edu.arizona.sista.reach.grounding

AdHocIMKBFactory

Related Doc: package grounding

class AdHocIMKBFactory extends Speciated with ReachKBKeyTransforms

Factory class for creating and loading an in-memory KB from a mixed-namespaced TSV file. Written by: Tom Hicks. 1/19/2016. Last Modified: Remove spurious import.

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ReachKBKeyTransforms, KBKeyTransforms, Speciated, AnyRef, Any
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  1. AdHocIMKBFactory
  2. ReachKBKeyTransforms
  3. KBKeyTransforms
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Instance Constructors

  1. new AdHocIMKBFactory()

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

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 hyphenatedProteinKey(text: String): String

    Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.

    Check for one of several types of hyphen-separated strings and, if found, extract and return the candidate text portion, else return the text unchanged.

    Definition Classes
    ReachKBKeyTransforms

  17. 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

  18. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  19. 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

  20. def make(kbFilename: String, metaInfo: IMKBMetaInfo): InMemoryKB

    Additional factory method to workaround meta info option.

  21. def make(kbFilename: String = "", metaInfo: Option[IMKBMetaInfo] = None): InMemoryKB

    Main factory method to create, fill, and return an encapsulated knowledge base.

  22. def makeCanonicalKey(text: String): String

    Canonicalize the given text string into a key for both storage and lookup.

    Canonicalize the given text string into a key for both storage and lookup.

    Definition Classes
    ReachKBKeyTransforms

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

    Definition Classes
    AnyRef

  24. final def notify(): Unit

    Definition Classes
    AnyRef

  25. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  26. def reachAlternateKeys(text: String, transformFns: KeyTransforms): Seq[String]

    Return alternate lookup keys created from the given text string and transform functions.

    Return alternate lookup keys created from the given text string and transform functions.

    Definition Classes
    ReachKBKeyTransforms

  27. def stripFamilySuffixes(text: String): String

    Return the portion of the text string minus one of the protein family suffixes, if found in the given text string, else return the text lowercased.

    Return the portion of the text string minus one of the protein family suffixes, if found in the given text string, else return the text lowercased.

    Definition Classes
    ReachKBKeyTransforms

  28. def stripMutantProtein(text: String): String

    Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return the text unchanged.

    Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return the text unchanged.

    Definition Classes
    ReachKBKeyTransforms

  29. def stripOrganCellTypeSuffixes(text: String): String

    Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return the text unchanged.

    Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return the text unchanged.

    Definition Classes
    ReachKBKeyTransforms

  30. def stripPTMPrefixes(text: String): String

    Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.

    Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return the text unchanged.

    Definition Classes
    ReachKBKeyTransforms

  31. def stripProteinSuffixes(text: String): String

    Return the portion of the text string minus one of the protein suffixes, if found in the given text string, else return the text lowercased.

    Return the portion of the text string minus one of the protein suffixes, if found in the given text string, else return the text lowercased.

    Definition Classes
    ReachKBKeyTransforms

  32. 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

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

    Definition Classes
    AnyRef

  34. def toString(): String

    Definition Classes
    AnyRef → Any

  35. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from ReachKBKeyTransforms

Inherited from KBKeyTransforms

Inherited from Speciated

Inherited from AnyRef

Inherited from Any

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