c

com.fulcrumgenomics.util

DnaFoldPredictor

class DnaFoldPredictor extends AnyRef

Class that wraps ViennaRNAs RNAFold utility which can be used to estimate the minimum free energy secondary structure of DNA and RNA molecules. When constructed a background process is started running RNAFold, calls to predict() then pipe input and output through RNAFold.

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Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
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Instance Constructors

  1. new DnaFoldPredictor(viennaRnaInstallDir: File, tm: Double)

Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to any2stringadd[DnaFoldPredictor] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (DnaFoldPredictor, B)
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to ArrowAssoc[DnaFoldPredictor] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
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  6. final def asInstanceOf[T0]: T0
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  7. def clone(): AnyRef
    Attributes
    protected[java.lang]
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    @throws( ... )
  8. def close(): Unit

    Kills the underlying process and makes future calls to predict() invalid.

  9. def ensuring(cond: (DnaFoldPredictor) ⇒ Boolean, msg: ⇒ Any): DnaFoldPredictor
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to Ensuring[DnaFoldPredictor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: (DnaFoldPredictor) ⇒ Boolean): DnaFoldPredictor
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to Ensuring[DnaFoldPredictor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean, msg: ⇒ Any): DnaFoldPredictor
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to Ensuring[DnaFoldPredictor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: Boolean): DnaFoldPredictor
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to Ensuring[DnaFoldPredictor] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  14. def equals(arg0: Any): Boolean
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  15. def finalize(): Unit
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    protected[java.lang]
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    @throws( classOf[java.lang.Throwable] )
  16. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to StringFormat[DnaFoldPredictor] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  17. final def getClass(): Class[_]
    Definition Classes
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  18. def hashCode(): Int
    Definition Classes
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  19. final def isInstanceOf[T0]: Boolean
    Definition Classes
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  20. final def ne(arg0: AnyRef): Boolean
    Definition Classes
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  21. final def notify(): Unit
    Definition Classes
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  22. final def notifyAll(): Unit
    Definition Classes
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  23. def predict(sequence: String): DnaFoldPrediction

    Creates the secondary structure prediction for the input sequence.

  24. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  25. def toString(): String
    Definition Classes
    AnyRef → Any
  26. final def wait(): Unit
    Definition Classes
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    @throws( ... )
  27. final def wait(arg0: Long, arg1: Int): Unit
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    @throws( ... )
  28. final def wait(arg0: Long): Unit
    Definition Classes
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    @throws( ... )
  29. def →[B](y: B): (DnaFoldPredictor, B)
    Implicit
    This member is added by an implicit conversion from DnaFoldPredictor to ArrowAssoc[DnaFoldPredictor] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from DnaFoldPredictor to any2stringadd[DnaFoldPredictor]

Inherited by implicit conversion StringFormat from DnaFoldPredictor to StringFormat[DnaFoldPredictor]

Inherited by implicit conversion Ensuring from DnaFoldPredictor to Ensuring[DnaFoldPredictor]

Inherited by implicit conversion ArrowAssoc from DnaFoldPredictor to ArrowAssoc[DnaFoldPredictor]

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