target stringlengths 20 113k | src_fm stringlengths 11 86.3k | src_fm_fc stringlengths 21 86.4k | src_fm_fc_co stringlengths 30 86.4k | src_fm_fc_ms stringlengths 42 86.8k | src_fm_fc_ms_ff stringlengths 43 86.8k |
|---|---|---|---|---|---|
@Test public void testSVSubstitutionIntergenic() throws InvalidGenomeVariant { final GenomeVariant change = new GenomeVariant(new GenomePosition(refDict, Strand.FWD, 1, 6640062, PositionType.ZERO_BASED), "CGAT", "TTTTA"); final Annotation anno = new StructuralVariantAnnotationBuilder(null, change).build(); Assert.asser... | public Annotation build() { final String ref = change.getRef(); final String alt = change.getAlt(); StringBuilder altRC = new StringBuilder(alt).reverse(); for (int i = 0; i < altRC.length(); ++i) if (altRC.charAt(i) == 'A') altRC.setCharAt(i, 'T'); else if (altRC.charAt(i) == 'T') altRC.setCharAt(i, 'A'); else if (alt... | StructuralVariantAnnotationBuilder { public Annotation build() { final String ref = change.getRef(); final String alt = change.getAlt(); StringBuilder altRC = new StringBuilder(alt).reverse(); for (int i = 0; i < altRC.length(); ++i) if (altRC.charAt(i) == 'A') altRC.setCharAt(i, 'T'); else if (altRC.charAt(i) == 'T') ... | StructuralVariantAnnotationBuilder { public Annotation build() { final String ref = change.getRef(); final String alt = change.getAlt(); StringBuilder altRC = new StringBuilder(alt).reverse(); for (int i = 0; i < altRC.length(); ++i) if (altRC.charAt(i) == 'A') altRC.setCharAt(i, 'T'); else if (altRC.charAt(i) == 'T') ... | StructuralVariantAnnotationBuilder { public Annotation build() { final String ref = change.getRef(); final String alt = change.getAlt(); StringBuilder altRC = new StringBuilder(alt).reverse(); for (int i = 0; i < altRC.length(); ++i) if (altRC.charAt(i) == 'A') altRC.setCharAt(i, 'T'); else if (altRC.charAt(i) == 'T') ... | StructuralVariantAnnotationBuilder { public Annotation build() { final String ref = change.getRef(); final String alt = change.getAlt(); StringBuilder altRC = new StringBuilder(alt).reverse(); for (int i = 0; i < altRC.length(); ++i) if (altRC.charAt(i) == 'A') altRC.setCharAt(i, 'T'); else if (altRC.charAt(i) == 'T') ... |
@Test public void testExonicOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946660), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTransc... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testNormalExtensionToHGVSString() { Assert.assertEquals("A124Text*23", normalExtension.toHGVSString()); Assert.assertEquals("Ala124Thrext*23", normalExtension.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("A124Text*23", normalExtension.toHGVSString(AminoAcidCode.ONE_LETTER)); } | @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(code), targetAA, "ext*?")); else re... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... |
@Test public void testIntronicFivePrimeOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58957157), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(ann... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testExonicFivePrimeOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946502), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testExonicThreePrimeOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012403), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testIntronicThreePrimeOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012355), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(an... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testUpstreamOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012449), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTran... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testDownstreamOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58942733), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTr... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testIntergenicOma1() { final SVMobileElementInsertion svIns = new SVMobileElementInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017449), 0, 0 ); final SVAnnotation anno = new SVMobileElementInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTr... | @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEMENT_INSERTION); } return new SVAnnotation(svMEIns, transcript, effects); ... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... | SVMobileElementInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation result = builder.build(); final EnumSet<VariantEffect> effects = EnumSet.copyOf(result.getEffects()); if (effects.contains(VariantEffect.INSERTION)) { effects.add(VariantEffect.MOBILE_ELEME... |
