Object

org.clulab.reach.grounding

EntityChecker

Related Doc: package grounding

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object EntityChecker extends App with LazyLogging

Program to lookup/check incoming BioPax model entities against local knowledge bases. Author: by Tom Hicks. 5/14/2015. Last Modified: Update for Bioentities KBs.

Linear Supertypes
LazyLogging, App, DelayedInit, AnyRef, Any
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Inherited
  1. EntityChecker
  2. LazyLogging
  3. App
  4. DelayedInit
  5. AnyRef
  6. Any
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Visibility
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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 ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any
  4. def args: Array[String]

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    Attributes
    protected
    Definition Classes
    App
    Annotations
    @deprecatedOverriding( "args should not be overridden" , "2.11.0" )
  5. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any
  6. val cellLocationSearcher: Seq[IMKBLookup]

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    Search sequence for sub cellular locations terms.

    Search sequence for sub cellular locations terms.

    Attributes
    protected
  7. val chemSearcher: Seq[IMKBLookup]

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    Search sequence for small molecules.

    Search sequence for small molecules.

    Attributes
    protected
  8. def clone(): AnyRef

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  9. val diseaseSearcher: Seq[IMKBLookup]

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    Search sequence for disease terms.

    Search sequence for disease terms.

    Attributes
    protected
  10. final def eq(arg0: AnyRef): Boolean

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

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    Definition Classes
    AnyRef → Any
  12. val executionStart: Long

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    Definition Classes
    App
  13. val filepath: String

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  14. def finalize(): Unit

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    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  15. val fis: FileInputStream

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

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    Definition Classes
    AnyRef → Any
  17. def hashCode(): Int

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    Definition Classes
    AnyRef → Any
  18. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any
  19. lazy val logger: Logger

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    Attributes
    protected
    Definition Classes
    LazyLogging
  20. def main(args: Array[String]): Unit

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    Definition Classes
    App
    Annotations
    @deprecatedOverriding( "main should not be overridden" , "2.11.0" )
  21. final def ne(arg0: AnyRef): Boolean

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

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

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    Definition Classes
    AnyRef
  24. val proteinSearcher: Seq[IMKBLookup]

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    Search sequence for resolving proteins.

    Search sequence for resolving proteins.

    Attributes
    protected
  25. def readAndCheckBioPax(fis: InputStream): Unit

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    Read the BioPAX model from the given input stream and check the entities.

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

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    Definition Classes
    AnyRef
  27. def toString(): String

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    Definition Classes
    AnyRef → Any
  28. final def wait(): Unit

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

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def delayedInit(body: ⇒ Unit): Unit

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    Definition Classes
    App → DelayedInit
    Annotations
    @deprecated
    Deprecated

    (Since version 2.11.0) The delayedInit mechanism will disappear.

Inherited from LazyLogging

Inherited from App

Inherited from DelayedInit

Inherited from AnyRef

Inherited from Any

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