From 099175cae8b08919de04d7fe9a2fd531c272c73c Mon Sep 17 00:00:00 2001 From: Jules Jacobsen Date: Tue, 13 Feb 2024 10:43:31 +0000 Subject: [PATCH] Alter PathogenicityData 'get' prefixed methods to remove the 'get' e.g. getPredictedPathogenicityScores() is now pathogenicityScores(), getPredictedScore(PathogenicitySource source) -> pathogenicityScore(PathogenicitySource source), getScore() -> pathogenicityScore() --- .../util/acmg/Acmg2015EvidenceAssigner.java | 14 ++--- .../core/genome/VariantDataServiceImpl.java | 4 +- .../core/model/VariantEvaluation.java | 4 +- .../core/model/frequency/FrequencyData.java | 2 +- .../pathogenicity/PathogenicityData.java | 16 +++--- .../VariantEffectPathogenicityScore.java | 2 +- .../core/writers/TsvVariantResultsWriter.java | 6 +-- .../src/main/resources/templates/results.html | 8 +-- .../core/genome/TestVariantDataService.java | 6 +-- .../genome/VariantDataServiceImplTest.java | 2 +- .../genome/VariantFactoryPerformanceTest.java | 2 +- .../genome/dao/ClinVarDaoMvStoreTest.java | 2 +- .../genome/dao/SvPathogenicityDaoTest.java | 2 +- .../core/model/VariantEvaluationTest.java | 6 +-- .../model/frequency/FrequencyDataTest.java | 14 ++--- .../pathogenicity/PathogenicityDataTest.java | 52 +++++++++---------- .../VariantEffectPathogenicityScoreTest.java | 50 +++++++++--------- .../src/main/resources/templates/results.html | 12 ++--- 18 files changed, 102 insertions(+), 102 deletions(-) diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java index 410aae62e..95914a360 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/analysis/util/acmg/Acmg2015EvidenceAssigner.java @@ -172,7 +172,7 @@ public AcmgEvidence assignVariantAcmgEvidence(VariantEvaluation variantEvaluatio assignPP4(acmgEvidenceBuilder, compatibleDiseaseMatches); PathogenicityData pathogenicityData = variantEvaluation.getPathogenicityData(); - ClinVarData clinVarData = variantEvaluation.getPathogenicityData().getClinVarData(); + ClinVarData clinVarData = variantEvaluation.getPathogenicityData().clinVarData(); if (!clinVarData.isEmpty()) { // PP5 "Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation" assignPP5(acmgEvidenceBuilder, clinVarData); @@ -281,7 +281,7 @@ private void assignPM3orBP2(AcmgEvidence.Builder acmgEvidenceBuilder, VariantEva if (contributingVariants.size() >= 2 && contributingVariants.contains(variantEvaluation)) { for (VariantEvaluation otherVariant : contributingVariants) { SampleGenotype otherVariantGenotype = otherVariant.getSampleGenotype(probandId); - ClinVarData otherClinVarData = otherVariant.getPathogenicityData().getClinVarData(); + ClinVarData otherClinVarData = otherVariant.getPathogenicityData().clinVarData(); if (otherClinVarData.getPrimaryInterpretation() == ClinVarData.ClinSig.PATHOGENIC && !otherVariant.equals(variantEvaluation)) { // X = this variant, P = other pathogenic variant boolean inTrans = inTrans(thisVariantGenotype, otherVariantGenotype); @@ -487,7 +487,7 @@ private void assignPP3orBP4(AcmgEvidence.Builder acmgEvidenceBuilder, Pathogenic // classification and ClinGen recommendations for clinical use of PP3/BP4 criteria" // https://www.biorxiv.org/content/10.1101/2022.03.17.484479v1 // - var revelScore = pathogenicityData.getPredictedScore(PathogenicitySource.REVEL); + var revelScore = pathogenicityData.pathogenicityScore(PathogenicitySource.REVEL); if (revelScore != null) { assignRevelBasedPP3BP4Classification(acmgEvidenceBuilder, revelScore); } else { @@ -538,18 +538,18 @@ else if (revel > 0.183f && revel <= 0.290f) { private void assignEnsembleBasedPP3BP4Classification(AcmgEvidence.Builder acmgEvidenceBuilder, PathogenicityData pathogenicityData) { int numBenign = 0; int numPathogenic = 0; - List predictedPathogenicityScores = pathogenicityData.getPredictedPathogenicityScores(); - for (PathogenicityScore pathogenicityScore : predictedPathogenicityScores) { + List pathogenicityScores = pathogenicityData.pathogenicityScores(); + for (PathogenicityScore pathogenicityScore : pathogenicityScores) { if (isPathogenic(pathogenicityScore)) { numPathogenic++; } else { numBenign++; } } - if (predictedPathogenicityScores.size() > 1 && numPathogenic > numBenign) { + if (pathogenicityScores.size() > 1 && numPathogenic > numBenign) { acmgEvidenceBuilder.add(PP3); } - if (predictedPathogenicityScores.size() > 1 && numBenign > numPathogenic) { + if (pathogenicityScores.size() > 1 && numBenign > numPathogenic) { acmgEvidenceBuilder.add(BP4); } } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImpl.