VariantEvaluation implements Comparable<VariantEvaluation>, Filterable, Inheritable, Variant { public boolean isPredictedPathogenic() { if (whiteListed) { return true; } if (variantEffect == VariantEffect.MISSENSE_VARIANT) { return true; } else { return getPathogenicityScore() >= DEFAULT_PATHOGENICITY_THRESHOLD; } } private  VariantEvaluation(Builder builder); @Override GenomeAssembly getGenomeAssembly(); @Override int getChromosome(); @Override String getChromosomeName(); @Override int getPosition(); @Override String getRef(); @Override String getAlt(); VariantContext getVariantContext(); int getAltAlleleId(); String getId(); double getPhredScore(); @Override VariantEffect getVariantEffect(); void setVariantEffect(VariantEffect ve); @Override String getGeneSymbol(); void setGeneSymbol(String symbol); @Override String getGeneId(); void setGeneId(String geneId); @Override List<TranscriptAnnotation> getTranscriptAnnotations(); void setAnnotations(List<TranscriptAnnotation> annotations); @Override boolean hasTranscriptAnnotations(); @JsonIgnore String getHgvsGenome(); @JsonIgnore String getGenotypeString(); Map<String, SampleGenotype> getSampleGenotypes(); SampleGenotype getSampleGenotype(String sampleId); @Override boolean addFilterResult(FilterResult filterResult); Set<FilterType> getPassedFilterTypes(); Set<FilterType> getFailedFilterTypes(); synchronized Set<FilterType> getFailedFilterTypesForMode(ModeOfInheritance modeOfInheritance); @Override synchronized boolean passedFilters(); @Override synchronized boolean passedFilter(FilterType filterType); FilterStatus getFilterStatus(); FilterStatus getFilterStatusForMode(ModeOfInheritance modeOfInheritance); float getVariantScore(); float getFrequencyScore(); float getPathogenicityScore(); boolean isPredictedPathogenic(); FrequencyData getFrequencyData(); void setFrequencyData(FrequencyData frequencyData); PathogenicityData getPathogenicityData(); void setPathogenicityData(PathogenicityData pathogenicityData); boolean isWhiteListed(); void setWhiteListed(boolean whiteListed); void setContributesToGeneScoreUnderMode(ModeOfInheritance modeOfInheritance); boolean contributesToGeneScore(); boolean contributesToGeneScoreUnderMode(ModeOfInheritance modeOfInheritance); @Override void setCompatibleInheritanceModes(Set<ModeOfInheritance> compatibleModes); @Override Set<ModeOfInheritance> getCompatibleInheritanceModes(); @Override boolean isCompatibleWith(ModeOfInheritance modeOfInheritance); @Override int compareTo(VariantEvaluation other); static int compareByRank(VariantEvaluation some, VariantEvaluation other); @Override int hashCode(); @Override boolean equals(Object obj); String toString(); static Builder builder(int chr, int pos, String ref, String alt);  }
@Test public void testIsPredictedPathogenicFalseByDefault() { assertThat(instance.isPredictedPathogenic(), is(false)); }
@Test public void testIsPredictedPathogenicMissenseVariant() { instance = testVariantBuilder().variantEffect(VariantEffect.MISSENSE_VARIANT).build(); assertThat(instance.isPredictedPathogenic(), is(true)); }
@Test public void testStopGainVariantIsPredictedPathogenicIsTrue() { instance = testVariantBuilder().variantEffect(VariantEffect.STOP_GAINED).build(); assertThat(instance.isPredictedPathogenic(), is(true)); }
@Test public void testDownstreamVariantIsPredictedPathogenicIsFalse() { instance = testVariantBuilder().variantEffect(VariantEffect.DOWNSTREAM_GENE_VARIANT).build(); assertThat(instance.isPredictedPathogenic(), is(false)); }