edu.arizona.sista.reach.grounding

ReachKBKeyTransforms

Related Docs: object ReachKBKeyTransforms | package grounding

trait ReachKBKeyTransforms extends KBKeyTransforms

REACH-related methods for transforming text strings into potential keys for lookup in KBs. Written by Tom Hicks. 11/10/2015. Last Modified: Restrict PTM patterns per issue #90.

Linear Supertypes
KBKeyTransforms, AnyRef, Any
Known Subclasses
AdHocIMKBFactory, AzFailsafeKBML, IMKBFamilyLookup, IMKBFamilyMentionLookup, IMKBLookup, IMKBMentionLookup, IMKBOrganCellTypeLookup, IMKBOrganCellTypeMentionLookup, IMKBProteinLookup, IMKBProteinMentionLookup, InMemoryKB, ReachKBKeyTransforms, TsvIMKBFactory
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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

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 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

  5. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  6. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  8. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  9. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  11. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  12. 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.

  13. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  14. def makeCanonicalKey(text: String): String

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

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

    Definition Classes
    AnyRef

  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
    AnyRef

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

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

  19. 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.

  20. 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.

  21. 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.

  22. 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.

  23. 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.

  24. 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

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

    Definition Classes
    AnyRef

  26. def toString(): String

    Definition Classes
    AnyRef → Any

  27. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from KBKeyTransforms

Inherited from AnyRef

Inherited from Any

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