replace functional for loop in smith waterman with simpler while loop…

… to improve performance

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWaterman.scala

@@ -48,38 +48,23 @@ abstract class SmithWaterman(xSequence: String, ySequence: String) extends Seria
  * @return Tuple of (i, j) coordinates.
  */
  private[smithwaterman] final def maxCoordinates(matrix: Array[Array[Double]]): (Int, Int) = {
- def maxInCol(col: Array[Double]): (Double, Int) = {
- def takeMax(a: (Double, Int), b: (Double, Int)): (Double, Int) = {
- if (a._1 > b._1) {
- a
- } else {
- b
- }
- }
-
- val c: Array[(Double, Int)] = col.zipWithIndex
-
- c.reduce(takeMax)
- }
-
- def maxCol(cols: Array[(Double, Int)]): (Int, Int) = {
- def takeMax(a: (Double, Int, Int), b: (Double, Int, Int)): (Double, Int, Int) = {
- if (a._1 > b._1) {
- a
- } else {
- b
+ var xMax = 0
+ var yMax = 0
+ var max = Double.MinValue
+ var x = 0
+ while (x < matrix.length) {
+ var y = 0
+ while (y < matrix(x).length) {
+ if (matrix(x)(y) >= max) {
+ max = matrix(x)(y)
+ xMax = x
+ yMax = y
  }
+ y += 1
  }
-
- val c: Array[((Double, Int), Int)] = cols.zipWithIndex
-
- val m: (Double, Int, Int) = c.map(kv => (kv._1._1, kv._1._2, kv._2))
- .reduce(takeMax)
-
- (m._2, m._3)
+ x += 1
  }
-
- maxCol(matrix.map(maxInCol))
+ (yMax, xMax)
  }
 
  /**

adam-core/src/main/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanGapScoringFromFn.scala

@@ -46,8 +46,10 @@ abstract class SmithWatermanGapScoringFromFn(
  }
 
  // score matrix
- for (i <- 1 to x) {
- for (j <- 1 to y) {
+ var i = 1
+ while (i <= x) {
+ var j = 1
+ while (j <= y) {
  val m = scoreMatrix(i - 1)(j - 1) + scoreFn(i, j, xSequence(i - 1), ySequence(j - 1))
  val d = scoreMatrix(i - 1)(j) + scoreFn(i, j, xSequence(i - 1), '_')
  val in = scoreMatrix(i)(j - 1) + scoreFn(i, j, '_', ySequence(j - 1))
@@ -64,7 +66,9 @@ abstract class SmithWatermanGapScoringFromFn(
 
  scoreMatrix(i)(j) = scoreUpdate
  moveMatrix(i)(j) = moveUpdate
+ j += 1
  }
+ i += 1
  }
 
  (scoreMatrix, moveMatrix)

adam-core/src/test/scala/org/bdgenomics/adam/algorithms/smithwaterman/SmithWatermanSuite.scala

@@ -19,6 +19,7 @@ package org.bdgenomics.adam.algorithms.smithwaterman
 
 import org.scalatest.FunSuite
 import scala.math.abs
+import scala.util.Random
 
 class SmithWatermanSuite extends FunSuite {
 
@@ -237,4 +238,13 @@ class SmithWatermanSuite extends FunSuite {
  assert(sw.xStart === 8)
  }
 
+ test("smithWaterman - simple alignment") {
+ val sw = new SmithWatermanConstantGapScoring("AAA",
+ "AAT",
+ 1.0, 0.0, -0.333, -0.333)
+ assert(sw.cigarX.toString === "3M")
+ assert(sw.cigarY.toString === "3M")
+ assert(sw.xStart === 0)
+ }
+
 }