Package | Description |
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org.biopax.paxtools.pattern |
Main package.
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org.biopax.paxtools.pattern.constraint |
Package for constraints.
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Modifier and Type | Class and Description |
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class |
MappedConst
This is a mapping from a constraint to the elements in a match.
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Modifier and Type | Method and Description |
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Constraint |
MappedConst.getConstr()
Getter for the constraint.
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Modifier and Type | Method and Description |
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void |
Pattern.add(Constraint constr,
String... label)
Creates a mapped constraint with the given generative constraint and the indexes it applies.
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void |
Pattern.insertPointConstraint(Constraint con,
int... ind)
A point constraint deals with only one element in a match, checks its validity.
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Constructor and Description |
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MappedConst(Constraint constr,
int... inds)
Constructor with the constraint and the index mapping.
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Pattern(Class<? extends BioPAXElement> startingClass,
Constraint firstConstraint,
String... label)
Constructor with the first constraint and labels it uses.
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Modifier and Type | Class and Description |
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class |
ActivityConstraint
Checks if the PhysicalEntity controls anything.
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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.
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class |
AND
Used for getting logical AND of a set of constraints.
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class |
ConstraintAdapter
This is a base class for a Constraint.
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class |
ConstraintChain
Used for using several constraints as a chain.
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class |
ControlsNotParticipant
Checks if a controller of this Control is also a participant of the controlled interactions.
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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.
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class |
Empty
Checks if the parameter constraint cannot generate any candidate.
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class |
Equality
Checks identity of two elements.
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class |
Field
Checks if an element has or has not a specific value for a field, or the field value of another
element.
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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.
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class |
HasAnID
Checks if the element has a valid ID.
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class |
IDConstraint
Checks if the element has the desired ID.
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class |
InterToPartER
This constraint is used to collect related EntityReference of the participant physical entities.
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class |
LinkedPE
Many times we want to link PhysicalEntities (PE) while traversing a relation.
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class |
ModificationChangeConstraint
This class checks if there exists a desired type of modification change among two PhysicalEntity.
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class |
MultiPathConstraint
Logical OR of several PathConstraints.
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class |
NonUbique
This is a non-generative constraint that checks if the small molecule is ubiquitous in any
context.
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class |
NOT
Negation of a constraint.
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class |
OR
Logical OR of several constraints.
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class |
OtherSide
Deprecated.
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class |
Participant
Gets input or output participants of a Conversion.
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class |
ParticipatesInConv
Gets the related Conversion where the PhysicalEntity is input or output, whichever is desired.
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class |
ParticipatingPE
Deprecated.
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class |
PathConstraint
PathConstraint encapsulates PathAccessor of Paxtools.
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class |
PEChainsIntersect
This constraint checks if two chains of linked physical entities are intersecting or not.
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class |
RelatedControl
After traversing a PhysicalEntity and the Conversion it participates, this constraint takes us to
the Control.
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class |
SelfOrThis
When a constraint excludes the origin element, but it is needed to be among them, use this
constraint.
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class |
Size
Checks the size of the generated elements of the wrapped constraint.
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class |
Type
Checks if a variable is a specific type or its subclass.
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class |
XOR
Used for getting logical XOR of a set of constraints.
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Modifier and Type | Method and Description |
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static Constraint |
ConBox.complexes()
From PhysicalEntity to its parent Complex recursively.
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static Constraint |
ConBox.complexMembers()
From Complex to its members recursively (also getting member of the inner complexes).
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static Constraint |
ConBox.compToER()
From Complex or SimplePhysicalEntity to the related EntityReference.
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static Constraint |
ConBox.controlled()
From Control to the controlled Process
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static Constraint |
ConBox.controllerPE()
From Control to the controller PhysicalEntity
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static Constraint |
ConBox.controlsConv()
From PhysicalEntity to the controlled Conversion, skipping the middle Control.
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static Constraint |
ConBox.controlsInteraction()
From PhysicalEntity to the controlled Interaction, skipping the middle Control.
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static Constraint |
ConBox.controlToConv()
From Control to the controlled Conversion, traversing downstream Controls recursively.
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static Constraint |
ConBox.controlToInter()
From Control to the controlled Interaction, traversing downstream Controls recursively.
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static Constraint |
ConBox.controlToTempReac()
From Control to the controlled TemplateReaction, traversing downstream Controls recursively.
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static Constraint |
ConBox.convToControl()
From Conversion to the upstream Control (and its upstream Control recursively).
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static Constraint |
ConBox.convToController()
From Conversion to the controller of the upstream Control (and its upstream Control
recursively).
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static Constraint |
ConBox.differentialActivity(boolean activating)
Gets a constraint to ensure that ensures only one of the two PhysicalEntities has an
activity.
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static Constraint |
ConBox.equal(boolean equal)
Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex
direction.
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static Constraint |
ConBox.erToPE()
From EntityReference to the member PhysicalEntity
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static Constraint |
ConBox.genericEquiv()
From PhysicalEntity to its generic equivalents, i.e.
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static Constraint |
ConBox.hasDifferentCompartments()
Checks if two physical entities have non-empty and different compartments.
