Class/Object

com.johnsnowlabs.nlp.annotators

DrugNormalizer

Related Docs: object DrugNormalizer | package annotators

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class DrugNormalizer extends AnnotatorModel[DrugNormalizer]

Annotator which normalizes raw text from clinical documents, e.g. scraped web pages or xml documents, from document type columns into Sentence. Removes all dirty characters from text following one or more input regex patterns. Can apply non wanted character removal which a specific policy. Can apply lower case normalization.

See DocumentNormalizer test class for examples examples of usage.

Linear Supertypes
AnnotatorModel[DrugNormalizer], CanBeLazy, RawAnnotator[DrugNormalizer], HasOutputAnnotationCol, HasInputAnnotationCols, HasOutputAnnotatorType, ParamsAndFeaturesWritable, HasFeatures, DefaultParamsWritable, MLWritable, Model[DrugNormalizer], Transformer, PipelineStage, Logging, Params, Serializable, Serializable, Identifiable, AnyRef, Any
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  2. By Inheritance
Inherited
  1. DrugNormalizer
  2. AnnotatorModel
  3. CanBeLazy
  4. RawAnnotator
  5. HasOutputAnnotationCol
  6. HasInputAnnotationCols
  7. HasOutputAnnotatorType
  8. ParamsAndFeaturesWritable
  9. HasFeatures
  10. DefaultParamsWritable
  11. MLWritable
  12. Model
  13. Transformer
  14. PipelineStage
  15. Logging
  16. Params
  17. Serializable
  18. Serializable
  19. Identifiable
  20. AnyRef
  21. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new DrugNormalizer()

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  2. new DrugNormalizer(uid: String)

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    uid

    required uid for storing annotator to disk

Type Members

  1. type AnnotationContent = Seq[Row]

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    Attributes
    protected
    Definition Classes
    AnnotatorModel
  2. type AnnotatorType = String

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    Definition Classes
    HasOutputAnnotatorType

Value Members

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

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    Definition Classes
    AnyRef → Any
  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any
  3. final def $[T](param: Param[T]): T

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    Attributes
    protected
    Definition Classes
    Params
  4. def $$[T](feature: StructFeature[T]): T

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    Attributes
    protected
    Definition Classes
    HasFeatures
  5. def $$[K, V](feature: MapFeature[K, V]): Map[K, V]

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    Attributes
    protected
    Definition Classes
    HasFeatures
  6. def $$[T](feature: SetFeature[T]): Set[T]

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    Attributes
    protected
    Definition Classes
    HasFeatures
  7. def $$[T](feature: ArrayFeature[T]): Array[T]

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    Attributes
    protected
    Definition Classes
    HasFeatures
  8. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  9. def _transform(dataset: Dataset[_], recursivePipeline: Option[PipelineModel]): DataFrame

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    Attributes
    protected
    Definition Classes
    AnnotatorModel
  10. val abbreviations: MapFeature[String, String]

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    abbreviation regex patterns which match will be extended in document

  11. def afterAnnotate(dataset: DataFrame): DataFrame

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    Attributes
    protected
    Definition Classes
    AnnotatorModel
  12. def annotate(annotations: Seq[Annotation]): Seq[Annotation]

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    Definition Classes
    DrugNormalizer → AnnotatorModel
  13. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  14. def beforeAnnotate(dataset: Dataset[_]): Dataset[_]

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    Attributes
    protected
    Definition Classes
    AnnotatorModel
  15. final def checkSchema(schema: StructType, inputAnnotatorType: String): Boolean

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    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  16. final def clear(param: Param[_]): DrugNormalizer.this.type

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    Definition Classes
    Params
  17. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  18. def copy(extra: ParamMap): DrugNormalizer

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    Definition Classes
    RawAnnotator → Model → Transformer → PipelineStage → Params
  19. def copyValues[T <: Params](to: T, extra: ParamMap): T

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    Attributes
    protected
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    Params
  20. final def defaultCopy[T <: Params](extra: ParamMap): T

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    Attributes
    protected
    Definition Classes
    Params
  21. def dfAnnotate: UserDefinedFunction

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    Attributes
    protected
    Definition Classes
    AnnotatorModel
  22. final def eq(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  23. def equals(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  24. def explainParam(param: Param[_]): String

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    Definition Classes
    Params
  25. def explainParams(): String

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    Definition Classes
    Params
  26. def extraValidate(structType: StructType): Boolean

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    Attributes
    protected
    Definition Classes
    RawAnnotator
  27. def extraValidateMsg: String

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    Attributes
    protected
    Definition Classes
    RawAnnotator
  28. final def extractParamMap(): ParamMap

