Merge a9ff433 into 5ae7cb0

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ASCIITable.scala

@@ -27,6 +27,7 @@ import org.bdgenomics.utils.instrumentation.Alignment.Alignment
  *
  * There must be an equal number of items in each row and in the header.
  */
+@deprecated("to be removed in version 0.3.0")
 class ASCIITable(header: Array[ASCIITableHeader], rows: Array[Array[String]]) {
 
   rows.foreach(row => {
@@ -99,4 +100,5 @@ class ASCIITable(header: Array[ASCIITableHeader], rows: Array[Array[String]]) {
 
 }
 
+@deprecated("to be removed in version 0.3.0")
 case class ASCIITableHeader(name: String, alignment: Alignment = Alignment.Right)

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/Alignment.scala

@@ -20,6 +20,7 @@ package org.bdgenomics.utils.instrumentation
 /**
  * Represents alignment of a cell in a table
  */
+@deprecated("to be removed in version 0.3.0")
 object Alignment extends Enumeration {
   type Alignment = Value
   val Left, Right, Center = Value

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/DurationFormatting.scala

@@ -27,6 +27,7 @@ import scala.concurrent.duration.Duration
  * - 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.
  */
+@deprecated("to be removed in version 0.3.0")
 object DurationFormatting {
 
   private val TwoDigitNumberFormatter = new DecimalFormat(".0#")

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/InstrumentationFunctions.scala

@@ -23,6 +23,7 @@ import java.io.PrintWriter
 /**
  * Helper functions for instrumentation
  */
+@deprecated("to be removed in version 0.3.0")
 object InstrumentationFunctions {
 
   def renderTable(name: String, timers: Seq[Monitor[_]], header: Seq[TableHeader]): String = {

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/Metrics.scala

@@ -51,6 +51,7 @@ import scala.util.DynamicVariable
  *
  * To switch-on recording of metrics for a specific thread, the companion [[Metrics]] object must be used.
  */
+@deprecated("to be removed in version 0.3.0")
 abstract class Metrics(val clock: Clock = new Clock()) extends Serializable {
   /**
    * Creates a timer with the specified name.
@@ -72,6 +73,7 @@ abstract class Metrics(val clock: Clock = new Clock()) extends Serializable {
  * 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.
  */
+@deprecated("to be removed in version 0.3.0")
 object Metrics {
 
   private implicit val accumulableParam = new ServoTimersAccumulableParam()
@@ -341,6 +343,7 @@ object Metrics {
 
 }
 
+@deprecated("to be removed in version 0.3.0")
 class Clock extends Serializable {
   def nanoTime() = System.nanoTime()
 }

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/MetricsListener.scala

@@ -31,6 +31,7 @@ import scala.concurrent.duration._
  * @note This class relies on being run in the same process as the driver. However,
  * this is the way that Spark seems to work.
  */
+@deprecated("to be removed in version 0.3.0")
 class MetricsListener(val metrics: RecordedMetrics) extends SparkListener {
 
   private val sparkMetrics = metrics.sparkMetrics

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/MetricsRecorder.scala

@@ -29,6 +29,7 @@ import scala.collection.mutable
  * 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!
  */
+@deprecated("to be removed in version 0.3.0")
 class MetricsRecorder(val accumulable: Accumulable[ServoTimers, RecordedTiming],
                       existingTimings: Option[Seq[TimingPath]] = None) extends Serializable {
 

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/MonitorTable.scala

@@ -34,6 +34,7 @@ import scala.collection.mutable.ArrayBuffer
  * - 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
  */
+@deprecated("to be removed in version 0.3.0")
 class MonitorTable(headerRow: Array[TableHeader], rows: Array[Monitor[_]]) {
 
   override def toString: String = {
@@ -65,9 +66,11 @@ class MonitorTable(headerRow: Array[TableHeader], rows: Array[Monitor[_]]) {
 /**
  * Specifies the title of a column, as well as how data is extracted to form the cells of this column
  */
+@deprecated("to be removed in version 0.3.0")
 case class TableHeader(name: String, valueExtractor: ValueExtractor, formatFunction: Option[(Any) => String] = None,
                        alignment: Alignment.Alignment = Alignment.Right)
 
+@deprecated("to be removed in version 0.3.0")
 object ValueExtractor {
   /**
    * Creates a [[ValueExtractor]] which extracts values from [[Monitor]]s matching the specified tag.
@@ -93,6 +96,7 @@ object ValueExtractor {
   }
 }
 
+@deprecated("to be removed in version 0.3.0")
 trait ValueExtractor {
   def extractValue(monitor: Monitor[_]): Option[Any]
 }