@Test public void testTranscriptDuplicationOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58929877), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59028960), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnotati... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testExonDuplicationOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58968128), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58994820), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnotationBuil... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testExonOverlapStartDuplicatedOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59004875), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59005052), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnn... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testNoTerExtensionToHGVSString() { Assert.assertEquals("A124Text*?", noTerExtension.toHGVSString()); Assert.assertEquals("Ala124Thrext*?", noTerExtension.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("A124Text*?", noTerExtension.toHGVSString(AminoAcidCode.ONE_LETTER)); } | @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(code), targetAA, "ext*?")); else re... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... | ProteinExtension extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isNoTerminalExtension()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSS... |
@Test public void testExonOverlapStopDuplicatedOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 5894659), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946671), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnot... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testExonOverlapDuplicationOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946844), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946946), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnotat... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testExonOverlapNoFrameshiftOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946843), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946946), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnota... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testIntronicOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58957157), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58963900), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnotationBuilder(oma... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testUpstreamOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012899), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnotationBuilder(oma... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testDownstreamOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58942733), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946074), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnotationBuilder(o... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testIntergenicOma1() { final SVDuplication svDup = new SVDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017899), 0, 0, 0, 0 ); final SVAnnotation anno = new SVDuplicationAnnotationBuilder(o... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTURAL_VARIANT ... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... | SVDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffec... |
@Test public void testTranscriptInversionOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58929877), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59028960), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBuilde... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testExonInversionOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58968128), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58994820), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBuilder(oma1... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testExonOverlapStartInvertedOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59004875), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59005052), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationB... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testEquals() { Assert.assertEquals(firstRange, firstRange2); Assert.assertNotEquals(secondRange, firstRange); } | @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinRange other = (ProteinRange) obj; if (first == null) { if (other.first != null) return false; } else if (!first.equals(other.first)) return false; if (last ==... | ProteinRange implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinRange other = (ProteinRange) obj; if (first == null) { if (other.first != null) return false; } else if (!fi... | ProteinRange implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinRange other = (ProteinRange) obj; if (first == null) { if (other.first != null) return false; } else if (!fi... | ProteinRange implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinRange other = (ProteinRange) obj; if (first == null) { if (other.first != null) return false; } else if (!fi... | ProteinRange implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinRange other = (ProteinRange) obj; if (first == null) { if (other.first != null) return false; } else if (!fi... |
@Test public void testExonOverlapStopInvertedOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946590), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946671), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBu... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testExonOverlapInversionOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946844), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946946), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBuild... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testExonOverlapNoFrameshiftOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946843), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946946), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBu... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testIntronicOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58957157), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58963900), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBuilder(oma1, svI... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testUpstreamOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012899), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBuilder(oma1, svI... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testDownstreamOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58942733), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946074), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBuilder(oma1, s... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testIntergenicOma1() { final SVInversion svInv = new SVInversion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017899), 0, 0, 0, 0 ); final SVAnnotation anno = new SVInversionAnnotationBuilder(oma1, s... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.INVERSION, VariantEffect.STRUCTURAL_VARIANT ))); } else if ... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... | SVInversionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svInv.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svInv, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.... |
@Test public void testTranscriptDuplicationOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58929877), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59028960), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTandemD... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testExonDuplicationOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58968128), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58994820), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTandemDuplica... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testExonOverlapStartDuplicatedOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59004875), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59005052), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTa... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testToHGVSStringWithOffset() { Assert.assertEquals("Gly126-1_Thr302-1", offsetRange.toHGVSString()); } | @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } } | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinRange(ProteinPointLocation first, ProteinPointLocation last); } | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinRange(ProteinPointLocation first, ProteinPointLocation last); static ProteinRange build(String firstAA, int first, String lastAA, int last); static ProteinRange buildWithO... | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinRange(ProteinPointLocation first, ProteinPointLocation last); static ProteinRange build(String firstAA, int first, String lastAA, int last); static ProteinRange buildWithO... |
@Test public void testExonOverlapStopDuplicatedOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946590), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946671), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTan... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testExonOverlapDuplicationOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946844), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946946), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTandem... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testExonOverlapNoFrameshiftOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946843), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946946), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTande... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testIntronicOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58957157), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58963900), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTandemDuplicationAnn... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testUpstreamOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012899), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTandemDuplicationAnn... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testDownstreamOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58942733), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946074), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTandemDuplicationA... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testIntergenicOma1() { final SVTandemDuplication svDup = new SVTandemDuplication( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017899), 0, 0, 0, 0 ); final SVAnnotation anno = new SVTandemDuplicationA... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.TRANSCRIPT_AMPLIFICATION, VariantEffect.STRUCTU... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... | SVTandemDuplicationAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svTandemDup.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svTandemDup, transcript, buildEffectSet(Sets.immutableEnu... |
