ReachKBKeyTransforms

Value Members

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

   

   Definition Classes

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2. final def ##(): Int

   

   Definition Classes

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

   

   Definition Classes

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4. val AllKeysSuffixPat: Regex

   

   The set of suffixes to remove from all keys to create a lookup key.

5. val CasedKeyTransforms: Seq[(String) ⇒ KeyCandidates]

   

   List of text transforms to use with a case-sensitive KB.

6. val DefaultKeyTransforms: Seq[(String) ⇒ KeyCandidates]

   

   Default list of text transforms to use with a KB.

7. val FamilyAuxKeyTransforms: Seq[(String) ⇒ KeyCandidates]

   

   List of transform methods to apply for alternate Protein Family lookups.

8. val FamilyPostAttributivePat: Regex

   

9. val GeneNameSuffixPat: Regex

   

   The set of suffixes to remove from all keys to create a lookup key.

10. val HyphenatedNamePat: Regex

    

    Pattern matching 2 text strings separated by a hyphen, case insensitive.

11. val IdentityKeyTransforms: Seq[(String) ⇒ KeyCandidates]

    

    Key transform sequence containing a single identity key transform (a NOP).

12. val KeyCharactersToRemove: Set[Char]

    

    The set of characters to remove from the text to create a lookup key.

13. val LeadingMutationPat: Regex

    

    Match mutation string at end of text string, case insensitive.

14. val OrganAuxKeyTransforms: Seq[(String) ⇒ KeyCandidates]

    

    List of transform methods to apply for alternate Organ lookups.

15. val OrganPostAttributivePat: Regex

    

    Match patterns to create an organ lookup key.

16. val PTMPrefixPat: Regex

    

    Match protein names beginning with special PTM-related prefix characters.

17. val PhosphorMutationPat: Regex

    

    Match phosphorylation mutation phrases, case insensitive.

18. val ProteinAuxKeyTransforms: Seq[(String) ⇒ KeyCandidates]

    

    List of transform methods to apply for alternate Protein lookups.

19. val ProteinPostAttributivePat: Regex

    

    Match patterns to create a protein lookup key.

20. val TrailingMutationPat: Regex

    

    Match mutation string at end of text string, case insensitive.

21. val UnderscoreFamilySuffixPat: Regex

    

    Match patterns to create a protein family lookup key.

22. def applyAllTransforms(transformFns: KeyTransforms, text: String): KeyCandidates

    

    Apply the given key transforms to the given string, returning a (possibly empty) sequence of potential key strings.

    Apply the given key transforms to the given string, returning a (possibly empty) sequence of potential key strings.

    Definition Classes

    KBKeyTransforms

23. def applyTransform(transformFn: KeyTransformFn, texts: Seq[String]): KeyCandidates

    

    Apply the given transform function to the given texts, return any non-empty result strings.

    Apply the given transform function to the given texts, return any non-empty result strings.

    Definition Classes

    KBKeyTransforms

24. def applyTransform(transformFn: KeyTransformFn, text: String): KeyCandidates

    

    Apply the given transform function to the given text, return any non-empty result strings.

    Apply the given transform function to the given text, return any non-empty result strings.

    Definition Classes

    KBKeyTransforms

25. final def asInstanceOf[T0]: T0

    

    Definition Classes

    Any

26. def canonicalKT(text: String): KeyCandidates

    

    A key transform which implements a canonicalization function for Strings.

    A key transform which implements a canonicalization function for Strings.

    Definition Classes

    ReachKBKeyTransforms

27. def canonicalKey(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

28. def clone(): AnyRef

    

    Attributes

    protected[java.lang]

    Definition Classes

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    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

30. def equals(arg0: Any): Boolean

    

    Definition Classes

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31. def finalize(): Unit

    

    Attributes

    protected[java.lang]

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

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

    

    Definition Classes

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33. def hashCode(): Int

    

    Definition Classes

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34. def identityKT(text: String): KeyCandidates

    

    A key transform which implements an Identity function for Strings.

    A key transform which implements an Identity function for Strings.

