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Improve alignment scores #1701

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merged 2 commits into from
Mar 7, 2024
Merged

Improve alignment scores #1701

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d1c41ec
improve alignment score
robinschmid Mar 6, 2024
b8a7b05
more precise alignment score tests
robinschmid Mar 7, 2024
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24 changes: 12 additions & 12 deletions mzmine-community/src/main/java/io/github/mzmine/util/FeatureListUtils.java
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Original file line number Diff line number Diff line change
Expand Up @@ -385,45 +385,45 @@ public static double getAlignmentScore(Double testMz, Float testRt, Float testMo
mobilityRange == null || mobilityRange.equals(Range.all()) ? null : mobilityRange;
ccsRange = ccsRange == null || ccsRange.equals(Range.all()) ? null : ccsRange;

int scorers = 0;
double totalWeight = 0;

double score = 0f;
double score = 0;
// values are "matched" if the given value exists in this class and falls within the tolerance.
if (mzWeight > 0 && mzRange != null && testMz != null) {
final double exactMass = RangeUtils.rangeCenter(mzRange);
double diff = Math.abs(testMz - exactMass);
double maxAllowedDiff = rangeLength(mzRange) / 2;
// no negative numbers
score += Math.max(0, (1 - diff / maxAllowedDiff) * mzWeight);
scorers += (int) Math.round(mzWeight);
score += Math.max(0, (1 - diff / maxAllowedDiff)) * mzWeight;
totalWeight += mzWeight;
}

if (rtWeight > 0 && rtRange != null && testRt != null) {
final Float rt = RangeUtils.rangeCenter(rtRange);
float diff = Math.abs(testRt - rt);
score += Math.max(0, 1 - (diff / (rangeLength(rtRange) / 2)) * rtWeight);
scorers += (int) Math.round(rtWeight);
score += Math.max(0, 1 - (diff / (rangeLength(rtRange) / 2))) * rtWeight;
totalWeight += rtWeight;
}

if (mobilityWeight > 0 && mobilityRange != null && testMobility != null) {
final Float mobility = RangeUtils.rangeCenter(mobilityRange);
float diff = Math.abs(testMobility - mobility);
score += Math.max(0, 1 - (diff / (rangeLength(mobilityRange) / 2)) * mobilityWeight);
scorers += (int) Math.round(mobilityWeight);
score += Math.max(0, 1 - (diff / (rangeLength(mobilityRange) / 2))) * mobilityWeight;
totalWeight += mobilityWeight;
}

if (ccsWeight > 0 && ccsRange != null && testCCS != null) {
final Float ccs = RangeUtils.rangeCenter(ccsRange);
float diff = Math.abs(testCCS - ccs);
score += Math.max(0, 1 - (diff / (rangeLength(ccsRange) / 2)) * ccsWeight);
scorers += (int) Math.round(ccsWeight);
score += Math.max(0, 1 - (diff / (rangeLength(ccsRange) / 2))) * ccsWeight;
totalWeight += ccsWeight;
}

if (scorers == 0) {
if (totalWeight == 0) {
return 0f;
}

return score / scorers;
return score / totalWeight;
}

/**
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14 changes: 14 additions & 0 deletions mzmine-community/src/test/java/io/github/mzmine/util/FeatureListUtilsTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@
import io.github.mzmine.datamodel.features.types.numbers.RTType;
import java.util.ArrayList;
import java.util.List;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
Expand Down Expand Up @@ -115,4 +116,17 @@ void binarySearch() {
assertEquals(10f, rows.get(FeatureListUtils.binarySearch(rows, 10)).getAverageRT());
}


@Test
void getAlignmentScore() {
double score = FeatureListUtils.getAlignmentScore(200.2, 5.1f, null, null,
Range.closed(200d, 201d), Range.closed(5f, 5.5f), null, null, 3, 1, 0, 0);
Assertions.assertTrue(score > 0);
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Can you double check the expected test results?

Assertions.assertTrue(score < 1);

score = FeatureListUtils.getAlignmentScore(200.5, 5.25f, null, null,
Range.closed(200d, 201d), Range.closed(5f, 5.5f), null, null, 3, 1, 0, 0);
Assertions.assertTrue(score > 0);
Assertions.assertTrue(score < 1);
}
}
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