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. def addAdjectivalModifiers(tokens: Seq[Int], deps: DirectedGraph[String]): Seq[Int]

   

   Adds adjectival modifiers to all elements in the given path This is necessary so we can properly inspect the semantic negatives, which are often not in the path, but modify tokens in it, "*decreased* PTPN13 expression increases phosphorylation of EphrinB1"

5. final def asInstanceOf[T0]: T0

   

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

   

   global action for EventEngine

7. def clone(): AnyRef

   

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   protected[java.lang]

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8. def consecutivePreps(path: Seq[Int], deps: DirectedGraph[String]): Boolean

   

9. def convertEventToEntity(event: BioEventMention): Option[BioMention]

   

   Gets a BioEventMention.

   Gets a BioEventMention. If it is not a SimpleEvent it returns None. If it is a SimpleEvent it will return an entity that represents the product of the event: a complex for a binding and an entity with a PTM for any other kind of SimpleEvent.

10. def countSemanticNegatives(trigger: Mention, arg: Mention, excluded: Set[Int]): Int

    

    Gets a trigger, an argument and a set of tokens to be ignored.

    Gets a trigger, an argument and a set of tokens to be ignored. Returns the number of semantic negatives found in the shortest possible path between the trigger and the argument.

11. val default: Action

    

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    Actions

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

    

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13. def equals(arg0: Any): Boolean

    

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14. def filterEventsWithExtraRecursion(mentions: Seq[Mention], state: State): Seq[Mention]

    

15. def finalize(): Unit

    

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    protected[java.lang]

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

16. def flipLabel(label: String): String

    

    gets a polarized label and returns it flipped

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

    

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18. def getModificationLabel(text: String): String

    

    retrieves the appropriate modification label

19. def getModifiers(token: Int, deps: DirectedGraph[String]): Seq[Int]

    

20. def hasController(mention: Mention): Boolean

    

    Test whether the given mention has a controller argument.

21. def hasDistinctControllerControlled(m: Mention): Boolean

    

    Gets a mention and checks that the controller and controlled are different.

    Gets a mention and checks that the controller and controlled are different. Returns true if either the controller or the controlled is missing, or if they are both present and are distinct.

22. def hasSynPathOverlap(m: Mention): Boolean

    

    checks if a mention has a controller/controlled arguments with syntactic paths from the trigger that overlap

23. def hashCode(): Int

    

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24. final def isInstanceOf[T0]: Boolean

    

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

    

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

    

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

    

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

    

29. 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

30. val mkEntities: Action

    

31. 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.

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

    

33. 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.

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

    

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35. final def notify(): Unit

    

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36. final def notifyAll(): Unit

    

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37. def preferSimpleEventControllers(mentions: Seq[Mention]): Seq[Mention]

    

    Gets a sequence of mentions and returns only the ones that have SimpleEvent controllers.

    Gets a sequence of mentions and returns only the ones that have SimpleEvent controllers. If none is found, returns all mentions.

38. def proteinBetween(trigger: Mention, arg: Mention, state: State): Boolean

    

39. def removeDummy(m: BioMention): BioMention

    

40. def sameEntityID(m1: BioMention, m2: BioMention): Boolean

    

    Returns true if both mentions are grounded to the same entity

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

    

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

42. def sortMentionsByController(mentions: Seq[Mention]): Seq[Mention]

    

    sorts a sequence of Mentions so that mentions with event controllers appear first

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

    

44. 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.

45. 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.

46. 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.

47. def switchLabel(mention: BioMention): BioMention

    

    Gets a mention.

    Gets a mention. If it is an EventMention with a polarized label and it is negated an odd number of times, returns a new mention with the label flipped. Or else it returns the mention unmodified

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

    

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49. def toString(): String

    

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50. 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.

51. def validArguments(mention: Mention, state: State): Boolean

    

52. final def wait(): Unit

    

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

    

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

    

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    @throws( ... )