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/RecordedMetrics.scala

@@ -20,6 +20,7 @@ package org.bdgenomics.utils.instrumentation
 /**
  * Currently this consists only of metrics collected from Spark, but there may be others in the future.
  */
+@deprecated("to be removed in version 0.3.0")
 class RecordedMetrics {
 
   val sparkMetrics = new RecordedSparkMetrics()

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimer.scala

@@ -41,6 +41,7 @@ import scala.collection.mutable
  * @param name the name of this timer; this is propagated to sub-monitors
  * @param tags the tags for this timer; these are propagated to sub-monitors
  */
+@deprecated("to be removed in version 0.3.0")
 class ServoTimer(name: String, @transient tags: Tag*) extends ConfigurableMonitor(name, tags)
     with CompositeMonitor[Object] {
 
@@ -216,6 +217,7 @@ class ServoTimer(name: String, @transient tags: Tag*) extends ConfigurableMonito
   }
 }
 
+@deprecated("to be removed in version 0.3.0")
 abstract class ConfigurableMonitor(val name: String, @transient tags: Seq[Tag])
     extends Taggable with Serializable {
 
@@ -255,6 +257,7 @@ abstract class ConfigurableMonitor(val name: String, @transient tags: Seq[Tag])
 
 private class SerializableTag(val key: String, val value: String) extends Serializable
 
+@deprecated("to be removed in version 0.3.0")
 object ServoTimer {
 
   private final val StatisticTagKey = "statistic"
@@ -276,6 +279,7 @@ object ServoTimer {
 
 }
 
+@deprecated("to be removed in version 0.3.0")
 trait Taggable {
   def addTag(tag: Tag)
 }

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/ServoTimersAccumulableParam.scala

@@ -25,6 +25,7 @@ import scala.collection.mutable
 /**
  * Implementation of [[AccumulableParam]] that records timings and returns a [[ServoTimers]] with the accumulated timings.
  */
+@deprecated("to be removed in version 0.3.0")
 class ServoTimersAccumulableParam extends AccumulableParam[ServoTimers, RecordedTiming] {
   override def addAccumulator(timers: ServoTimers, newTiming: RecordedTiming): ServoTimers = {
     timers.recordTiming(newTiming)
@@ -46,6 +47,7 @@ class ServoTimersAccumulableParam extends AccumulableParam[ServoTimers, Recorded
  * 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.
  */
+@deprecated("to be removed in version 0.3.0")
 class ServoTimers extends Serializable {
 
   val timerMap = new ConcurrentHashMap[TimingPath, ServoTimer]()
@@ -85,11 +87,13 @@ class ServoTimers extends Serializable {
 /**
  * Specifies a timing that is to recorded
  */
+@deprecated("to be removed in version 0.3.0")
 case class RecordedTiming(timingNanos: Long, pathToRoot: TimingPath) extends Serializable
 
 /**
  * Specifies a timer name, along with all of its ancestors.
  */
+@deprecated("to be removed in version 0.3.0")
 class TimingPath(val timerName: String, val parentPath: Option[TimingPath], val sequenceId: Int = 0,
                  val isRDDOperation: Boolean = false, val shouldRecord: Boolean = true) extends Serializable {
 
@@ -164,6 +168,7 @@ class TimingPath(val timerName: String, val parentPath: Option[TimingPath], val
 
 }
 
+@deprecated("to be removed in version 0.3.0")
 class TimingPathKey(val timerName: String, val sequenceId: Int,
                     val isRDDOperation: Boolean, val shouldRecord: Boolean = true) {
   private val cachedHashCode = computeHashCode()

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/SparkMetrics.scala

@@ -31,6 +31,7 @@ import scala.concurrent.duration._
 /**
  * Allows metrics for Spark to be captured and rendered in tabular form.
  */
+@deprecated("to be removed in version 0.3.0")
 abstract class SparkMetrics {
 
   private val taskTimers = new mutable.ArrayBuffer[TaskTimer]()
@@ -131,12 +132,14 @@ abstract class SparkMetrics {
 
 }
 
+@deprecated("to be removed in version 0.3.0")
 protected object SparkMetrics {
   final val HostTagKey = "host"
   final val StageNameTagKey = "stageName"
   final val StageIdTagKey = "stageId"
 }
 
+@deprecated("to be removed in version 0.3.0")
 class TaskTimer(name: String) {
   val overallTimings = buildTimer(name)
   val timingsByHost = new mutable.HashMap[String, ServoTimer]
@@ -168,6 +171,8 @@ class TaskTimer(name: String) {
   }
 }
 
+@deprecated("to be removed in version 0.3.0")
 case class SparkTaskContext(executorId: String, stageId: Int)
 
