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Merge pull request #16 from vickumar1981/smith-waterman-score
Smith waterman score
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7 changes: 7 additions & 0 deletions
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src/main/java/com/github/vickumar1981/stringdistance/util/SmithWatermanImpl.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,7 @@ | ||
| package com.github.vickumar1981.stringdistance.util; | ||
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| import com.github.vickumar1981.stringdistance.SmithWatermanImplWrapper; | ||
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| public class SmithWatermanImpl extends SmithWatermanImplWrapper { | ||
| public SmithWatermanImpl() {} | ||
| } |
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118 changes: 118 additions & 0 deletions
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src/main/scala/com/github/vickumar1981/stringdistance/impl/SmithWatermanImpl.scala
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,118 @@ | ||
| package com.github.vickumar1981.stringdistance.impl | ||
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| import scala.math.{max, min} | ||
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| trait SmithWatermanImpl extends GapSubstitution { | ||
| def smithWaterman(s1: String, s2: String, | ||
| gap: Gap = ConstantGap(), | ||
| windowSize: Int = Integer.MAX_VALUE): Double = { | ||
| require(gap.matchValue > 0, "Smith Waterman match value must be a number > 0.") | ||
| require(gap.misMatchValue < 0, "Smith Waterman mismatch value must be a number < 0.") | ||
| require(windowSize > 0, "Smith Waterman window size must be a number > 0") | ||
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| if (s1.isEmpty || s2.isEmpty) 0d | ||
| else { | ||
| val maxDist = min(s1.length, s2.length) * max(gap.matchValue, gap.min) | ||
| val calcScore = calculateSmithWaterman(s1, s2, gap, windowSize) | ||
| 1 - ((calcScore - maxDist) / maxDist) | ||
| } | ||
| } | ||
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| def smithWatermanGotoh(s1: String, s2: String, gap: ConstantGap = ConstantGap()): Double = { | ||
| require(gap.matchValue > 0, "Smith Waterman Gotoh match value must be a number > 0.") | ||
| require(gap.misMatchValue < 0, "Smith Waterman Gotoh mismatch value must be a number < 0.") | ||
| if (s1.isEmpty || s2.isEmpty) 0d | ||
| else { | ||
| val maxDist = min(s1.length, s2.length) * max(gap.matchValue, gap.gapValue) | ||
| val calcScore = calculateSmithWatermanGotoh(s1, s2, gap) | ||
| (maxDist - calcScore) / maxDist | ||
| } | ||
| } | ||
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| // scalastyle:off | ||
| private def calculateSmithWaterman(s1: String, s2: String, gap: Gap, windowSize: Int): Double = { | ||
| val (s1Len, s2Len) = (s1.length, s2.length) | ||
| val d = Array.ofDim[Double](s1Len, s2Len) | ||
| var maxValue: Double = max(0d, subst(s1, 0, s2, 0, gap)) | ||
| d(0)(0) = maxValue | ||
| s1.indices.foreach { | ||
| i => { | ||
| // Get the optimal deletion | ||
| var maxGapCost = 0d | ||
| (max(1, i - windowSize) until i).foreach { | ||
| k => maxGapCost = max(maxGapCost, d(i - k)(0) + gap.value(i - k, i)) | ||
| } | ||
| d(i)(0) = max(max(0, maxGapCost), subst(s1, i, s2, 0, gap)) | ||
| maxValue = max(maxValue, d(i)(0)) | ||
| } | ||
| } | ||
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| (1 until s2Len).foreach { | ||
| j => { | ||
| // Get the optimal insertion | ||
| var maxGapCost = 0d | ||
| (max(1, j - windowSize) until j).foreach { | ||
| k => maxGapCost = max(maxGapCost, d(0)(j - k) + gap.value(j - k, j)) | ||
| } | ||
| d(0)(j) = max(max(0d, maxGapCost), subst(s1, 0, s2, j, gap)) | ||
| maxValue = max(maxValue, d(0)(j)) | ||
| } | ||
| } | ||
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| // Build 2-d array | ||
| (1 until s1Len).foreach { | ||
| i => { | ||
| (1 until s2Len).foreach { | ||
| j => { | ||
| var maxGapCost = 0d | ||
| (max(1, i - windowSize) until i).foreach { | ||
| k => maxGapCost = max(maxGapCost, d(i - k)(j) + gap.value(i - k, i)) | ||
| } | ||
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| (max(1, j - windowSize) until j).foreach { | ||
| k => maxGapCost = max(maxGapCost, d(i)(j - k) + gap.value(j - k, j)) | ||
| } | ||
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| d(i)(j) = max(max(0d, maxGapCost), d(i - 1)(j - 1) + subst(s1, i, s2, j, gap)) | ||
| maxValue = max(maxValue, d(i)(j)) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| maxValue | ||
| } | ||
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| // scalastyle: on | ||
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| private def calculateSmithWatermanGotoh(s1: String, s2: String, gap: ConstantGap): Double = { | ||
| val (s1Len, s2Len) = (s1.length, s2.length) | ||
| val v0 = Array.ofDim[Double](s2Len) | ||
| val v1 = Array.ofDim[Double](s2Len) | ||
| var maxValue = max(max(0, gap.gapValue), subst(s1, 0, s2, 0, gap)) | ||
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| (1 until s2Len).foreach { | ||
| j => v0(j) = max(max(0, v0(j - 1) + gap.gapValue), subst(s1, 0, s2, j, gap)) | ||
| } | ||
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| (1 until s1Len).foreach { | ||
| i => { | ||
| v1(0) = max(max(0, v0(0) + gap.gapValue), subst(s1, i, s2, 0, gap)) | ||
| maxValue = max(maxValue, v1(0)) | ||
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| (1 until s2Len).foreach { | ||
| j => { | ||
| v1(j) = max(max(0, v0(j) + gap.gapValue), v0(j - 1) + subst(s1, i, s2, j, gap)) | ||
| maxValue = max(maxValue, v1(j)) | ||
| } | ||
| } | ||
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| s2.indices.foreach { | ||
| j => v0(j) = v1(j) | ||
| } | ||
| } | ||
| } | ||
| maxValue | ||
| } | ||
| } | ||
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