ReachKBUtils

Value Members

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

   

   Definition Classes

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2. final def ##(): Int

   

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

   

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

   

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   Speciated

5. final def asInstanceOf[T0]: T0

   

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6. def clone(): AnyRef

   

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   protected[java.lang]

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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

   

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10. def equals(arg0: Any): Boolean

    

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11. def finalize(): Unit

    

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    protected[java.lang]

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

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

    

    Definition Classes

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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 isFamilyGrounded(mention: BioMention): Boolean

    

    Tell whether the given mention is grounded from a protein family KB or not.

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. def isProteinGrounded(mention: BioMention): Boolean

    

    Tell whether the given mention is grounded from a protein KB or not.

20. def makeFileInKBDir(filename: String): File

    

    Return a file for the given filename in the knowledge bases directory.

21. def makeFileInUserDir(filename: String): File

    

    Return a file for the given filename in the current user working directory.

22. def makeNamespaceId(namespace: String, id: String): String

    

    Return a formatted string containing this entry's namespace and ID.

23. def makePathInKBDir(filename: String): String

    

    Return a resource path string for the given filename in the knowledge bases directory.

24. def makePathInUserDir(filename: String): String

    

    Return a path string for the given filename in the current user working directory.

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

    

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26. final def notify(): Unit

    

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27. final def notifyAll(): Unit

    

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28. def readLines(filename: String): List[String]

    

    Read and return all the lines from the specified file.

29. def selectASpecies(resolutions: Seq[KBResolution], species: String): Seq[KBResolution]

    

    Filter sequence to return only resolutions (sorted) with the given species.

30. def selectByNotSpecies(resolutions: Seq[KBResolution], species: Set[String]): Seq[KBResolution]

    

    Filter sequence to return only resolutions (sorted) without a species in the given set.

31. def selectBySpecies(resolutions: Seq[KBResolution], species: Set[String]): Seq[KBResolution]

    

    Filter sequence to return only resolutions (sorted) with a species in the given set.

32. def selectHuman(resolutions: Seq[KBResolution]): Seq[KBResolution]

    

    Filter sequence to return human resolutions (sorted).

33. def selectNoSpecies(resolutions: Seq[KBResolution]): Seq[KBResolution]

    

    Filter sequence to return resolutions which have no species.

34. def selectNotASpecies(resolutions: Seq[KBResolution], species: String): Seq[KBResolution]

    

    Filter sequence to return only resolutions (sorted) without the given species.

35. def selectNotHuman(resolutions: Seq[KBResolution]): Seq[KBResolution]

    

    Filter sequence to return only resolutions (sorted) with a non-human species.

36. def sourceFromResource(resourcePath: String): Source

    

    Return a Scala Source object created from the given resource path string.

    Return a Scala Source object created from the given resource path string. If the resource path ends with ".gz" the source is created around a gzip input stream.

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

    

    Definition Classes

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38. def toString(): String

    

    Definition Classes

    AnyRef → Any

39. def tsvRowToFields(row: String): Seq[String]

    

    Convert a single row string from a TSV file to a sequence of string fields.

40. def tsvValidateFields(fields: Seq[String]): Boolean

    

    Check for required fields in one row of a TSV input file.

41. final def wait(): Unit

    

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    @throws( ... )

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

    

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    @throws( ... )

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

    

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    @throws( ... )