Transvar implements ProteinResolver { @Override @NotNull public List<VariantHotspot> extractHotspotsFromProteinAnnotation(@NotNull String gene, @Nullable String specificTranscript, @NotNull String proteinAnnotation) { List<VariantHotspot> hotspots = extractHotspotsForAnnotation(gene, specificTranscript, proteinAnnotation); String proteinKey = ProteinKeyFormatter.toProteinKey(gene, specificTranscript, proteinAnnotation); LOGGER.debug("Converted '{}' to {} hotspot(s)", proteinKey, hotspots.size()); if (hotspots.isEmpty()) { unresolvedProteinAnnotations.add(proteinKey); } return hotspots; } @VisibleForTesting  Transvar(@NotNull TransvarProcess process, @NotNull TransvarInterpreter interpreter,
            @NotNull Map<String, HmfTranscriptRegion> transcriptPerGeneMap); @NotNull static Transvar withRefGenome(@NotNull RefGenomeVersion refGenomeVersion, @NotNull String refGenomeFastaFile); @Override @NotNull List<VariantHotspot> extractHotspotsFromProteinAnnotation(@NotNull String gene, @Nullable String specificTranscript,
            @NotNull String proteinAnnotation); @Override @NotNull Set<String> unresolvedProteinAnnotations();  }
@Test public void noHotspotsWhenTransvarProcessReturnsEmpty() { Transvar transvar = returnsNoTransvarRecord(); assertTrue(transvar.extractHotspotsFromProteinAnnotation("BRAF", "ENST00000288602", "V600E").isEmpty()); }
@Test public void noHotspotsWhenGeneIsUnknown() { Transvar transvar = returnsSingleTransvarRecord(createTestRecord()); assertTrue(transvar.extractHotspotsFromProteinAnnotation("DoesNotExist", null, Strings.EMPTY).isEmpty()); }
@Test public void noHotspotsWhenRecordIsNotOnSpecificTranscript() { Transvar transvar = returnsSingleTransvarRecord(createTestRecord()); assertTrue(transvar.extractHotspotsFromProteinAnnotation("BRAF", "DoesNotExist", Strings.EMPTY).isEmpty()); }