edu.arizona.sista.reach.grounding

KBLookup

Related Doc: package grounding

trait KBLookup extends Speciated

Trait for simple and species-specific string lookup in local knowledge bases. Written by Tom Hicks. 10/28/2015. Last Modified: Redo to return resolution sequences.

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Speciated, AnyRef, Any
Known Subclasses
AzFailsafeKBML, IMKBFamilyLookup, IMKBFamilyMentionLookup, IMKBLookup, IMKBMentionLookup, IMKBOrganCellTypeLookup, IMKBOrganCellTypeMentionLookup, IMKBProteinLookup, IMKBProteinMentionLookup, KBMentionLookup
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Type Members

  1. type SpeciesNameSet = Set[String]

    Species name sets.

    Species name sets.

    Definition Classes
    Speciated

Abstract Value Members

  1. abstract def resolve(text: String): Resolutions

    Resolve the given text string to an optional entry in a knowledge base.

    Resolve the given text string to an optional entry in a knowledge base. Return a resolution for the entry, if any found. NB: This is an abstract method, to be overridden by each child class.

  2. abstract def resolveByASpecies(text: String, species: String): Resolutions

    Resolve the given text string to an optional entry in a knowledge base, for the single named species.

    Resolve the given text string to an optional entry in a knowledge base, for the single named species. Return a resolution for the entry, if any found. NB: This is an abstract method, to be overridden by each child class.

  3. abstract def resolveBySpecies(text: String, speciesSet: SpeciesNameSet): Resolutions

    Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB.

    Resolve the given text string to an optional group of entries in a knowledge base, returning resolutions for all species entries found in the KB. NB: This is an abstract method, to be overridden by each child class.

  4. abstract def resolveHuman(text: String): Resolutions

    Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans.

    Resolve the given text string to an optional entry in a knowledge base, failing if the entry is not for humans. Return a resolution for a human entry, if any found. NB: This is an abstract method, to be overridden by each child class.

  5. abstract def resolveNoSpecies(text: String): Resolutions

    Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species.

    Resolve the given text string to an optional entry in a knowledge base which explicitly does not have an associated species. Fail if all entries have species. Return a resolution for the entry, if any found. NB: This is an abstract method, to be overridden by each child class.

Concrete Value Members

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

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef → Any

  4. def SpeciesNameSet(xs: String*): Set[String]

    Definition Classes
    Speciated

  5. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  6. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  7. def containsHumanNsId(nsIdSeq: Seq[String]): Boolean

    Tell whether the given sequence of namespace/ID strings contains a human nsId.

    Tell whether the given sequence of namespace/ID strings contains a human nsId.

    Definition Classes
    Speciated

  8. def containsHumanSpecies(speciesSeq: Seq[String]): Boolean

    Tell whether the given sequence of species strings contain a human species label.

    Tell whether the given sequence of species strings contain a human species label.

    Definition Classes
    Speciated

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
    AnyRef → Any

  13. def hasHumanNsId(nsId: String): Boolean

    Tell whether the given namespace/ID string is an ID for humans or not.

    Tell whether the given namespace/ID string is an ID for humans or not.

    Definition Classes
    Speciated

  14. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  15. def isHumanSpecies(species: String): Boolean

    Tell whether the given species string is label for humans or not.

    Tell whether the given species string is label for humans or not.

    Definition Classes
    Speciated

  16. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  17. def isMemberOf(species: String, speciesSet: SpeciesNameSet): Boolean

    Tell whether the given species string is a member of the given set of species.

    Tell whether the given species string is a member of the given set of species.

    Definition Classes
    Speciated

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

    Definition Classes
    AnyRef

  19. final def notify(): Unit

    Definition Classes
    AnyRef

  20. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

    Definition Classes
    AnyRef

  22. def toString(): String

    Definition Classes
    AnyRef → Any

  23. final def wait(): Unit

    Definition Classes
    AnyRef
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    @throws( ... )

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

    Definition Classes
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    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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