DarpaActions

Value Members

1. final def !=(arg0: Any): Boolean

   

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2. final def ##(): Int

   

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3. final def ==(arg0: Any): Boolean

   

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4. final def asInstanceOf[T0]: T0

   

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5. def cleanupEvents(mentions: Seq[Mention], state: State): Seq[Mention]

   

   global action for EventEngine

6. def clone(): AnyRef

   

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7. val default: Action

   

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8. final def eq(arg0: AnyRef): Boolean

   

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9. def equals(arg0: Any): Boolean

   

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10. def finalize(): Unit

    

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    protected[java.lang]

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    @throws( classOf[java.lang.Throwable] )

11. final def getClass(): Class[_]

    

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12. def handleAutoEvent(mentions: Seq[Mention], state: State): Seq[Mention]

    

    1.

    1. Checks that the cause and theme of an "auto" event (ex. autophosphorylation) are the same
    2. Splits valid event into BioEventMention (sans cause) and a BioRelationMention for a Regulation where the original cause serves as the controller.
    NOTE: we cannot call splitSimpleEvent, as it requires that the controlled and controller do not overlap

13. def hashCode(): Int

    

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14. final def isInstanceOf[T0]: Boolean

    

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15. def keepIfValidArgs(mentions: Seq[Mention], state: State): Seq[Mention]

    

16. lazy val logger: Logger

    

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    LazyLogging

17. def mkActivation(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Identical to mkRegulation, except mkActivation will only allow activations where no overlapping regulation is present

18. def mkBinding(mentions: Seq[Mention], state: State): Seq[Mention]

    

19. def mkBindingsFromPairs(pairs: Seq[Seq[BioMention]], original: EventMention): Seq[Mention]

    

20. def mkBioMention(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Converts mentions to biomentions.

    Converts mentions to biomentions. They are returned as mentions but they are biomentions with grounding, modifications, etc

21. val mkEntities: Action

    

22. def mkNERMentions(mentions: Seq[Mention], state: State): Seq[Mention]

    

    This action handles the creation of mentions from labels generated by the NER system.

    This action handles the creation of mentions from labels generated by the NER system. Rules that use this action should run in an iteration following and rules recognizing "custom" entities. This action will only create mentions if no other mentions overlap with a NER label sequence.

23. def mkNaryBinding(mentions: Seq[Mention], state: State): Seq[Mention]

    

    For bindings that should not be split into pairs

24. def mkRegulation(mentions: Seq[Mention], state: State): Seq[Mention]

    

25. def mkUbiquitination(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Gets a sequence of mentions that are candidates for becoming Ubiquitination events and filters out the ones that have ubiquitin as a theme, since a ubiquitin can't be ubiquitinated.

    Gets a sequence of mentions that are candidates for becoming Ubiquitination events and filters out the ones that have ubiquitin as a theme, since a ubiquitin can't be ubiquitinated. Events that have ubiquitin as a cause are also filtered out.

26. final def ne(arg0: AnyRef): Boolean

    

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27. final def notify(): Unit

    

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28. final def notifyAll(): Unit

    

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29. def siteSniffer(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Promote any Sites in the Modifications of a SimpleEvent argument to an event argument "site"

30. def splitSimpleEvents(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Splits a SimpleEvent with a theme and a cause into a ComplexEvent.

    Splits a SimpleEvent with a theme and a cause into a ComplexEvent. Requires that the controlled and controller do not overlap

31. def storeEventSite(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Gets RelationMentions that represent an EventSite, and attaches the site to the corresponding entities in-place.

    Gets RelationMentions that represent an EventSite, and attaches the site to the corresponding entities in-place. Later, if these entities are matched as participants in an event, these sites will be "promoted" to that event and removed from the entity (see siteSniffer for details) This action always returns Nil and assumes that the arguments are already in the state.

32. def storeMutants(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Gets RelationMentions that represent a Mutant, and attaches the mutation to the corresponding event in-place.

    Gets RelationMentions that represent a Mutant, and attaches the mutation to the corresponding event in-place. This action always returns Nil and assumes that the arguments are already in the state.

33. def storePTM(mentions: Seq[Mention], state: State): Seq[Mention]

    

    This action gets RelationMentions that represents a PTM, and attaches the modification to the target entity in place.

    This action gets RelationMentions that represents a PTM, and attaches the modification to the target entity in place. This action modifies mentions in-place. This action always returns Nil, it assumes that the arguments are already in the state.

34. final def synchronized[T0](arg0: ⇒ T0): T0

    

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35. def toString(): String

    

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36. def unpackRelations(mentions: Seq[Mention], state: State): Seq[Mention]

    

    Unpacks RelationMentions into its arguments.

    Unpacks RelationMentions into its arguments. A new BioTextBoundMention will be created for each argument with the labels of the original RelationMention. This is relying on Odin's behavior of assigning the same label of the RelationMention to its arguments captured with a pattern (not mention captures). This is required for RelationMentions whose arguments are used directly by subsequent rules. WARNING This method only handles RelationMentions. Other types of Mentions are deleted.

37. final def wait(): Unit

    

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38. final def wait(arg0: Long, arg1: Int): Unit

    

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39. final def wait(arg0: Long): Unit

    

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