@Test public void testInsertion() { Assert.assertEquals("100_101insCGAT", new GenomicNucleotideChangeBuilder(varIns).build().toHGVSString()); } | public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt()); } GenomePosition position = ... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... |
@Test public void testDeletion() { Assert.assertEquals("101_104delCGAT", new GenomicNucleotideChangeBuilder(varDel).build().toHGVSString()); } | public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt()); } GenomePosition position = ... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... |
@Test public void testSNV() { Assert.assertEquals("101C>T", new GenomicNucleotideChangeBuilder(varSNV).build().toHGVSString()); } | public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt()); } GenomePosition position = ... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... |
@Test public void testToHGVSStringDownstreamOfTerminal() { Assert.assertEquals("Gly*126_Thr*302", downstreamOfTerminalRange.toHGVSString()); } | @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } } | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinRange(ProteinPointLocation first, ProteinPointLocation last); } | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinRange(ProteinPointLocation first, ProteinPointLocation last); static ProteinRange build(String firstAA, int first, String lastAA, int last); static ProteinRange buildWithO... | ProteinRange implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinRange(ProteinPointLocation first, ProteinPointLocation last); static ProteinRange build(String firstAA, int first, String lastAA, int last); static ProteinRange buildWithO... |
@Test public void testSubstitution() { Assert.assertEquals("101_103delCGAinsTTT", new GenomicNucleotideChangeBuilder(varSub).build().toHGVSString()); } | public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt()); } GenomePosition position = ... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... |
@Test public void testInversion() { Assert.assertEquals("101_104inv", new GenomicNucleotideChangeBuilder(varInv).build().toHGVSString()); } | public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt()); } GenomePosition position = ... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... | GenomicNucleotideChangeBuilder { public NucleotideChange build() { final String ref; final String alt; if (variant.getGenomeInterval().getStrand() == Strand.FWD) { ref = variant.getRef(); alt = variant.getAlt(); } else { ref = DNAUtils.reverseComplement(variant.getRef()); alt = DNAUtils.reverseComplement(variant.getAlt... |
@Test public void testIsFounderTrue() { PedPerson person = new PedPerson("fam", "name", "0", "0", Sex.MALE, Disease.AFFECTED); Assert.assertTrue(person.isFounder()); } | public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } } | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease,
Collection<String> extraFields); PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease dis... | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease,
Collection<String> extraFields); PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease dis... | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease,
Collection<String> extraFields); PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease dis... |
@Test public void testIsFounderFalse() { PedPerson person = new PedPerson("fam", "name", "father", "0", Sex.MALE, Disease.AFFECTED); Assert.assertFalse(person.isFounder()); } | public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } } | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease,
Collection<String> extraFields); PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease dis... | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease,
Collection<String> extraFields); PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease dis... | PedPerson { public boolean isFounder() { return ("0".equals(father) && "0".equals(mother)); } PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease disease,
Collection<String> extraFields); PedPerson(String pedigree, String name, String father, String mother, Sex sex, Disease dis... |
@Test public void testWrite() throws IOException { ImmutableList.Builder<PedPerson> individuals = new ImmutableList.Builder<PedPerson>(); individuals.add(new PedPerson("fam", "father", "0", "0", Sex.MALE, Disease.UNKNOWN)); individuals.add(new PedPerson("fam", "mother", "0", "0", Sex.FEMALE, Disease.UNKNOWN)); individu... | public void write(PedFileContents contents) throws IOException { FileOutputStream fos = new FileOutputStream(file); BufferedOutputStream stream = new BufferedOutputStream(fos); write(contents, stream); stream.close(); fos.close(); } | PedFileWriter { public void write(PedFileContents contents) throws IOException { FileOutputStream fos = new FileOutputStream(file); BufferedOutputStream stream = new BufferedOutputStream(fos); write(contents, stream); stream.close(); fos.close(); } } | PedFileWriter { public void write(PedFileContents contents) throws IOException { FileOutputStream fos = new FileOutputStream(file); BufferedOutputStream stream = new BufferedOutputStream(fos); write(contents, stream); stream.close(); fos.close(); } PedFileWriter(File file); } | PedFileWriter { public void write(PedFileContents contents) throws IOException { FileOutputStream fos = new FileOutputStream(file); BufferedOutputStream stream = new BufferedOutputStream(fos); write(contents, stream); stream.close(); fos.close(); } PedFileWriter(File file); void write(PedFileContents contents); static ... | PedFileWriter { public void write(PedFileContents contents) throws IOException { FileOutputStream fos = new FileOutputStream(file); BufferedOutputStream stream = new BufferedOutputStream(fos); write(contents, stream); stream.close(); fos.close(); } PedFileWriter(File file); void write(PedFileContents contents); static ... |
