edu.arizona.sista.reach.grounding

KBAltLookup

Related Doc: package grounding

trait KBAltLookup extends Speciated with KBKeyTransforms

Trait for simple and species-specific string lookup in local knowledge bases using alternate key resolutions. Written by Tom Hicks. 11/15/2015. Last Modified: Redo to return resolution sequences.

Linear Supertypes
KBKeyTransforms, Speciated, AnyRef, Any
Known Subclasses
AzFailsafeKBML, IMKBFamilyLookup, IMKBFamilyMentionLookup, IMKBLookup, IMKBMentionLookup, IMKBOrganCellTypeLookup, IMKBOrganCellTypeMentionLookup, IMKBProteinLookup, IMKBProteinMentionLookup, KBAltMentionLookup
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  2. KBKeyTransforms
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Type Members

  1. type KeyTransforms = Seq[(String) ⇒ String]

    Type alias for functions which take a text string and return a potential key string.

    Type alias for functions which take a text string and return a potential key string.

    Definition Classes
    KBKeyTransforms

  2. type SpeciesNameSet = Set[String]

    Species name sets.

    Species name sets.

    Definition Classes
    Speciated

Abstract Value Members

  1. abstract def resolveAlt(text: String, transforms: KeyTransforms): 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. If the text is not found, use the given text transforming functions to create and lookup alternate keys. 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 resolveByASpeciesAlt(text: String, species: String, transforms: KeyTransforms): 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. If the text is not found, use the given text transforming functions to create and lookup alternate keys. 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 resolveBySpeciesAlt(text: String, speciesSet: SpeciesNameSet, transforms: KeyTransforms): 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. If the text is not found, use the given text transforming functions to create and lookup alternate keys. NB: This is an abstract method, to be overridden by each child class.

  4. abstract def resolveHumanAlt(text: String, transforms: KeyTransforms): 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. If the text is not found, use the given text transforming functions to create and lookup alternate keys. 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 resolveNoSpeciesAlt(text: String, transforms: KeyTransforms): 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. If the text is not found, use the given text transforming functions to create and lookup alternate keys. 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. def applyTransforms(text: String, transformFns: KeyTransforms): Seq[String]

    Return a sequence of alternate keys, one for each of the given key transforms.

    Return a sequence of alternate keys, one for each of the given key transforms.

    Definition Classes
    KBKeyTransforms

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

  8. 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

  9. 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

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

    Definition Classes
    AnyRef

  11. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  12. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  14. 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

  15. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  16. 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

  17. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  18. 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

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

    Definition Classes
    AnyRef

  20. final def notify(): Unit

    Definition Classes
    AnyRef

  21. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  22. def stripSuffixes(suffixes: Seq[String], text: String): String

    Try to remove all of the suffixes in the given set from the given text.

    Try to remove all of the suffixes in the given set from the given text.

    Definition Classes
    KBKeyTransforms

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

    Definition Classes
    AnyRef

  24. def toString(): String

    Definition Classes
    AnyRef → Any

  25. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from KBKeyTransforms

Inherited from Speciated

Inherited from AnyRef

Inherited from Any

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