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static Constraint |
ConBox.hasXref(String xrefID)
Makes sure that the object has an Xref with the given ID.
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static Constraint |
ConBox.inSamePathway()
Makes sure that the two interactions are members of the same pathway.
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static Constraint |
ConBox.interToControl()
From Interaction to the upstream Control (and its upstream Control recursively).
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static Constraint |
ConBox.interToController()
From Interaction to the controlling Controls recursively, and their controller PEs.
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static Constraint |
ConBox.interToPE()
From Interaction to the related PhysicalEntity.
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static Constraint |
ConBox.isBait()
Checks if the molecule is a bait of a Y2H experiment.
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static Constraint |
ConBox.isHuman()
Makes sure the EntityReference or the PhysicalEntity belongs to human.
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static Constraint |
ConBox.isPrey()
Checks if the molecule is a prey of a Y2H experiment.
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static Constraint |
ConBox.left()
From Conversion to its left participants.
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static Constraint |
ConBox.linkedER(boolean up) |
static Constraint |
ConBox.linkToComplex()
Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex
direction.
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static Constraint |
ConBox.linkToComplex(Blacklist blacklist)
Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards complex
direction.
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static Constraint |
ConBox.linkToSimple(Blacklist blacklist)
Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member
direction.
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static Constraint |
ConBox.linkToSpecific()
Makes a linker constraint from PhysicalEntity to its linked PhysicalEntity towards member
direction.
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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.
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static Constraint |
ConBox.modificationConstraint(String modifTerm)
Makes sure that the PhysicalEntity or any linked PE contains the modification term.
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static Constraint |
ConBox.moreControllerThanParticipant()
Makes sure that the PhysicalEntity is controlling more reactions than it participates
(excluding complex assembly).
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static Constraint |
ConBox.nameEquals(String... name)
Filters Named to contain a name from the input set.
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static Constraint |
ConBox.nameEquals(String name)
Filters Named to contain a specific name.
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static Constraint |
ConBox.nextInteraction()
Starts from an Interaction and gets next Interactions in temporal order, if ever defined in
a Pathway.
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static Constraint |
ConBox.notAParticipant()
Makes sure that the second element (PhysicalEntity) is not a participant of the first element
(Interaction).
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static Constraint |
ConBox.notControlled()
Makes sure the Interaction has no Control
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static Constraint |
ConBox.notControlsThis()
Makes sure the second element (Control) is not a controller to the first element
(Interaction).
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static Constraint |
ConBox.notGeneric()
Makes sure that the PhysicalEntity do not have member physical entities..
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static Constraint |
ConBox.notLabeledInactive()
Makes sure a PhysicalEntity of any linked member PhysicalEntities toward members are not
labeled as inactive.
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static Constraint |
ConBox.participant()
From Interaction to its PhysicalEntity participants.
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static Constraint |
ConBox.participantER()
From Interaction to the related EntityReference of its participants.
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static Constraint |
ConBox.participatesInConv()
From PhysicalEntity to the Conversion that it participates.
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static Constraint |
ConBox.participatesInInter()
From PhysicalEntity to the Interaction that it participates.
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static Constraint |
ConBox.peNotRelatedToER()
Makes sure that the given physical entity is not related to the entity reference.
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static Constraint |
ConBox.peToControl()
From PhysicalEntity to the downstream Control
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static Constraint |
ConBox.peToControlledConv()
From PhysicalEntity to the downstream Conversion.
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static Constraint |
ConBox.peToControlledInter()
From PhysicalEntity to the downstream Interaction.
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static Constraint |
ConBox.peToER()
From SimplePhysicalEntity to its EntityReference.
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static Constraint |
ConBox.peToInter()
From PhysicalEntity to the related Interaction.
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static Constraint |
ConBox.product()
From TemplateReaction to its products.
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static Constraint |
ConBox.right()
From Conversion to its right participants.
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static Constraint |
ConBox.simpleMembers()
From complex to its simple members (members which are of type SimplePhysicalEntity)
recursively.
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static Constraint |
ConBox.simplePEToConv(RelType type)
From simple PhysicalEntity to related Conversion.
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static Constraint |
ConBox.source(String dbname) |
static Constraint |
ConBox.type(Class<? extends BioPAXElement> clazz)
Creates an element type constraint.
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static Constraint |
ConBox.withComplexes()
From PhysicalEntity to parent Complex recursively, or to itself.
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static Constraint |
ConBox.withComplexMembers()
From Complex to its members, or the complex itself.
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static Constraint |
ConBox.withSimpleMembers()
From complex to its simple members recursively, or the Complex itself
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Constructor and Description |
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ConstraintChain(Constraint... con)
Constructor with the chained constraints.
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Empty(Constraint con)
Constructor with the generative Constraint.
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NOT(Constraint con)
Constructor with the wrapped constraint.
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SelfOrThis(Constraint con)
Constructor with the wrapped constraint.
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SelfOrThis(Constraint con,
int selfIndex)
Constructor with the wrapped constraint and index of self.
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Size(Constraint con,
int size,
Size.Type type)
Constructor with parameters.
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Copyright © 2015 BioPAX. All rights reserved.