@Test public void testIsParentOfAffected() { Assert.assertTrue(decorator.isParentOfAffected(pedigree.getMembers().get(0))); Assert.assertTrue(decorator.isParentOfAffected(pedigree.getMembers().get(1))); Assert.assertFalse(decorator.isParentOfAffected(pedigree.getMembers().get(2))); Assert.assertFalse(decorator.isParent... | public boolean isParentOfAffected(Person person) { for (Person member : pedigree.getMembers()) if (member.getFather() == person || member.getMother() == person) return true; return false; } | PedigreeQueryDecorator { public boolean isParentOfAffected(Person person) { for (Person member : pedigree.getMembers()) if (member.getFather() == person || member.getMother() == person) return true; return false; } } | PedigreeQueryDecorator { public boolean isParentOfAffected(Person person) { for (Person member : pedigree.getMembers()) if (member.getFather() == person || member.getMother() == person) return true; return false; } PedigreeQueryDecorator(Pedigree pedigree); } | PedigreeQueryDecorator { public boolean isParentOfAffected(Person person) { for (Person member : pedigree.getMembers()) if (member.getFather() == person || member.getMother() == person) return true; return false; } PedigreeQueryDecorator(Pedigree pedigree); Pedigree getPedigree(); boolean isParentOfAffected(Person pers... | PedigreeQueryDecorator { public boolean isParentOfAffected(Person person) { for (Person member : pedigree.getMembers()) if (member.getFather() == person || member.getMother() == person) return true; return false; } PedigreeQueryDecorator(Pedigree pedigree); Pedigree getPedigree(); boolean isParentOfAffected(Person pers... |
@Test public void testGetUnaffectedNames() { Assert.assertEquals(ImmutableSet.of("father"), decorator.getUnaffectedNames()); } | public ImmutableSet<String> getUnaffectedNames() { ImmutableSet.Builder<String> resultNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) resultNames.add(member.getName()); return resultNames.build(); } | PedigreeQueryDecorator { public ImmutableSet<String> getUnaffectedNames() { ImmutableSet.Builder<String> resultNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) resultNames.add(member.getName()); return resultNames.build(); } } | PedigreeQueryDecorator { public ImmutableSet<String> getUnaffectedNames() { ImmutableSet.Builder<String> resultNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) resultNames.add(member.getName()); return resultNames.build(); } PedigreeQ... | PedigreeQueryDecorator { public ImmutableSet<String> getUnaffectedNames() { ImmutableSet.Builder<String> resultNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) resultNames.add(member.getName()); return resultNames.build(); } PedigreeQ... | PedigreeQueryDecorator { public ImmutableSet<String> getUnaffectedNames() { ImmutableSet.Builder<String> resultNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) resultNames.add(member.getName()); return resultNames.build(); } PedigreeQ... |
@Test public void testGetParentNames() { Assert.assertEquals(ImmutableSet.of("father", "mother"), decorator.getParentNames()); } | public ImmutableSet<String> getParentNames() { ImmutableSet.Builder<String> parentNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.add(member.getMother().ge... | PedigreeQueryDecorator { public ImmutableSet<String> getParentNames() { ImmutableSet.Builder<String> parentNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.... | PedigreeQueryDecorator { public ImmutableSet<String> getParentNames() { ImmutableSet.Builder<String> parentNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.... | PedigreeQueryDecorator { public ImmutableSet<String> getParentNames() { ImmutableSet.Builder<String> parentNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.... | PedigreeQueryDecorator { public ImmutableSet<String> getParentNames() { ImmutableSet.Builder<String> parentNames = new ImmutableSet.Builder<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.... |