    Definition Classes

    KBKeyTransforms

35. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

36. def lowercaseKT(text: String): KeyCandidates

    

    A key transform which implements a minimal canonicalization function for Strings.

    A key transform which implements a minimal canonicalization function for Strings.

    Definition Classes

    KBKeyTransforms

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

    

    Definition Classes

    AnyRef

38. final def notify(): Unit

    

    Definition Classes

    AnyRef

39. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

40. def stripAllKeysSuffixes(text: String): String

    

    Remove suffixes from all keys candidates.

    Remove suffixes from all keys candidates.

    Definition Classes

    ReachKBKeyTransforms

41. def stripAllSuffixes(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

42. def stripAllSuffixesKT(suffixes: Seq[String], text: String): KeyCandidates

    

    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

43. def stripFamilyPostAttributivesKT(text: String): KeyCandidates

    

    Return the portion of the text string minus one of the protein family postpositional attributives, if found in the given text string, else return no candidates.

    Return the portion of the text string minus one of the protein family postpositional attributives, if found in the given text string, else return no candidates.

    Definition Classes

    ReachKBKeyTransforms

44. def stripGeneNameAffixesKT(text: String): KeyCandidates

    

    Try to remove some specific affixes from the given hyphenated text and return a dash-concatenated string of non-affixes, or no candidates if no affixes removed.

    Try to remove some specific affixes from the given hyphenated text and return a dash-concatenated string of non-affixes, or no candidates if no affixes removed.

    Definition Classes

    ReachKBKeyTransforms

45. def stripMutantProteinKT(text: String): KeyCandidates

    

    Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return no candidates.

    Return the portion of the text string before a trailing mutation phrase, if found in the given text string, else return no candidates.

    Definition Classes

    ReachKBKeyTransforms

46. def stripOrganPostAttributivesKT(text: String): KeyCandidates

    

    Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return no candidates.

    Return the portion of the text string minus one of the organ-cell-type suffixes, if found in the given text string, else return no candidates.

    Definition Classes

    ReachKBKeyTransforms

47. def stripPTMPrefixesKT(text: String): KeyCandidates

    

    Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return no candidates.

    Return the portion of the text string minus any of the PTM-related prefixes, if found in the given text string, else return no candidates.

    Definition Classes

    ReachKBKeyTransforms

48. def stripProteinDomainKT(text: String): KeyCandidates

    

    Check for hyphen-separated strings where the RHS is a protein domain specification.

    Check for hyphen-separated strings where the RHS is a protein domain specification. Extract and return the candidate text portion, else return no candidates.

    Definition Classes

    ReachKBKeyTransforms

49. def stripProteinPostAttributivesKT(text: String): KeyCandidates

    

    Return the portion of the text string minus one of the protein postpositional attributives, if found in the given text string, else return no candidates.

    Return the portion of the text string minus one of the protein postpositional attributives, if found in the given text string, else return no candidates.

    Definition Classes

    ReachKBKeyTransforms

50. def stripSuffixByPattern(pattern: Regex, text: String): String

    

    Remove suffix(es) matching given pattern from text, return matched part or text.

    Remove suffix(es) matching given pattern from text, return matched part or text. Trims matching part or text as a side effect.

    Definition Classes

    ReachKBKeyTransforms

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

    

    Definition Classes

    AnyRef

52. def toKeyCandidates(candidates: Seq[String]): KeyCandidates

    

    Transform the given sequence of strings into (a possibly empty) key candidates.

    Transform the given sequence of strings into (a possibly empty) key candidates.

    Definition Classes

    KBKeyTransforms

53. def toKeyCandidates(text: String): KeyCandidates

    

    Transform the given string into (a possibly empty) key candidates.

    Transform the given string into (a possibly empty) key candidates.

    Definition Classes

    KBKeyTransforms

54. def toString(): String

    

    Definition Classes

    AnyRef → Any

55. final def wait(): Unit

    

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    @throws( ... )

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

    

    Definition Classes

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    @throws( ... )

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

    

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    @throws( ... )