KrakenReportToJson

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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. def aboutText: String

   

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5. def argsParser: ArgsParser

   

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   KrakenReportToJson → ToolCommand

6. final def asInstanceOf[T0]: T0

   

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   Any

7. var cladeIDs: ArrayBuffer[Long]

   

8. def clone(): AnyRef

   

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9. def cmdArrayToArgs(args: Array[String]): Args

   

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10. def contactText: String

    

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11. def contributingText: String

    

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12. def descriptionText: String

    

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    KrakenReportToJson → ToolCommand

13. def documentationText: String

    

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14. def emptyArgs: Args

    

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    KrakenReportToJson → ToolCommand

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

    

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16. def equals(arg0: Any): Boolean

    

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17. def example(args: String*): String

    

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18. def exampleText: String

    

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19. def finalize(): Unit

    

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20. def generateDocumentation(outputDirectory: File, version: String, release: Boolean): Unit

    

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21. def generateReadme(outputFile: File): Unit

    

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

    

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23. def hashCode(): Int

    

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24. def installationText: String

    

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25. final def isInstanceOf[T0]: Boolean

    

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26. def logger: Logger

    

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27. def main(args: Array[String]): Unit

    

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    KrakenReportToJson → ToolCommand

28. def mainPageContents: List[(String, String)]

    

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29. def manualText: String

    

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    KrakenReportToJson → ToolCommand

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

    

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31. final def notify(): Unit

    

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32. final def notifyAll(): Unit

    

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33. def parseLine(krakenRawHit: String, skipNames: Boolean): Map[Long, KrakenHit]

    

    Takes a line from the kraken report, converts into Map with taxonID and information on this hit as KrakenHit.

    Takes a line from the kraken report, converts into Map with taxonID and information on this hit as KrakenHit. KrakenHit is used later on for building the tree

    krakenRawHit

    Line from the KrakenReport output

    skipNames

    Specify to skip names in the report output to reduce size of JSON

34. def readmeContents: List[(String, String)]

    

    Definition Classes

    ToolCommand

35. def reportToJson(reportRaw: File, skipNames: Boolean): String

    

    Read the KrakenReport output and transform into Map by TaxonID and KrakenHit A JSON-string output is given.

    Read the KrakenReport output and transform into Map by TaxonID and KrakenHit A JSON-string output is given.

    reportRaw

    The KrakenReport output

    skipNames

    Specify to skip names in the report output to reduce size of JSON

36. val spacePattern: Regex

    

37. def sparkExample(args: String*): String

    

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38. def sparkUnsafeExample(args: String*): String

    

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

    

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40. def toString(): String

    

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41. def toolName: String

    

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42. def unsafeExample(args: String*): String

    

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43. def urlToolName: String

    

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44. def usageText: String

    

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45. final def wait(): Unit

    

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

    

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

    

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