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImpl.java index e509996ca..d935e1fc0 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImpl.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImpl.java @@ -147,7 +147,7 @@ public PathogenicityData getVariantPathogenicityData(Variant variant, Set pathogenicityDataCompletableFuture : futurePathData) { PathogenicityData pathogenicityData = pathogenicityDataCompletableFuture.join(); - allPathScores.addAll(pathogenicityData.getPredictedPathogenicityScores()); + allPathScores.addAll(pathogenicityData.pathogenicityScores()); } defaultPathogenicityData = futureDefaultData.join(); } else { @@ -173,7 +173,7 @@ private boolean containsTabixSource(Set pathogenicitySource } private void addAllWantedScores(Set pathogenicitySources, PathogenicityData defaultPathogenicityData, List allPathScores) { - for (PathogenicityScore score : defaultPathogenicityData.getPredictedPathogenicityScores()) { + for (PathogenicityScore score : defaultPathogenicityData.pathogenicityScores()) { if (pathogenicitySources.contains(score.getSource())) { allPathScores.add(score); } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java index b2b82e94a..12e9cd8ef 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/VariantEvaluation.java @@ -379,8 +379,8 @@ public float getPathogenicityScore() { if (whiteListed) { return 1f; } - float predictedScore = pathogenicityData.getScore(); - float variantEffectScore = VariantEffectPathogenicityScore.getPathogenicityScoreOf(variantEffect); + float predictedScore = pathogenicityData.pathogenicityScore(); + float variantEffectScore = VariantEffectPathogenicityScore.pathogenicityScoreOf(variantEffect); if (this.isSymbolic()) { // SvAnna scoring https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-022-01046-6/tables/1 // | element contains v diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java index d0142b355..8b10ecc09 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyData.java @@ -155,7 +155,7 @@ public boolean containsFrequencySource(FrequencySource frequencySource) { } @Nullable - public Frequency frequencyForSource(FrequencySource source) { + public Frequency frequency(FrequencySource source) { int i = frequencySourceIndex(source); return i < 0 ? null : frequency(i); } diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityData.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityData.java index 9eb7c58dc..e7a698ccc 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityData.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityData.java @@ -98,7 +98,7 @@ private PathogenicityData(ClinVarData clinVarData, Collection getPredictedPathogenicityScores() { + public List pathogenicityScores() { return new ArrayList<>(pathogenicityScores.values()); } @@ -136,27 +136,27 @@ public boolean hasPredictedScore(PathogenicitySource pathogenicitySource) { * @param pathogenicitySource * @return */ - public PathogenicityScore getPredictedScore(PathogenicitySource pathogenicitySource) { + public PathogenicityScore pathogenicityScore(PathogenicitySource pathogenicitySource) { return pathogenicityScores.get(pathogenicitySource); } /** * @return the predicted pathogenicity score for this data set. The score is ranked from 0 (non-pathogenic) to 1 (highly pathogenic) */ - public float getScore() { + public float pathogenicityScore() { if (pathogenicityScores.isEmpty()) { return VariantEffectPathogenicityScore.NON_PATHOGENIC_SCORE; } - return getPredictedPathScore(); + return maxPredictedPathScore(); } - private float getPredictedPathScore() { + private float maxPredictedPathScore() { // Once upon a time we used score-specific cutoffs. These are present in the score classes: // Mutation Taster: >0.95 assumed pathogenic, prediction categories not shown // Polyphen2 (HVAR): "D" (> 0.956,probably damaging), "P": [0.447-0.955], possibly damaging, and "B", <0.447, benign. // SIFT: "D"<0.05, damaging and "T">0.05, tolerated // TODO: re-implement this and add isPredictedPathogenic() to the PathogenicityScore - PathogenicityScore mostPathogenicPredictedScore = getMostPathogenicScore(); + PathogenicityScore