes in org.biopax.paxtools.pattern.constraint that implement Constraint

Modifier and Type	Class	Description
class	ActivityConstraint	Checks if the PhysicalEntity controls anything.
class	ActivityModificationChangeConstraint	This is a very specialized constraint that checks if two PhysicalEntity of the same EntityReference have differential features, such that we can predict an activity change based on gain or loss of these features.
class	AND	Used for getting logical AND of a set of constraints.
class	ConstraintAdapter	This is a base class for a Constraint.
class	ConstraintChain	Used for using several constraints as a chain.
class	ControlsNotParticipant	Checks if a controller of this Control is also a participant of the controlled interactions.
class	ControlToControllerER	This constraint is used to collect related EntityReference of the controllers of a Control.
class	ConversionSide	Given Conversion and its one of the participants (at the left or right), traverses to either the participants at the other side or the same side.
class	Empty	Checks if the parameter constraint cannot generate any candidate.
class	Equality	Checks identity of two elements.
class	Field	Checks if an element has or has not a specific value for a field, or the field value of another element.
class	FieldOfMultiple	Checks if generated elements has or has not a specific value for a field, or the field value of another set of generated elements.
class	HasAnID	Checks if the element has a valid ID.
class	IDConstraint	Checks if the element has the desired ID.
class	InterToPartER	This constraint is used to collect related EntityReference of the participant physical entities.
class	LinkedPE	Many times we want to link PhysicalEntities (PE) while traversing a relation.
class	ModificationChangeConstraint	This class checks if there exists a desired type of modification change among two PhysicalEntity.
class	MultiPathConstraint	Logical OR of several PathConstraints.
class	NonUbique	This is a non-generative constraint that checks if the small molecule is ubiquitous in any context.
class	NOT	Negation of a constraint.
class	OR	Logical OR of several constraints.
class	Participant	Gets input or output participants of a Conversion.
class	ParticipatesInConv	Gets the related Conversion where the PhysicalEntity is input or output, whichever is desired.
class	PathConstraint	PathConstraint encapsulates PathAccessor of Paxtools.
class	PEChainsIntersect	This constraint checks if two chains of linked physical entities are intersecting or not.
class	RelatedControl	After traversing a PhysicalEntity and the Conversion it participates, this constraint takes us to the Control.
class	SelfOrThis	When a constraint excludes the origin element, but it is needed to be among them, use this constraint.
class	Size	Checks the size of the generated elements of the wrapped constraint.
class	Type	Checks if a variable is a specific type or its subclass.
class	XOR	Used for getting logical XOR of a set of constraints.

