Package org.biopax.paxtools.pattern.constraint

package org.biopax.paxtools.pattern.constraint

Package for constraints. ConBox is a special class, not a constraint, but has static methods for creation of frequently used constraints.

Related Packages

Package	Description
org.biopax.paxtools.pattern	Main package.
org.biopax.paxtools.pattern.example
org.biopax.paxtools.pattern.miner	Package for pattern miner utility.
org.biopax.paxtools.pattern.util	Package for several utility classes.

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