mostPathogenicPredictedScore = mostPathogenicScore(); if (mostPathogenicPredictedScore != null) { // As of v12.0.0 scores are normalised internally so SIFT scores no longer need to be inverted here. return mostPathogenicPredictedScore.getScore(); @@ -168,7 +168,7 @@ private float getPredictedPathScore() { * @return The most pathogenic score or null if there are no predicted scores */ @Nullable - public PathogenicityScore getMostPathogenicScore() { + public PathogenicityScore mostPathogenicScore() { // Add filter step using PathogenicityScore::isPredictedPathogenic? // n.b. here min() is referring to the *first* element in a sorted list, rather than the minimum numeric value // PathogenicityScore compareTo returns the most pathogenic first e.g. 1.0, 0.9, 0.8 ... which is the reverse of diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScore.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScore.java index 709c62566..5fb6020f2 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScore.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScore.java @@ -84,7 +84,7 @@ private VariantEffectPathogenicityScore() { //Uninstantiable. This class should be an enum, but then it doesn't code nicely :( } - public static float getPathogenicityScoreOf(VariantEffect variantEffect) { + public static float pathogenicityScoreOf(VariantEffect variantEffect) { switch (variantEffect) { case SEQUENCE_VARIANT: return NON_PATHOGENIC_SCORE; diff --git a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriter.java b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriter.java index 19d0bb5db..1c8e54adb 100644 --- a/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriter.java +++ b/exomiser-core/src/main/java/org/monarchinitiative/exomiser/core/writers/TsvVariantResultsWriter.java @@ -163,7 +163,7 @@ private List buildVariantRecord(int rank, VariantEvaluation ve, GeneScor fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseId()).orElse("")); fields.add(assignment.map(acmgAssignment -> acmgAssignment.disease().getDiseaseName()).orElse("")); PathogenicityData pathogenicityData = ve.getPathogenicityData(); - ClinVarData clinVarData = pathogenicityData.getClinVarData(); + ClinVarData clinVarData = pathogenicityData.clinVarData(); fields.add(clinVarData.getVariationId()); fields.add(clinVarData.getPrimaryInterpretation()); fields.add(clinVarData.starRating()); @@ -175,10 +175,10 @@ private List buildVariantRecord(int rank, VariantEvaluation ve, GeneScor fields.add(maxFreq == null ? "" : maxFreq.source()); fields.add(maxFreq == null ? "" : maxFreq.frequency()); fields.add(toVcfFreqInfo(frequencyData.frequencies())); - PathogenicityScore maxPath = pathogenicityData.getMostPathogenicScore(); + PathogenicityScore maxPath = pathogenicityData.mostPathogenicScore(); fields.add(maxPath == null ? "" : maxPath.getSource()); fields.add(maxPath == null ? "" : maxPath.getScore()); - fields.add(toVcfPathInfo(pathogenicityData.getPredictedPathogenicityScores())); + fields.add(toVcfPathInfo(pathogenicityData.pathogenicityScores())); return fields; } diff --git a/exomiser-core/src/main/resources/templates/results.html b/exomiser-core/src/main/resources/templates/results.html index 87060587b..01cdb1640 100644 --- a/exomiser-core/src/main/resources/templates/results.html +++ b/exomiser-core/src/main/resources/templates/results.html @@ -378,10 +378,10 @@

Variant Score: 1.00 -
No +
No pathogenicity data
-
Mutation Taster: 0.999 (P)
@@ -519,10 +519,10 @@

Variant Score: 1.00 -
No +
No pathogenicity data
-
Mutation Taster: 0.999 (P)
diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestVariantDataService.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestVariantDataService.java index 1db781f68..f0d42d1fb 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestVariantDataService.