Package

org.bdgenomics.utils

instrumentation

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package instrumentation

Deprecated in version 0.2.16, will be removed in version 0.3.0.

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Type Members

  1. class ASCIITable extends AnyRef

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    Renders a table using ASCII characters.

    Renders a table using ASCII characters. The table is represented by a header row, consisting of ASCIITableHeader objects which define the column label and the column alignment, and multiple rows, each of which contains an array of values to go in each row.

    There must be an equal number of items in each row and in the header.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  2. case class ASCIITableHeader(name: String, alignment: Alignment = Alignment.Right) extends Product with Serializable

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  3. class Clock extends Serializable

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  4. abstract class ConfigurableMonitor extends Taggable with Serializable

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  5. abstract class Metrics extends Serializable

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    Allows metrics to be created for an application.

    Allows metrics to be created for an application. Currently only timers are supported, but other types of metrics may be supported in the future.

    Classes should extend this class to provide collections of metrics for an application. For example, typical usage might be:

    object Timers extends Metrics {
      val Operation1 = timer("Operation 1")
      val Operation2 = timer("Operation 2")
    }

    This creates two timers: one for Operation 1, and one for Operation 2.

    To switch-on recording of metrics for a specific thread, the companion Metrics object must be used.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  6. class MetricsListener extends SparkListener

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    Spark listener that accumulates metrics in the passed-in RecordedMetrics object at stage completion time.

    Spark listener that accumulates metrics in the passed-in RecordedMetrics object at stage completion time.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

    Note

    This class relies on being run in the same process as the driver. However, this is the way that Spark seems to work.

  7. class MetricsRecorder extends Serializable

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    Allows metrics to be recorded.

    Allows metrics to be recorded. Currently only timings are supported, but other metrics may be supported in the future. Use the startPhase method to start recording a timing and the finishPhase method to finish recording it. If timings are nested the hierarchy is preserved.

    Note: this class is intended to be used in a thread-local context, and therefore it is not thread-safe. Do not attempt to call it concurrently from multiple threads!

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  8. class MonitorTable extends AnyRef

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    Tabular representation of a set of Monitors.

    Tabular representation of a set of Monitors. A MonitorTable consists of a list of TableHeaders, which specify not only the titles of the columns, but also how the data is extracted from the rows, as well as a list of rows which are Monitors containing the data. Each header can specify the following:

    - name: the name of the column; this will be the text that is used in the header row - valueExtractor: specifies how data will be extracted from a monitor; the functions in the ValueExtractor object can be used to create ValueExtractors for a particular purpose - formatFunction (optional): a function which formats the value extracted from the monitor as a String - alignment (optional): specifies how the data in a cell is aligned; defaults to right-alignment

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  9. class RecordedMetrics extends AnyRef

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    Currently this consists only of metrics collected from Spark, but there may be others in the future.

    Currently this consists only of metrics collected from Spark, but there may be others in the future.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  10. case class RecordedTiming(timingNanos: Long, pathToRoot: TimingPath) extends Serializable with Product

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    Specifies a timing that is to recorded

    Specifies a timing that is to recorded

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  11. class ServoTimer extends ConfigurableMonitor with CompositeMonitor[AnyRef]

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    Timer that implements the com.netflix.servo.monitor.CompositeMonitor interface.

    Timer that implements the com.netflix.servo.monitor.CompositeMonitor interface. Sub-monitors contain specific metrics, and can be identified using the following tags: - Total Time: ServoTimer.TotalTimeTag - Count: ServoTimer.CountTag - Mean: ServoTimer.MeanTag - Max: ServoTimer.MaxTag - Min: ServoTimer.MinTag All timings are returned in nanoseconds.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  12. class ServoTimers extends Serializable

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    Holds a collection of ServoTimers.

    Holds a collection of ServoTimers. Each instance of a timer is stored against a TimingPath, which specifies all of its ancestors. Timings can be recorded using the recordTiming method, which will either update an existing timer if the specified TimingPath exists already, or will create a new timer.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  13. class ServoTimersAccumulableParam extends AccumulableParam[ServoTimers, RecordedTiming]

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    Implementation of AccumulableParam that records timings and returns a ServoTimers with the accumulated timings.

    Implementation of AccumulableParam that records timings and returns a ServoTimers with the accumulated timings.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  14. abstract class SparkMetrics extends AnyRef

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    Allows metrics for Spark to be captured and rendered in tabular form.

    Allows metrics for Spark to be captured and rendered in tabular form.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  15. case class SparkTaskContext(executorId: String, stageId: Int) extends Product with Serializable

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  16. case class StageTiming(stageId: Int, stageName: Option[String], duration: Duration) extends Product with Serializable

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  17. case class TableHeader(name: String, valueExtractor: ValueExtractor, formatFunction: Option[(Any) ⇒ String] = None, alignment: Alignment = Alignment.Right) extends Product with Serializable

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    Specifies the title of a column, as well as how data is extracted to form the cells of this column

    Specifies the title of a column, as well as how data is extracted to form the cells of this column

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  18. trait Taggable extends AnyRef

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  19. class TaskTimer extends AnyRef

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  20. class TimingPath extends Serializable

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    Specifies a timer name, along with all of its ancestors.

    Specifies a timer name, along with all of its ancestors.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  21. class TimingPathKey extends AnyRef

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  22. trait ValueExtractor extends AnyRef

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

Deprecated Value Members

  1. object Alignment extends Enumeration

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    Represents alignment of a cell in a table

    Represents alignment of a cell in a table

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  2. object DurationFormatting

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    Functions for formatting durations.

    Functions for formatting durations. The following rules are applied: - Durations greater than one hour are formatted as "X hours X mins X secs" - Durations greater than one minute, but less than one hour are formatted as "X mins X secs" - Durations less than one minute are formatted with two digits after the decimal point. Zeros are suppressed.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  3. object InstrumentationFunctions

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    Helper functions for instrumentation

    Helper functions for instrumentation

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  4. object Metrics extends Serializable

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    Manages recording of metrics in an application.

    Manages recording of metrics in an application. Metrics collection is turned on for a particular thread by calling the initialize method. After initialize is called the Metrics.Recorder field is set, and the application can use that to record metrics. To print metrics, call the print method, and to stop recording metrics for a particular thread, call the stopRecording method.

    If an application does not want to record metrics, it can simply avoid calling the initialize method (or can call the stopRecording method if there is a chance that initialize has been called on that thread previously). Attempting to record metrics when the initialize method has not been called will not produce an error, and incurs very little overhead. However, attempting to call the print method to print the metrics will produce an error.

    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  5. object ServoTimer extends Serializable

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  6. object SparkMetrics

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    Attributes
    protected
    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

  7. object ValueExtractor

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    Annotations
    @deprecated
    Deprecated

    to be removed in version 0.3.0

Inherited from AnyRef

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