Methods in org.biopax.paxtools.pattern.constraint that return Constraint

Modifier and Type	Method	Description
static Constraint	ConBox.complexes()	From PhysicalEntity to its parent Complex recursively.
static Constraint	ConBox.complexMembers()	From Complex to its members recursively (also getting member of the inner complexes).
static Constraint	ConBox.compToER()	From Complex or SimplePhysicalEntity to the related EntityReference.
static Constraint	ConBox.controlled()	From Control to the controlled Process
static Constraint	ConBox.controllerPE()	From Control to the controller PhysicalEntity
static Constraint	ConBox.controlsConv()	From PhysicalEntity to the controlled Conversion, skipping the middle Control.
static Constraint	ConBox.controlsInteraction()	From PhysicalEntity to the controlled Interaction, skipping the middle Control.
static Constraint	ConBox.controlToConv()	From Control to the controlled Conversion, traversing downstream Controls recursively.
static Constraint	ConBox.controlToInter()	From Control to the controlled Interaction, traversing downstream Controls recursively.
static Constraint	ConBox.controlToTempReac()	From Control to the controlled TemplateReaction, traversing downstream Controls recursively.
static Constraint	ConBox.convToControl()	From Conversion to the upstream Control (and its upstream Control recursively).
static Constraint	ConBox.convToController()	From Conversion to the controller of the upstream Control (and its upstream Control recursively).
static Constraint	ConBox.differentialActivity(boolean activating)	Gets a constraint to ensure that ensures only one of the two PhysicalEntities has an activity.
static Constraint	ConBox.equal(boolean equal)	Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
static Constraint	ConBox.erToPE()	From EntityReference to the member PhysicalEntity
static Constraint	ConBox.genericEquiv()	From PhysicalEntity to its generic equivalents, i.e.
static Constraint	ConBox.hasDifferentCompartments()	Checks if two physical entities have non-empty and different compartments.
static Constraint	ConBox.hasProvenance(String name)	Makes sure that the object is associated with a Provenance with the given name.
static Constraint	ConBox.hasXref(String xrefID)	Makes sure that the object has an Xref with the given ID.
static Constraint	ConBox.inSamePathway()	Makes sure that the two interactions are members of the same pathway.
static Constraint	ConBox.interToControl()	From Interaction to the upstream Control (and its upstream Control recursively).
static Constraint	ConBox.interToController()	From Interaction to the controlling Controls recursively, and their controller PEs.
static Constraint	ConBox.interToPE()	From Interaction to the related PhysicalEntity.
static Constraint	ConBox.isBait()	Checks if the molecule is a bait of a Y2H experiment.
static Constraint	ConBox.isHuman()	Makes sure the EntityReference or the PhysicalEntity belongs to human.
static Constraint	ConBox.isPrey()	Checks if the molecule is a prey of a Y2H experiment.
static Constraint	ConBox.left()	From Conversion to its left participants.
static Constraint	ConBox.linkedER(boolean up)
static Constraint	ConBox.linkToComplex()	Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
static Constraint	ConBox.linkToComplex(Blacklist blacklist)	Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex direction.
static Constraint	ConBox.linkToSimple(Blacklist blacklist)	Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
static Constraint	ConBox.linkToSpecific()	Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member direction.
static Constraint	ConBox.maxDegree(int limit)	Makes sure the participant degree (number of Conversions that this is a participant) of the PhysicalEntity is less than or equal to the parameter.
static Constraint	ConBox.modificationConstraint(String modifTerm)	Makes sure that the PhysicalEntity or any linked PE contains the modification term.
static Constraint	ConBox.moreControllerThanParticipant()	Makes sure that the PhysicalEntity is controlling more reactions than it participates (excluding complex assembly).
static Constraint	ConBox.nameEquals(String name)	Filters Named to contain a specific name.
static Constraint	ConBox.nameEquals(String... name)	Filters Named to contain a name from the input set.
static Constraint	ConBox.nextInteraction()	Starts from an Interaction and gets next Interactions in temporal order, if ever defined in a Pathway.
static Constraint	ConBox.notAParticipant()	Makes sure that the second element (PhysicalEntity) is not a participant of the first element (Interaction).
static Constraint	ConBox.notControlled()	Makes sure the Interaction has no Control
static Constraint	ConBox.notControlsThis()	Makes sure the second element (Control) is not a controller to the first element (Interaction).
static Constraint	ConBox.notGeneric()	Makes sure that the PhysicalEntity do not have member physical entities..
static Constraint	ConBox.notLabeledInactive()	Makes sure a PhysicalEntity of any linked member PhysicalEntities toward members are not labeled as inactive.
static Constraint	ConBox.participant()	From Interaction to its PhysicalEntity participants.
static Constraint	ConBox.participantER()	From Interaction to the related EntityReference of its participants.
static Constraint	ConBox.participatesInConv()	From PhysicalEntity to the Conversion that it participates.
static Constraint	ConBox.participatesInInter()	From PhysicalEntity to the Interaction that it participates.
static Constraint	ConBox.peNotRelatedToER()	Makes sure that the given physical entity is not related to the entity reference.
static Constraint	ConBox.peToControl()	From PhysicalEntity to the downstream Control
static Constraint	ConBox.peToControlledConv()	From PhysicalEntity to the downstream Conversion.
static Constraint	ConBox.peToControlledInter()	From PhysicalEntity to the downstream Interaction.
static Constraint	ConBox.peToER()	From SimplePhysicalEntity to its EntityReference.
static Constraint	ConBox.peToInter()	From PhysicalEntity to the related Interaction.
static Constraint	ConBox.product()	From TemplateReaction to its products.
static Constraint	ConBox.right()	From Conversion to its right participants.
static Constraint	ConBox.simpleMembers()	From complex to its simple members (members which are of type SimplePhysicalEntity) recursively.
static Constraint	ConBox.simplePEToConv(RelType type)	From simple PhysicalEntity to related Conversion.
static Constraint	ConBox.source(String dbname)
static Constraint	ConBox.type(Class<? extends BioPAXElement> clazz)	Creates an element type constraint.
static Constraint	ConBox.withComplexes()	From PhysicalEntity to parent Complex recursively, or to itself.
static Constraint	ConBox.withComplexMembers()	From Complex to its members, or the complex itself.
static Constraint	ConBox.withSimpleMembers()	From complex to its simple members recursively, or the Complex itself

Constructors in org.biopax.paxtools.pattern.constraint with parameters of type Constraint

Modifier	Constructor	Description
	ConstraintChain(Constraint... con)	Constructor with the chained constraints.
	Empty(Constraint con)	Constructor with the generative Constraint.
	NOT(Constraint con)	Constructor with the wrapped constraint.
	SelfOrThis(Constraint con)	Constructor with the wrapped constraint.
	SelfOrThis(Constraint con, int selfIndex)	Constructor with the wrapped constraint and index of self.
	Size(Constraint con, int size, Size.Type type)	Constructor with parameters.