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/TestVariantDataService.java @@ -111,12 +111,12 @@ public FrequencyData getVariantFrequencyData(Variant variant, Set pathogenicitySources) { PathogenicityData pathData = expectedPathogenicityData.getOrDefault(variant, PathogenicityData.empty()); - List wanted = pathData.getPredictedPathogenicityScores() + List wanted = pathData.pathogenicityScores() .stream() .filter(pathogenicity -> pathogenicitySources.contains(pathogenicity.getSource())) - .collect(Collectors.toList()); + .toList(); - return PathogenicityData.of(pathData.getClinVarData(), wanted); + return PathogenicityData.of(pathData.clinVarData(), wanted); } public static Builder builder() { diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImplTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImplTest.java index be4963a58..e8ff886ca 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImplTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantDataServiceImplTest.java @@ -147,7 +147,7 @@ public void serviceReturnsSpecifiedPathogenicityDataForMissenseVariant() { public void serviceReturnsCaddDataForMissenseVariant() { variant = buildVariantOfType(VariantEffect.MISSENSE_VARIANT); PathogenicityData result = instance.getVariantPathogenicityData(variant, EnumSet.of(PathogenicitySource.CADD)); - assertThat(result, equalTo(PathogenicityData.of(PATH_CLINVAR_DATA, CADD_DATA.getPredictedScore(PathogenicitySource.CADD)))); + assertThat(result, equalTo(PathogenicityData.of(PATH_CLINVAR_DATA, CADD_DATA.pathogenicityScore(PathogenicitySource.CADD)))); } @Test diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryPerformanceTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryPerformanceTest.java index ca6d11ed5..f0d3ec6f1 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryPerformanceTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/VariantFactoryPerformanceTest.java @@ -180,7 +180,7 @@ private Consumer printVariant() { variantEvaluation.getTranscriptAnnotations().get(0).getHgvsCdna(), variantEvaluation.getVariantScore(), variantEvaluation.getFrequencyScore(), variantEvaluation.getFrequencyData().maxFreq(), - variantEvaluation.getPathogenicityScore(), variantEvaluation.getPathogenicityData().getPredictedPathogenicityScores() + variantEvaluation.getPathogenicityScore(), variantEvaluation.getPathogenicityData().pathogenicityScores() ); } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/ClinVarDaoMvStoreTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/ClinVarDaoMvStoreTest.java index 30c549b0e..f01ac5e5e 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/ClinVarDaoMvStoreTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/ClinVarDaoMvStoreTest.java @@ -287,7 +287,7 @@ void manualDataExplorer() { if (pathogenicityData.isEmpty()) { System.out.println("\t-"); } else { - pathogenicityData.getPredictedPathogenicityScores().forEach(path -> System.out.println("\t" + path)); + pathogenicityData.pathogenicityScores().forEach(path -> System.out.println("\t" + path)); } } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDaoTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDaoTest.java index a481d55da..69c921a31 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDaoTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/genome/dao/SvPathogenicityDaoTest.java @@ -57,6 +57,6 @@ class SvPathogenicityDaoTest { void getPathogenicityData(int chr, int start, int end, String alt, int changeLength, ClinVarData.ClinSig expected) { Variant variant = TestFactory.variantBuilder(chr, start, end, "", alt, changeLength).build(); PathogenicityData result = instance.getPathogenicityData(variant); - assertThat(result.getClinVarData().getPrimaryInterpretation(), equalTo(expected)); + assertThat(result.clinVarData().getPrimaryInterpretation(), equalTo(expected)); } } \ No newline at end of file diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java index 651a63732..7ae87b28c 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/VariantEvaluationTest.java @@ -379,7 +379,7 @@ public void testGetPathogenicityScoreNonMissenseVariantNoPredictions() { VariantEffect type = VariantEffect.DOWNSTREAM_GENE_VARIANT; instance = testVariantBuilder().variantEffect(type).build(); - float expected = VariantEffectPathogenicityScore.getPathogenicityScoreOf(type); + float expected = VariantEffectPathogenicityScore.pathogenicityScoreOf(type); assertThat(instance.getPathogenicityScore(), equalTo(expected)); } @@ -389,7 +389,7 @@ public void testGetPathogenicityScoreNonMissenseVariantWithPredictions() { PathogenicityData pathData = PathogenicityData.of(CaddScore.of(1f)); instance = testVariantBuilder().pathogenicityData(pathData).variantEffect(type).build(); - assertThat(instance.getPathogenicityScore(), equalTo(pathData.getScore())); + assertThat(instance.getPathogenicityScore(), equalTo(pathData.pathogenicityScore())); } @Test @@ -397,7 +397,7 @@ public void testGetPathogenicityScoreMissenseVariantNoPredictions() { VariantEffect type = VariantEffect.MISSENSE_VARIANT; instance = testVariantBuilder().variantEffect(type).build(); - float expected = VariantEffectPathogenicityScore.getPathogenicityScoreOf(type); + float expected = VariantEffectPathogenicityScore.pathogenicityScoreOf(type); assertThat(instance.getPathogenicityScore(), equalTo(expected)); } diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java index ccc9faea2..1f09347aa 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/frequency/FrequencyDataTest.java @@ -114,37 +114,37 @@ public void testGetRsId() { @Test public void testGetNonExistentFrequency() { - assertThat(EMPTY_DATA.frequencyForSource(THOUSAND_GENOMES), equalTo(null)); + assertThat(EMPTY_DATA.frequency(THOUSAND_GENOMES), equalTo(null)); } @Test public void testGetDbSnpMaf() { - assertThat(FREQUENCY_DATA.frequencyForSource(THOUSAND_GENOMES), equalTo(DBSNP_PASS)); + assertThat(FREQUENCY_DATA.frequency(THOUSAND_GENOMES), equalTo(DBSNP_PASS)); } @Test public void testGetEspEaMaf() { - assertThat(FREQUENCY_DATA.frequencyForSource(ESP_EA), equalTo(ESP_EA_PASS)); + assertThat(FREQUENCY_DATA.frequency(ESP_EA), equalTo(ESP_EA_PASS)); } @Test public void testGetEspAaMaf() { - assertThat(FREQUENCY_DATA.frequencyForSource(ESP_AA), equalTo(ESP_AA_PASS)); + assertThat(FREQUENCY_DATA.frequency(ESP_AA), equalTo(ESP_AA_PASS)); } @Test public void testGetEspAllMaf() { - assertThat(FREQUENCY_DATA.frequencyForSource(ESP_ALL), equalTo(ESP_ALL_PASS)); + assertThat(FREQUENCY_DATA.frequency(ESP_ALL), equalTo(ESP_ALL_PASS)); } @Test public void testGetFrequencyForUnavailableSource() { - assertThat(FREQUENCY_DATA.frequencyForSource(GNOMAD_E_NFE), equalTo(null)); + assertThat(FREQUENCY_DATA.frequency(GNOMAD_E_NFE), equalTo(null)); } @Test public void testGetFrequencyForUnavailableSourceBefore() { - assertThat(FREQUENCY_DATA.frequencyForSource(UNKNOWN), equalTo(null)); + assertThat(FREQUENCY_DATA.frequency(UNKNOWN), equalTo(null)); } @Test diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityDataTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityDataTest.java index 6d251fac3..af0cc45db 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityDataTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/PathogenicityDataTest.java @@ -61,9 +61,9 @@ public class PathogenicityDataTest { public void testEmptyData() { PathogenicityData instance = PathogenicityData.empty(); assertThat(instance.hasPredictedScore(), is(false)); - assertThat(instance.getPredictedPathogenicityScores().isEmpty(), is(true)); - assertThat(instance.getMostPathogenicScore(), nullValue()); - assertThat(instance.getScore(), equalTo(0f)); + assertThat(instance.pathogenicityScores().isEmpty(), is(true)); + assertThat(instance.mostPathogenicScore(), nullValue()); + assertThat(instance.pathogenicityScore(), equalTo(0f)); } @Test @@ -76,8 +76,8 @@ public void testHasPredictedScoreReturnsFalseWhenNullsUsedInConstructor() { @Test public void testGetPredictedPathogenicityScoresIsEmptyWhenNullsUsedInConstructor() { PathogenicityData instance = PathogenicityData.of(ClinVarData.empty(), Collections.emptySet()); - assertThat(instance.getClinVarData().isEmpty(), is(true)); - assertThat(instance.getPredictedPathogenicityScores().isEmpty(), is(true)); + assertThat(instance.clinVarData().isEmpty(), is(true)); + assertThat(instance.pathogenicityScores().isEmpty(), is(true)); assertThat(instance.isEmpty(), is(true)); assertThat(instance, equalTo(PathogenicityData.empty())); assertThat(PathogenicityData.of(), equalTo(PathogenicityData.empty())); @@ -93,62 +93,62 @@ public void testVarArgsPathScores() { @Test public void testPathogenicityDataRemovesNullsUsedInConstructor() { PathogenicityData instance = PathogenicityData.of(POLYPHEN_FAIL, null); - assertThat(instance.getPredictedPathogenicityScores().isEmpty(), is(false)); - assertThat(instance.getPredictedPathogenicityScores().size(), equalTo(1)); + assertThat(instance.pathogenicityScores().isEmpty(), is(false)); + assertThat(instance.pathogenicityScores().size(), equalTo(1)); } @Test public void testGetMostPathogenicScoreReturnsNullWhenNoScorePresent() { - PathogenicityScore mostPathogenicScore = PathogenicityData.empty().getMostPathogenicScore(); + PathogenicityScore mostPathogenicScore = PathogenicityData.empty().mostPathogenicScore(); assertThat(mostPathogenicScore, nullValue()); } @Test public void testGetMostPathogenicScoreReturnsOnlyScoreWhenOneScorePresent() { PathogenicityData instance = PathogenicityData.of(POLYPHEN_FAIL); - PathogenicityScore mostPathogenicScore = instance.getMostPathogenicScore(); + PathogenicityScore mostPathogenicScore = instance.mostPathogenicScore(); assertThat(mostPathogenicScore, equalTo(POLYPHEN_FAIL)); } @Test public void testConstructorWithCollectionReturnsMostPathogenicScore() { PathogenicityData instance = PathogenicityData.of(Arrays.asList(POLYPHEN_FAIL, SIFT_PASS)); - PathogenicityScore mostPathogenicScore = instance.getMostPathogenicScore(); + PathogenicityScore mostPathogenicScore = instance.mostPathogenicScore(); assertThat(mostPathogenicScore, equalTo(SIFT_PASS)); } @Test public void testGetMostPathogenicScoreReturnsMostPathogenicScore() { PathogenicityData instance = PathogenicityData.of(POLYPHEN_FAIL, SIFT_PASS); - PathogenicityScore mostPathogenicScore = instance.getMostPathogenicScore(); + PathogenicityScore mostPathogenicScore = instance.mostPathogenicScore(); assertThat(mostPathogenicScore, equalTo(SIFT_PASS)); } @Test public void testGetPolyPhenScore() { PathogenicityData instance = PathogenicityData.of(POLYPHEN_FAIL); - PathogenicityScore result = instance.getPredictedScore(PathogenicitySource.POLYPHEN); + PathogenicityScore result = instance.pathogenicityScore(PathogenicitySource.POLYPHEN); assertThat(result, equalTo(POLYPHEN_FAIL)); } @Test public void testGetMutationTasterScore() { PathogenicityData instance = PathogenicityData.of(MTASTER_PASS); - PathogenicityScore result = instance.getPredictedScore(PathogenicitySource.MUTATION_TASTER); + PathogenicityScore result = instance.pathogenicityScore(PathogenicitySource.MUTATION_TASTER); assertThat(result, equalTo(MTASTER_PASS)); } @Test public void testGetSiftScore() { PathogenicityData instance = PathogenicityData.of(SIFT_FAIL); - PathogenicityScore result = instance.getPredictedScore(PathogenicitySource.SIFT); + PathogenicityScore result = instance.pathogenicityScore(PathogenicitySource.SIFT); assertThat(result, equalTo(SIFT_FAIL)); } @Test public void testGetRemmScore() { PathogenicityData instance = PathogenicityData.of(RemmScore.of(1f)); - PathogenicityScore result = instance.getPredictedScore(PathogenicitySource.REMM); + PathogenicityScore result = instance.pathogenicityScore(PathogenicitySource.REMM); assertThat(result, equalTo(RemmScore.of(1f))); } @@ -156,7 +156,7 @@ public void testGetRemmScore() { public void testGetCaddScore() { CaddScore caddScore = CaddScore.of(POLYPHEN_PASS_SCORE); PathogenicityData instance = PathogenicityData.of(caddScore); - PathogenicityScore result = instance.getPredictedScore(PathogenicitySource.CADD); + PathogenicityScore result = instance.pathogenicityScore(PathogenicitySource.CADD); assertThat(result, equalTo(caddScore)); } @@ -165,7 +165,7 @@ public void testGetPredictedPathogenicityScores() { PathogenicityData instance = PathogenicityData.of(POLYPHEN_PASS, MTASTER_PASS, SIFT_FAIL); List expResult = ImmutableList.of(POLYPHEN_PASS, MTASTER_PASS, SIFT_FAIL); - List result = instance.getPredictedPathogenicityScores(); + List result = instance.pathogenicityScores(); assertThat(result, equalTo(expResult)); } @@ -174,9 +174,9 @@ public void testGetPredictedPathogenicityScoresIsImmutable() { PathogenicityData instance = PathogenicityData.of(POLYPHEN_PASS, MTASTER_PASS, SIFT_FAIL); List expResult = ImmutableList.of(POLYPHEN_PASS, MTASTER_PASS, SIFT_FAIL); //try and add another score to the instance post-construction - instance.getPredictedPathogenicityScores().add(SIFT_PASS); + instance.pathogenicityScores().add(SIFT_PASS); - List result = instance.getPredictedPathogenicityScores(); + List result = instance.pathogenicityScores(); assertThat(result, equalTo(expResult)); } @@ -200,7 +200,7 @@ public void testHasPredictedScoreForSourceIsFalse() { @Test public void testGetPredictedScoreWhenScorePresent() { PathogenicityData instance = PathogenicityData.of(POLYPHEN_PASS); - PathogenicityScore result = instance.getPredictedScore(PathogenicitySource.POLYPHEN); + PathogenicityScore result = instance.pathogenicityScore(PathogenicitySource.POLYPHEN); assertThat(result.getScore(), equalTo(POLYPHEN_PASS.getScore())); assertThat(result.getSource(), equalTo(POLYPHEN_PASS.getSource())); assertThat(result, equalTo(POLYPHEN_PASS)); @@ -208,7 +208,7 @@ public void testGetPredictedScoreWhenScorePresent() { @Test public void testGetPredictedScoreScoreMissingReturnsNull() { - assertThat(EMPTY_DATA.getPredictedScore(PathogenicitySource.POLYPHEN), is(nullValue())); + assertThat(EMPTY_DATA.pathogenicityScore(PathogenicitySource.POLYPHEN), is(nullValue())); } @Test @@ -228,7 +228,7 @@ public void testHasNoClinVarData() { @Test public void testEmptyClinVarData() { - assertThat(EMPTY_DATA.getClinVarData(), equalTo(ClinVarData.empty())); + assertThat(EMPTY_DATA.clinVarData(), equalTo(ClinVarData.empty())); } @Test @@ -236,7 +236,7 @@ public void testClinVarData() { ClinVarData clinVarData = ClinVarData.builder().variationId("12345").primaryInterpretation(ClinVarData.ClinSig.PATHOGENIC).build(); PathogenicityData instance = PathogenicityData.of(clinVarData, POLYPHEN_PASS); assertThat(instance.hasClinVarData(), is(true)); - assertThat(instance.getClinVarData(), equalTo(clinVarData)); + assertThat(instance.clinVarData(), equalTo(clinVarData)); } @Test @@ -259,19 +259,19 @@ public void testNotEquals() { @Test public void testGetScoreNoPredictedData() { - assertThat(PathogenicityData.empty().getScore(), equalTo(0f)); + assertThat(PathogenicityData.empty().pathogenicityScore(), equalTo(0f)); } @Test public void testGetScoreNonSiftPredictedData() { PathogenicityData instance = PathogenicityData.of(MTASTER_PASS, POLYPHEN_FAIL); - assertThat(instance.getScore(), equalTo(MTASTER_PASS_SCORE)); + assertThat(instance.pathogenicityScore(), equalTo(MTASTER_PASS_SCORE)); } @Test public void testGetScoreReturnsNormalisedSiftScore() { PathogenicityData instance = PathogenicityData.of(MTASTER_FAIL, SIFT_PASS); - assertThat(instance.getScore(), equalTo(1 - SIFT_PASS_SCORE)); + assertThat(instance.pathogenicityScore(), equalTo(1 - SIFT_PASS_SCORE)); } @Test diff --git a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScoreTest.java b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScoreTest.java index 2c1385e9f..1656ac0af 100644 --- a/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScoreTest.java +++ b/exomiser-core/src/test/java/org/monarchinitiative/exomiser/core/model/pathogenicity/VariantEffectPathogenicityScoreTest.java @@ -41,91 +41,91 @@ public class VariantEffectPathogenicityScoreTest { @Test void sequenceVariantScore() { - assertThat(getPathogenicityScoreOf(SEQUENCE_VARIANT), equalTo(NON_PATHOGENIC_SCORE)); + assertThat(pathogenicityScoreOf(SEQUENCE_VARIANT), equalTo(NON_PATHOGENIC_SCORE)); } @Test public void testGetPathogenicityScoreForDefaultMissense() { - assertThat(getPathogenicityScoreOf(MISSENSE_VARIANT), equalTo(DEFAULT_MISSENSE_SCORE)); + assertThat(pathogenicityScoreOf(MISSENSE_VARIANT), equalTo(DEFAULT_MISSENSE_SCORE)); } @Test void synonymousVariantScore() { - assertThat(getPathogenicityScoreOf(SYNONYMOUS_VARIANT), equalTo(SYNONYMOUS_SCORE)); + assertThat(pathogenicityScoreOf(SYNONYMOUS_VARIANT), equalTo(SYNONYMOUS_SCORE)); } @Test void frameShiftScores() { - assertThat(getPathogenicityScoreOf(FRAMESHIFT_ELONGATION), equalTo(FRAMESHIFT_SCORE)); - assertThat(getPathogenicityScoreOf(FRAMESHIFT_TRUNCATION), equalTo(FRAMESHIFT_SCORE)); - assertThat(getPathogenicityScoreOf(FRAMESHIFT_VARIANT), equalTo(FRAMESHIFT_SCORE)); + assertThat(pathogenicityScoreOf(FRAMESHIFT_ELONGATION), equalTo(FRAMESHIFT_SCORE)); + assertThat(pathogenicityScoreOf(FRAMESHIFT_TRUNCATION), equalTo(FRAMESHIFT_SCORE)); + assertThat(pathogenicityScoreOf(FRAMESHIFT_VARIANT), equalTo(FRAMESHIFT_SCORE)); } @Test void