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    Definition Classes
    Params
  29. final def extractParamMap(extra: ParamMap): ParamMap

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    Definition Classes
    Params
  30. val features: ArrayBuffer[Feature[_, _, _]]

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    Definition Classes
    HasFeatures
  31. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  32. def get[T](feature: StructFeature[T]): Option[T]

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    Attributes
    protected
    Definition Classes
    HasFeatures
  33. def get[K, V](feature: MapFeature[K, V]): Option[Map[K, V]]

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    Attributes
    protected
    Definition Classes
    HasFeatures
  34. def get[T](feature: SetFeature[T]): Option[Set[T]]

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    Attributes
    protected
    Definition Classes
    HasFeatures
  35. def get[T](feature: ArrayFeature[T]): Option[Array[T]]

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    Attributes
    protected
    Definition Classes
    HasFeatures
  36. final def get[T](param: Param[T]): Option[T]

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    Definition Classes
    Params
  37. final def getClass(): Class[_]

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    Definition Classes
    AnyRef → Any
  38. final def getDefault[T](param: Param[T]): Option[T]

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    Definition Classes
    Params
  39. def getInputCols: Array[String]

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    Definition Classes
    HasInputAnnotationCols
  40. def getLazyAnnotator: Boolean

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    Definition Classes
    CanBeLazy
  41. def getLowercase: Boolean

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    Lowercase tokens, default false

  42. final def getOrDefault[T](param: Param[T]): T

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    Definition Classes
    Params
  43. final def getOutputCol: String

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    Definition Classes
    HasOutputAnnotationCol
  44. def getParam(paramName: String): Param[Any]

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    Definition Classes
    Params
  45. def getPolicy: String

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    Policy to remove patterns from text.

    Policy to remove patterns from text. Defaults "all".

  46. final def hasDefault[T](param: Param[T]): Boolean

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    Definition Classes
    Params
  47. def hasParam(paramName: String): Boolean

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    Definition Classes
    Params
  48. def hasParent: Boolean

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    Definition Classes
    Model
  49. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  50. def initializeLogIfNecessary(isInterpreter: Boolean, silent: Boolean): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  51. def initializeLogIfNecessary(isInterpreter: Boolean): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  52. val inputAnnotatorTypes: Array[AnnotatorType]

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    Input annotator type : DOCUMENT

    Input annotator type : DOCUMENT

    Definition Classes
    DrugNormalizer → HasInputAnnotationCols
  53. final val inputCols: StringArrayParam

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    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  54. final def isDefined(param: Param[_]): Boolean

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    Definition Classes
    Params
  55. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  56. final def isSet(param: Param[_]): Boolean

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    Definition Classes
    Params
  57. def isTraceEnabled(): Boolean

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    Attributes
    protected
    Definition Classes
    Logging
  58. val lazyAnnotator: BooleanParam

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    Definition Classes
    CanBeLazy
  59. def log: Logger

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    Attributes
    protected
    Definition Classes
    Logging
  60. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  61. def logDebug(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  62. def logError(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  63. def logError(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  64. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  65. def logInfo(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  66. def logName: String

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    Attributes
    protected
    Definition Classes
    Logging
  67. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  68. def logTrace(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  69. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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    Attributes
    protected
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    Logging
  70. def logWarning(msg: ⇒ String): Unit

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    Attributes
    protected
    Definition Classes
    Logging
  71. val lowercase: BooleanParam

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    whether to convert strings to lowercase

  72. def msgHelper(schema: StructType): String

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    Attributes
    protected
    Definition Classes
    HasInputAnnotationCols
  73. final def ne(arg0: AnyRef): Boolean

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    Definition Classes
    AnyRef
  74. final def notify(): Unit

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    Definition Classes
    AnyRef
  75. final def notifyAll(): Unit

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    Definition Classes
    AnyRef
  76. def onWrite(path: String, spark: SparkSession): Unit

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    Attributes
    protected
    Definition Classes
    ParamsAndFeaturesWritable
  77. val outputAnnotatorType: AnnotatorType

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    Input annotator type : DOCUMENT

    Input annotator type : DOCUMENT

    Definition Classes
    DrugNormalizer → HasOutputAnnotatorType
  78. final val outputCol: Param[String]

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    Attributes
    protected
    Definition Classes
    HasOutputAnnotationCol
  79. lazy val params: Array[Param[_]]

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    Definition Classes
    Params
  80. var parent: Estimator[DrugNormalizer]

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    Definition Classes
    Model
  81. val patterns: MapFeature[String, String]

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    normalization regex patterns which match will be normalized document

  82. val policy: Param[String]

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    removalPolicy to remove patterns from text with a given policy

