ReachKBUtils

Value Members

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

   

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2. final def ##(): Int

   

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

   

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4. final def asInstanceOf[T0]: T0

   

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5. def clone(): AnyRef

   

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

   

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7. def equals(arg0: Any): Boolean

   

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8. def finalize(): Unit

   

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

   

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10. def hashCode(): Int

    

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11. def isFamilyGrounded(mention: BioMention): Boolean

    

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

12. final def isInstanceOf[T0]: Boolean

    

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13. def isProteinGrounded(mention: BioMention): Boolean

    

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

14. def makeFileInKBDir(filename: String): File

    

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

15. def makeFileInUserDir(filename: String): File

    

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

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

    

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

17. def makePathInKBDir(filename: String): String

    

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

18. def makePathInUserDir(filename: String): String

    

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

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

    

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20. final def notify(): Unit

    

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21. final def notifyAll(): Unit

    

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22. def orderResolutions(resSeq: Seq[KBResolution]): Seq[KBResolution]

    

    Return given sequence of resolutions ordered in the application default manner.

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

    

    Read and return all the lines from the specified file.

24. def selectASpecies(resSeq: Seq[KBResolution], species: String): Seq[KBResolution]

    

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

25. def selectByNotSpecies(resSeq: Seq[KBResolution], species: Speciated.SpeciesNameSet): Seq[KBResolution]

    

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

26. def selectBySpecies(resSeq: Seq[KBResolution], species: Speciated.SpeciesNameSet): Seq[KBResolution]

    

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

27. def selectHuman(resSeq: Seq[KBResolution]): Seq[KBResolution]

    

    Filter sequence to return human resolutions (sorted).

28. def selectNoSpecies(resSeq: Seq[KBResolution]): Seq[KBResolution]

    

    Filter sequence to return resolutions which have no species.

29. def selectNotASpecies(resSeq: Seq[KBResolution], species: String): Seq[KBResolution]

    

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

30. def selectNotHuman(resSeq: Seq[KBResolution]): Seq[KBResolution]

    

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

31. 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.

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

    

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33. def toString(): String

    

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

    

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

35. final def wait(): Unit

    

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

    

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

    

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