@Test public void testGetParents() { Assert.assertEquals(ImmutableList.of(pedigree.getMembers().get(0), pedigree.getMembers().get(1)), decorator.getParents()); } | public ImmutableList<Person> getParents() { ImmutableSet<String> parentNames = getParentNames(); ImmutableList.Builder<Person> builder = new ImmutableList.Builder<Person>(); for (Person member : pedigree.getMembers()) if (parentNames.contains(member.getName())) builder.add(member); return builder.build(); } | PedigreeQueryDecorator { public ImmutableList<Person> getParents() { ImmutableSet<String> parentNames = getParentNames(); ImmutableList.Builder<Person> builder = new ImmutableList.Builder<Person>(); for (Person member : pedigree.getMembers()) if (parentNames.contains(member.getName())) builder.add(member); return build... | PedigreeQueryDecorator { public ImmutableList<Person> getParents() { ImmutableSet<String> parentNames = getParentNames(); ImmutableList.Builder<Person> builder = new ImmutableList.Builder<Person>(); for (Person member : pedigree.getMembers()) if (parentNames.contains(member.getName())) builder.add(member); return build... | PedigreeQueryDecorator { public ImmutableList<Person> getParents() { ImmutableSet<String> parentNames = getParentNames(); ImmutableList.Builder<Person> builder = new ImmutableList.Builder<Person>(); for (Person member : pedigree.getMembers()) if (parentNames.contains(member.getName())) builder.add(member); return build... | PedigreeQueryDecorator { public ImmutableList<Person> getParents() { ImmutableSet<String> parentNames = getParentNames(); ImmutableList.Builder<Person> builder = new ImmutableList.Builder<Person>(); for (Person member : pedigree.getMembers()) if (parentNames.contains(member.getName())) builder.add(member); return build... |
@Test public void testGetNumberOfParents() { Assert.assertEquals(2, decorator.getNumberOfParents()); } | public int getNumberOfParents() { HashSet<String> parentNames = new HashSet<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.add(member.getMother().getName()); } return parentNames.size(); ... | PedigreeQueryDecorator { public int getNumberOfParents() { HashSet<String> parentNames = new HashSet<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.add(member.getMother().getName()); } re... | PedigreeQueryDecorator { public int getNumberOfParents() { HashSet<String> parentNames = new HashSet<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.add(member.getMother().getName()); } re... | PedigreeQueryDecorator { public int getNumberOfParents() { HashSet<String> parentNames = new HashSet<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.add(member.getMother().getName()); } re... | PedigreeQueryDecorator { public int getNumberOfParents() { HashSet<String> parentNames = new HashSet<String>(); for (Person member : pedigree.getMembers()) { if (member.getFather() != null) parentNames.add(member.getFather().getName()); if (member.getMother() != null) parentNames.add(member.getMother().getName()); } re... |
@Test public void testEquals() { Assert.assertTrue(location1.equals(location2)); Assert.assertTrue(location2.equals(location1)); Assert.assertFalse(location1.equals(location3)); Assert.assertFalse(location3.equals(location1)); } | @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinPointLocation other = (ProteinPointLocation) obj; if (aa == null) { if (other.aa != null) return false; } else if (!aa.equals(other.aa)) return false; if (dow... | ProteinPointLocation implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinPointLocation other = (ProteinPointLocation) obj; if (aa == null) { if (other.aa != null) return fal... | ProteinPointLocation implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinPointLocation other = (ProteinPointLocation) obj; if (aa == null) { if (other.aa != null) return fal... | ProteinPointLocation implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinPointLocation other = (ProteinPointLocation) obj; if (aa == null) { if (other.aa != null) return fal... | ProteinPointLocation implements ConvertibleToHGVSString { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; ProteinPointLocation other = (ProteinPointLocation) obj; if (aa == null) { if (other.aa != null) return fal... |
@Test public void testGetNumberOfAffecteds() { Assert.assertEquals(1, decorator.getNumberOfAffecteds()); } | public int getNumberOfAffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.AFFECTED) result += 1; return result; } | PedigreeQueryDecorator { public int getNumberOfAffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.AFFECTED) result += 1; return result; } } | PedigreeQueryDecorator { public int getNumberOfAffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.AFFECTED) result += 1; return result; } PedigreeQueryDecorator(Pedigree pedigree); } | PedigreeQueryDecorator { public int getNumberOfAffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.AFFECTED) result += 1; return result; } PedigreeQueryDecorator(Pedigree pedigree); Pedigree getPedigree(); boolean isParentOfAffected(Person person); ImmutableSet<S... | PedigreeQueryDecorator { public int getNumberOfAffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.AFFECTED) result += 1; return result; } PedigreeQueryDecorator(Pedigree pedigree); Pedigree getPedigree(); boolean isParentOfAffected(Person person); ImmutableSet<S... |
@Test public void testGetNumberOfUnaffecteds() { Assert.assertEquals(1, decorator.getNumberOfUnaffecteds()); } | public int getNumberOfUnaffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) result += 1; return result; } | PedigreeQueryDecorator { public int getNumberOfUnaffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) result += 1; return result; } } | PedigreeQueryDecorator { public int getNumberOfUnaffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) result += 1; return result; } PedigreeQueryDecorator(Pedigree pedigree); } | PedigreeQueryDecorator { public int getNumberOfUnaffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) result += 1; return result; } PedigreeQueryDecorator(Pedigree pedigree); Pedigree getPedigree(); boolean isParentOfAffected(Person person); ImmutableS... | PedigreeQueryDecorator { public int getNumberOfUnaffecteds() { int result = 0; for (Person member : pedigree.getMembers()) if (member.getDisease() == Disease.UNAFFECTED) result += 1; return result; } PedigreeQueryDecorator(Pedigree pedigree); Pedigree getPedigree(); boolean isParentOfAffected(Person person); ImmutableS... |