nonFrameShiftIndelScores() { - assertThat(getPathogenicityScoreOf(MNV), equalTo(NONFRAMESHIFT_INDEL_SCORE)); - assertThat(getPathogenicityScoreOf(FEATURE_TRUNCATION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); - assertThat(getPathogenicityScoreOf(DISRUPTIVE_INFRAME_DELETION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); - assertThat(getPathogenicityScoreOf(DISRUPTIVE_INFRAME_INSERTION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); - assertThat(getPathogenicityScoreOf(INFRAME_DELETION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); - assertThat(getPathogenicityScoreOf(INFRAME_INSERTION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); - assertThat(getPathogenicityScoreOf(INTERNAL_FEATURE_ELONGATION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); - assertThat(getPathogenicityScoreOf(COMPLEX_SUBSTITUTION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(MNV), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(FEATURE_TRUNCATION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(DISRUPTIVE_INFRAME_DELETION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(DISRUPTIVE_INFRAME_INSERTION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(INFRAME_DELETION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(INFRAME_INSERTION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(INTERNAL_FEATURE_ELONGATION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); + assertThat(pathogenicityScoreOf(COMPLEX_SUBSTITUTION), equalTo(NONFRAMESHIFT_INDEL_SCORE)); } @Test void spliceAcceptorDonorScore() { - assertThat(getPathogenicityScoreOf(SPLICE_ACCEPTOR_VARIANT), equalTo(SPLICE_DONOR_ACCEPTOR_SCORE)); - assertThat(getPathogenicityScoreOf(SPLICE_DONOR_VARIANT), equalTo(SPLICE_DONOR_ACCEPTOR_SCORE)); + assertThat(pathogenicityScoreOf(SPLICE_ACCEPTOR_VARIANT), equalTo(SPLICE_DONOR_ACCEPTOR_SCORE)); + assertThat(pathogenicityScoreOf(SPLICE_DONOR_VARIANT), equalTo(SPLICE_DONOR_ACCEPTOR_SCORE)); } @Test void testSpliceRegionScore() { assertThat(SPLICE_REGION_VARIANT.getImpact(), equalTo(PutativeImpact.LOW)); // LOW impact scores usually have a score of 0 - assertThat(getPathogenicityScoreOf(SPLICE_REGION_VARIANT), equalTo(SPLICE_REGION_SCORE)); + assertThat(pathogenicityScoreOf(SPLICE_REGION_VARIANT), equalTo(SPLICE_REGION_SCORE)); } @Test void startLossScore() { - assertThat(getPathogenicityScoreOf(START_LOST), equalTo(STARTLOSS_SCORE)); + assertThat(pathogenicityScoreOf(START_LOST), equalTo(STARTLOSS_SCORE)); } @Test void stopLossScore() { - assertThat(getPathogenicityScoreOf(STOP_LOST), equalTo(STOPLOSS_SCORE)); + assertThat(pathogenicityScoreOf(STOP_LOST), equalTo(STOPLOSS_SCORE)); } @Test void stopGainScore() { - assertThat(getPathogenicityScoreOf(STOP_GAINED), equalTo(NONSENSE_SCORE)); + assertThat(pathogenicityScoreOf(STOP_GAINED), equalTo(NONSENSE_SCORE)); } @Test public void inversionScore() { - assertThat(getPathogenicityScoreOf(INVERSION), equalTo(INVERSION_SCORE)); + assertThat(pathogenicityScoreOf(INVERSION), equalTo(INVERSION_SCORE)); } @Test public void testGetPathogenicityScoreForNonPathogenicVariantType() { - assertThat(getPathogenicityScoreOf(DOWNSTREAM_GENE_VARIANT), equalTo(NON_PATHOGENIC_SCORE)); + assertThat(pathogenicityScoreOf(DOWNSTREAM_GENE_VARIANT), equalTo(NON_PATHOGENIC_SCORE)); } @Test public void testGetPathogenicityScoreForUnListedHighImpactVariantEffect() { assertThat(COPY_NUMBER_CHANGE.getImpact(), equalTo(PutativeImpact.HIGH)); - assertThat(getPathogenicityScoreOf(COPY_NUMBER_CHANGE), equalTo(DEFAULT_HIGH_SCORE)); + assertThat(pathogenicityScoreOf(COPY_NUMBER_CHANGE), equalTo(DEFAULT_HIGH_SCORE)); } @Test public void testGetPathogenicityScoreForUnListedModerateImpactVariantEffect() { assertThat(THREE_PRIME_UTR_TRUNCATION.getImpact(), equalTo(PutativeImpact.MODERATE)); - assertThat(getPathogenicityScoreOf(THREE_PRIME_UTR_TRUNCATION), equalTo(DEFAULT_MISSENSE_SCORE)); + assertThat(pathogenicityScoreOf(THREE_PRIME_UTR_TRUNCATION), equalTo(DEFAULT_MISSENSE_SCORE)); } @Test public void testGetPathogenicityScoreForUnListedLowImpactVariantEffect() { assertThat(CODING_TRANSCRIPT_INTRON_VARIANT.getImpact(), equalTo(PutativeImpact.LOW)); - assertThat(getPathogenicityScoreOf(CODING_TRANSCRIPT_INTRON_VARIANT), equalTo(NON_PATHOGENIC_SCORE)); + assertThat(pathogenicityScoreOf(CODING_TRANSCRIPT_INTRON_VARIANT), equalTo(NON_PATHOGENIC_SCORE)); } } diff --git a/exomiser-web/src/main/resources/templates/results.html b/exomiser-web/src/main/resources/templates/results.html index 191c3bb65..669d7bec1 100644 --- a/exomiser-web/src/main/resources/templates/results.html +++ b/exomiser-web/src/main/resources/templates/results.html @@ -296,10 +296,10 @@

Analyzed samples

- + - + @@ -557,10 +557,10 @@

Variant Score: 1.00 -
No +
No pathogenicity data
-
Mutation Taster: 0.999 (P)
@@ -698,10 +698,10 @@

Variant Score: 1.00 -
No +
No pathogenicity data
-
Mutation Taster: 0.999 (P)