+@deprecated("to be removed in version 0.3.0")
 case class StageTiming(stageId: Int, stageName: Option[String], duration: Duration)

utils-metrics/src/main/scala/org/bdgenomics/utils/instrumentation/package.scala

@@ -0,0 +1,23 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.utils
+
+/**
+ * Deprecated in version 0.2.16, will be removed in version 0.3.0.
+ */
+package object instrumentation {}

utils-metrics/src/main/scala/org/bdgenomics/utils/metrics/Collection.scala

@@ -17,6 +17,7 @@
  */
 package org.bdgenomics.utils.metrics
 
+@deprecated("to be removed in version 0.3.0")
 class Collection[T](val values: Seq[T]) extends Serializable {
 }
 

utils-metrics/src/main/scala/org/bdgenomics/utils/metrics/Histogram.scala

@@ -20,6 +20,7 @@ package org.bdgenomics.utils.metrics
 import java.io.{ StringWriter, Writer }
 import org.bdgenomics.utils.metrics.aggregators.Aggregated
 
+@deprecated("to be removed in version 0.3.0")
 class Histogram[T](val valueToCount: Map[T, Int]) extends Aggregated[T] with Serializable {
 
   /**
@@ -82,6 +83,7 @@ class Histogram[T](val valueToCount: Map[T, Int]) extends Aggregated[T] with Ser
   }
 }
 
+@deprecated("to be removed in version 0.3.0")
 object Histogram {
 
   def apply[T](valueToCount: Map[T, Int]): Histogram[T] =

utils-metrics/src/main/scala/org/bdgenomics/utils/metrics/aggregators/Aggregator.scala

@@ -20,6 +20,7 @@ package org.bdgenomics.utils.metrics.aggregators
 import java.io.Writer
 import org.bdgenomics.utils.metrics.{ Collection, Histogram }
 
+@deprecated("to be removed in version 0.3.0")
 trait Aggregator[SingleType, AggType <: Aggregated[SingleType]] extends Serializable {
 
   /**
@@ -46,15 +47,18 @@ trait Aggregator[SingleType, AggType <: Aggregated[SingleType]] extends Serializ
 
 }
 
+@deprecated("to be removed in version 0.3.0")
 trait Writable {
   def write(stream: Writer)
 }
 
+@deprecated("to be removed in version 0.3.0")
 trait Aggregated[+T] extends Writable with Serializable {
   def count(): Long
   def countIdentical(): Long
 }
 
+@deprecated("to be removed in version 0.3.0")
 class AggregatedCollection[T, U <: Aggregated[T]](val values: Seq[U])
     extends Aggregated[Collection[Seq[T]]]
     with Serializable {
@@ -68,10 +72,12 @@ class AggregatedCollection[T, U <: Aggregated[T]](val values: Seq[U])
   }
 }
 
+@deprecated("to be removed in version 0.3.0")
 object AggregatedCollection {
   def apply[T, U <: Aggregated[T]](values: Seq[U]) = new AggregatedCollection[T, U](values)
 }
 
+@deprecated("to be removed in version 0.3.0")
 class CombinedAggregator[Single, Agg <: Aggregated[Single]](aggs: Seq[Aggregator[Single, Agg]])
     extends Aggregator[Collection[Seq[Single]], AggregatedCollection[Single, Agg]] {
 
@@ -96,6 +102,7 @@ class CombinedAggregator[Single, Agg <: Aggregated[Single]](aggs: Seq[Aggregator
     })
 }
 
+@deprecated("to be removed in version 0.3.0")
 class UniqueAggregator[T] extends Aggregator[T, UniqueWritable[T]] {
   /**
    * An initial value for the aggregation
@@ -110,6 +117,7 @@ class UniqueAggregator[T] extends Aggregator[T, UniqueWritable[T]] {
   def combine(first: UniqueWritable[T], second: UniqueWritable[T]): UniqueWritable[T] = first.union(second)
 }
 
+@deprecated("to be removed in version 0.3.0")
 class HistogramAggregator[T] extends Aggregator[T, Histogram[T]] {
   /**
    * An initial value for the aggregation
@@ -125,6 +133,7 @@ class HistogramAggregator[T] extends Aggregator[T, Histogram[T]] {
 
 }
 
+@deprecated("to be removed in version 0.3.0")
 class UniqueWritable[T](vals: T*) extends Aggregated[T] with Serializable {
 
   val count = vals.size.toLong

utils-metrics/src/main/scala/org/bdgenomics/utils/metrics/aggregators/package.scala

@@ -0,0 +1,23 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.utils.metrics
+
+/**
+ * Deprecated in version 0.2.16, will be removed in version 0.3.0.
+ */
+package object aggregators {}

utils-metrics/src/main/scala/org/bdgenomics/utils/metrics/package.scala

@@ -0,0 +1,23 @@
+/**
+ * Licensed to Big Data Genomics (BDG) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The BDG licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.bdgenomics.utils
+
+/**
+ * Deprecated in version 0.2.16, will be removed in version 0.3.0.
+ */
+package object metrics {}