c

com.fulcrumgenomics.util

ProgressLogger

class ProgressLogger extends AbstractProgressLogger

A subclass of HTSJDK's progress logger that uses fgbio's logging system.

Linear Supertypes
AbstractProgressLogger, ProgressLoggerInterface, AnyRef, Any
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Inherited
  1. ProgressLogger
  2. AbstractProgressLogger
  3. ProgressLoggerInterface
  4. AnyRef
  5. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new ProgressLogger(logger: Logger, noun: String = "record", verb: String = "processed", unit: Int = 1000 * 1000)

Abstract Value Members

  1. abstract def log(arg0: <repeated...>[String]): Unit
    Attributes
    protected[htsjdk.samtools.util]
    Definition Classes
    AbstractProgressLogger

Concrete 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 ProgressLogger to any2stringadd[ProgressLogger] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (ProgressLogger, B)
    Implicit
    This member is added by an implicit conversion from ProgressLogger to ArrowAssoc[ProgressLogger] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  7. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  8. def ensuring(cond: (ProgressLogger) ⇒ Boolean, msg: ⇒ Any): ProgressLogger
    Implicit
    This member is added by an implicit conversion from ProgressLogger to Ensuring[ProgressLogger] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  9. def ensuring(cond: (ProgressLogger) ⇒ Boolean): ProgressLogger
    Implicit
    This member is added by an implicit conversion from ProgressLogger to Ensuring[ProgressLogger] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  10. def ensuring(cond: Boolean, msg: ⇒ Any): ProgressLogger
    Implicit
    This member is added by an implicit conversion from ProgressLogger to Ensuring[ProgressLogger] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  11. def ensuring(cond: Boolean): ProgressLogger
    Implicit
    This member is added by an implicit conversion from ProgressLogger to Ensuring[ProgressLogger] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  14. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  15. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from ProgressLogger to StringFormat[ProgressLogger] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  16. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  17. def getCount(): Long
    Definition Classes
    AbstractProgressLogger
  18. def getElapsedSeconds(): Long
    Definition Classes
    AbstractProgressLogger
  19. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  20. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  21. def log(message: String*): Unit
  22. val logger: Logger
  23. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  24. final def notify(): Unit
    Definition Classes
    AnyRef
  25. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  26. def record(): Unit

    Method to use to record progress when genome location isn't available or relevant.

  27. def record(arg0: <repeated...>[SAMRecord]): Boolean
    Definition Classes
    AbstractProgressLogger → ProgressLoggerInterface
  28. def record(arg0: SAMRecord): Boolean
    Definition Classes
    AbstractProgressLogger → ProgressLoggerInterface
  29. def record(arg0: String, arg1: Int): Boolean
    Definition Classes
    AbstractProgressLogger → ProgressLoggerInterface
  30. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  31. def toString(): String
    Definition Classes
    AnyRef → Any
  32. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  33. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  34. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  35. def →[B](y: B): (ProgressLogger, B)
    Implicit
    This member is added by an implicit conversion from ProgressLogger to ArrowAssoc[ProgressLogger] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AbstractProgressLogger

Inherited from ProgressLoggerInterface

Inherited from AnyRef

Inherited from Any

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

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

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

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

Ungrouped