IndexCardOutput

Value Members

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

   

   Definition Classes

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2. final def ##(): Int

   

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

   

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4. def addLocation(f: PropMap, prefix: String, loc: CorefMention): Unit

   

5. def addMeta(f: PropMap, mention: CorefMention, paperId: String, startTime: Date, endTime: Date, otherMetaData: Map[String, String]): Unit

   

6. def addMutation(f: PropMap, base: String, site: Int): Unit

   

7. def addUnspecifiedMutation(f: PropMap): Unit

   

8. final def asInstanceOf[T0]: T0

   

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9. def clone(): AnyRef

   

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   protected[java.lang]

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   @throws( ... )

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

    

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11. def equals(arg0: Any): Boolean

    

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12. def finalize(): Unit

    

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    protected[java.lang]

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

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

    

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14. def hashCode(): Int

    

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15. final def isInstanceOf[T0]: Boolean

    

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    Any

16. lazy val logger: Logger

    

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    protected

    Definition Classes

    LazyLogging

17. def mkActivationIndexCard(mention: CorefMention): Option[PropMap]

    

    Creates a card for an activation event

18. def mkArgument(arg: CorefMention): Any

    

19. def mkBindingIndexCard(mention: CorefMention): Option[PropMap]

    

    Creates a card for a complex-assembly event

20. def mkCards(paperId: String, allMentions: Seq[Mention], startTime: Date, endTime: Date, otherMetaData: Map[String, String]): Iterable[PropMap]

    

    Creates annotations from all events read from this paper.

    Creates annotations from all events read from this paper. This needs to be done in 2 passes: 1) save recursive events 2) save simple events that are not part of recursive events

21. def mkComplexArgument(complex: CorefMention): FrameList

    

22. def mkContext(f: PropMap, mention: CorefMention): Unit

    

    Add the properties of the given context map to the given property map.

23. def mkEventModification(mention: CorefMention): PropMap

    

24. def mkFeatures(arg: CorefMention): FrameList

    

25. def mkHedging(f: PropMap, mention: CorefMention): Unit

    

26. def mkIdentifier(grounding: KBResolution): String

    

27. def mkIndexCard(mention: CorefMention): Option[PropMap]

    

    Main annotation dispatcher method.

28. def mkIndexCardFileName(paperId: String, count: Int): String

    

    Return a new filename for each card.

29. def mkModificationIndexCard(mention: CorefMention, positiveModification: Boolean = true): Option[PropMap]

    

    Creates a card for a simple, modification event

30. def mkMutantFeature(m: Mutant): PropMap

    

31. def mkPTMFeature(ptm: PTM): PropMap

    

32. def mkRegulationIndexCard(mention: CorefMention, simpleEventsInRegs: HashSet[Mention]): Option[PropMap]

    

    Creates a card for a regulation event

33. def mkSimpleEventIndexCard(mention: CorefMention, label: String): Option[PropMap]

    

    Creates a card for a simple events

34. def mkSingleArgument(arg: CorefMention): PropMap

    

35. def mkTranslocationIndexCard(mention: CorefMention): Option[PropMap]

    

    Creates a card for a translocation event

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

    

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37. final def notify(): Unit

    

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38. final def notifyAll(): Unit

    

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

    

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40. def toJSON(paperId: String, allMentions: Seq[Mention], paperPassages: Seq[FriesEntry], startTime: Date, endTime: Date, outFilePrefix: String): String

    

    Returns the given mentions in the index-card JSON format, as one big string.

    Returns the given mentions in the index-card JSON format, as one big string. All index cards are concatenated into a single JSON string.

    Definition Classes

    IndexCardOutput → JsonOutputter

41. def toJSON(paperId: String, allMentions: Seq[Mention], nxmldoc: NxmlDocument, startTime: Date, endTime: Date, outFilePrefix: String): String

    

    Returns the given mentions in some JSON-based format, as one big string.

    Returns the given mentions in some JSON-based format, as one big string. Alternate interface: takes document and extracts passages to output mentions. The processing start and stop date/times are given. The output filename prefix is provided for use by the generator routines, as needed.

    Definition Classes

    JsonOutputter

42. def toString(): String

    

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43. final def wait(): Unit

    

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    @throws( ... )

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

    

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

    

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46. def writeJSON(paperId: String, allMentions: Seq[Mention], paperPassages: Seq[FriesEntry], startTime: Date, endTime: Date, outFilePrefix: String): Unit

    

    Writes the given mentions to output files in IndexCard JSON format.

    Writes the given mentions to output files in IndexCard JSON format. Separate output files are written for sentences, entities, and events. Each output file is prefixed with the given prefix string.

    Definition Classes

    IndexCardOutput → JsonOutputter

47. def writeJSON(paperId: String, allMentions: Seq[Mention], nxmldoc: NxmlDocument, startTime: Date, endTime: Date, outFilePrefix: String): Unit

    

    Definition Classes

    JsonOutputter

48. def writeJSON(paperId: String, allMentions: Seq[Mention], paperPassages: Seq[FriesEntry], startTime: Date, endTime: Date, outFilePrefix: String, assemblyAPI: Assembler): Unit

    

    Outputs the given mentions to the given output file in some JSON-based format, including additional information from the assembly process.

    Outputs the given mentions to the given output file in some JSON-based format, including additional information from the assembly process. The processing start and stop date/times are given. The output file is given as a prefix, in case outputters choose to generate multiple output files (e.g., see FriesOutput).

    Definition Classes

    JsonOutputter