  83. def save(path: String): Unit

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    Definition Classes
    MLWritable
    Annotations
    @Since( "1.6.0" ) @throws( ... )
  84. def set[T](feature: StructFeature[T], value: T): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  85. def set[K, V](feature: MapFeature[K, V], value: Map[K, V]): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  86. def set[T](feature: SetFeature[T], value: Set[T]): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  87. def set[T](feature: ArrayFeature[T], value: Array[T]): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  88. final def set(paramPair: ParamPair[_]): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    Params
  89. final def set(param: String, value: Any): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    Params
  90. final def set[T](param: Param[T], value: T): DrugNormalizer.this.type

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    Definition Classes
    Params
  91. def setDefault[T](feature: StructFeature[T], value: () ⇒ T): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  92. def setDefault[K, V](feature: MapFeature[K, V], value: () ⇒ Map[K, V]): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  93. def setDefault[T](feature: SetFeature[T], value: () ⇒ Set[T]): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  94. def setDefault[T](feature: ArrayFeature[T], value: () ⇒ Array[T]): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    HasFeatures
  95. final def setDefault(paramPairs: ParamPair[_]*): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    Params
  96. final def setDefault[T](param: Param[T], value: T): DrugNormalizer.this.type

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    Attributes
    protected
    Definition Classes
    Params
  97. final def setInputCols(value: String*): DrugNormalizer.this.type

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    Definition Classes
    HasInputAnnotationCols
  98. final def setInputCols(value: Array[String]): DrugNormalizer.this.type

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    Definition Classes
    HasInputAnnotationCols
  99. def setLazyAnnotator(value: Boolean): DrugNormalizer.this.type

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    Definition Classes
    CanBeLazy
  100. def setLowercase(value: Boolean): DrugNormalizer.this.type

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    Lower case tokens, default false

  101. final def setOutputCol(value: String): DrugNormalizer.this.type

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    Definition Classes
    HasOutputAnnotationCol
  102. def setParent(parent: Estimator[DrugNormalizer]): DrugNormalizer

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    Definition Classes
    Model
  103. def setPolicy(value: String): DrugNormalizer.this.type

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    Removal policy to apply.

    Removal policy to apply. Valid policy values are: "all", "abbreviations", "dosages"

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

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    Definition Classes
    AnyRef
  105. def toString(): String

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    Definition Classes
    Identifiable → AnyRef → Any
  106. final def transform(dataset: Dataset[_]): DataFrame

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    Definition Classes
    AnnotatorModel → Transformer
  107. def transform(dataset: Dataset[_], paramMap: ParamMap): DataFrame

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    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" )
  108. def transform(dataset: Dataset[_], firstParamPair: ParamPair[_], otherParamPairs: ParamPair[_]*): DataFrame

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    Definition Classes
    Transformer
    Annotations
    @Since( "2.0.0" ) @varargs()
  109. final def transformSchema(schema: StructType): StructType

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    Definition Classes
    RawAnnotator → PipelineStage
  110. def transformSchema(schema: StructType, logging: Boolean): StructType

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    Attributes
    protected
    Definition Classes
    PipelineStage
    Annotations
    @DeveloperApi()
  111. val uid: String

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    required uid for storing annotator to disk

    required uid for storing annotator to disk

    Definition Classes
    DrugNormalizer → Identifiable
  112. def validate(schema: StructType): Boolean

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    Attributes
    protected
    Definition Classes
    RawAnnotator
  113. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  114. final def wait(arg0: Long, arg1: Int): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  115. final def wait(arg0: Long): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  116. def wrapColumnMetadata(col: Column): Column

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    Attributes
    protected
    Definition Classes
    RawAnnotator
  117. def write: MLWriter

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    Definition Classes
    ParamsAndFeaturesWritable → DefaultParamsWritable → MLWritable

Inherited from AnnotatorModel[DrugNormalizer]

Inherited from CanBeLazy

Inherited from RawAnnotator[DrugNormalizer]

Inherited from HasOutputAnnotationCol

Inherited from HasInputAnnotationCols

Inherited from HasOutputAnnotatorType

Inherited from ParamsAndFeaturesWritable

Inherited from HasFeatures

Inherited from DefaultParamsWritable

Inherited from MLWritable

Inherited from Model[DrugNormalizer]

Inherited from Transformer

Inherited from PipelineStage

Inherited from Logging

Inherited from Params

Inherited from Serializable

Inherited from Serializable

Inherited from Identifiable

Inherited from AnyRef

Inherited from Any

Parameters

A list of (hyper-)parameter keys this annotator can take. Users can set and get the parameter values through setters and getters, respectively.

Parameters

Annotator types

Required input and expected output annotator types

Members

Parameter setters

Parameter getters