au.csiro.variantspark.data.Feature.scala Maven / Gradle / Ivy

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Genomic variants interpretation toolkit

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package au.csiro.variantspark.data

import org.apache.spark.mllib.linalg.{Vector, Vectors}
import org.apache.spark.rdd.RDD

/**
  * TODO: Rethingk this inheritance
  */
trait Feature extends Data {
  def label: String
  def variableType: VariableType
  def data: Data
  def at(i: Int): Double = data.at(i)
  def size: Int = data.size
  def value: Any = data.value
  def valueAsByteArray: Array[Byte] = data.valueAsByteArray
  def valueAsIntArray: Array[Int] = data.valueAsIntArray
  def valueAsVector: Vector = data.valueAsVector
  def valueAsStrings: List[String] = data.valueAsStrings
}

case class StdFeature(label: String, variableType: VariableType, data: Data) extends Feature

object StdFeature {
  def from[V](label: String, variableType: VariableType, v: V)(
      implicit db: DataBuilder[V]): Feature = {
    StdFeature(label, variableType, db.from(v))
  }
  def from[V](label: String, v: V)(implicit db: DataBuilder[V]): Feature =
    from(label, db.defaultVariableType, v)
  def from[V](label: String, variableType: VariableType, v: List[String])(
      implicit db: DataBuilder[V]): Feature = StdFeature(label, variableType, db.from(v))
}

trait FeatureBuilder {
  def from(label: String, variableType: VariableType, l: List[String]): Feature
}

class ToFeature[V](val v: RDD[V]) extends AnyVal {
  def asFeature(variableType: VariableType)(implicit db: DataBuilder[V]): RDD[(Feature, Long)] = {
    v.map(v => StdFeature.from(null, variableType, v)).zipWithIndex
  }
}