@Test public void testIsFounderTrue() { Person index = new Person("name", null, null, Sex.MALE, Disease.AFFECTED); Assert.assertTrue(index.isFounder()); } | public boolean isFounder() { return (father == null && mother == null); } | Person { public boolean isFounder() { return (father == null && mother == null); } } | Person { public boolean isFounder() { return (father == null && mother == null); } Person(String name, Person father, Person mother, Sex sex, Disease disease, Collection<String> extraFields); Person(String name, Person father, Person mother, Sex sex, Disease disease); Person(PedPerson pedPerson, PedFileContents pedF... | Person { public boolean isFounder() { return (father == null && mother == null); } Person(String name, Person father, Person mother, Sex sex, Disease disease, Collection<String> extraFields); Person(String name, Person father, Person mother, Sex sex, Disease disease); Person(PedPerson pedPerson, PedFileContents pedF... | Person { public boolean isFounder() { return (father == null && mother == null); } Person(String name, Person father, Person mother, Sex sex, Disease disease, Collection<String> extraFields); Person(String name, Person father, Person mother, Sex sex, Disease disease); Person(PedPerson pedPerson, PedFileContents pedF... |
@Test public void testIsFounderFalse() { Person father = new Person("father", null, null, Sex.MALE, Disease.AFFECTED); Person index = new Person("name", father, null, Sex.MALE, Disease.AFFECTED); Assert.assertFalse(index.isFounder()); } | public boolean isFounder() { return (father == null && mother == null); } | Person { public boolean isFounder() { return (father == null && mother == null); } } | Person { public boolean isFounder() { return (father == null && mother == null); } Person(String name, Person father, Person mother, Sex sex, Disease disease, Collection<String> extraFields); Person(String name, Person father, Person mother, Sex sex, Disease disease); Person(PedPerson pedPerson, PedFileContents pedF... | Person { public boolean isFounder() { return (father == null && mother == null); } Person(String name, Person father, Person mother, Sex sex, Disease disease, Collection<String> extraFields); Person(String name, Person father, Person mother, Sex sex, Disease disease); Person(PedPerson pedPerson, PedFileContents pedF... | Person { public boolean isFounder() { return (father == null && mother == null); } Person(String name, Person father, Person mother, Sex sex, Disease disease, Collection<String> extraFields); Person(String name, Person father, Person mother, Sex sex, Disease disease); Person(PedPerson pedPerson, PedFileContents pedF... |
@Test public void testIsNamesEqual() { Assert.assertTrue(list.namesEqual(pedigree1)); Assert.assertFalse(list.namesEqual(pedigree2)); } | public boolean namesEqual(Pedigree pedigree) { return (pedigree.getNames().equals(names)); } | GenotypeList { public boolean namesEqual(Pedigree pedigree) { return (pedigree.getNames().equals(names)); } } | GenotypeList { public boolean namesEqual(Pedigree pedigree) { return (pedigree.getNames().equals(names)); } GenotypeList(String geneID, List<String> names, boolean isXChromosomal,
ImmutableList<ImmutableList<Genotype>> calls); } | GenotypeList { public boolean namesEqual(Pedigree pedigree) { return (pedigree.getNames().equals(names)); } GenotypeList(String geneID, List<String> names, boolean isXChromosomal,
ImmutableList<ImmutableList<Genotype>> calls); String getGeneName(); ImmutableList<String> getNames(); boolean isXChromosomal(); Immut... | GenotypeList { public boolean namesEqual(Pedigree pedigree) { return (pedigree.getNames().equals(names)); } GenotypeList(String geneID, List<String> names, boolean isXChromosomal,
ImmutableList<ImmutableList<Genotype>> calls); String getGeneName(); ImmutableList<String> getNames(); boolean isXChromosomal(); Immut... |
@Test public void testParseWithHeader() throws PedParseException, IOException { PedFileReader reader = new PedFileReader(this.tmpFileWithHeader); PedFileContents pedFileContents = reader.read(); Assert.assertEquals(pedFileContents.getExtraColumnHeaders().size(), 0); ImmutableList.Builder<PedPerson> individuals = new Im... | public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } PedFileReader(File file); } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } PedFileReader(File file); PedFileContents read(); static PedFileContents read(InputStream stream); } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } PedFileReader(File file); PedFileContents read(); static PedFileContents read(InputStream stream); } |
@Test public void testParseWithoutHeader() throws PedParseException, IOException { PedFileReader reader = new PedFileReader(this.tmpFileWithoutHeader); PedFileContents pedFileContents = reader.read(); Assert.assertEquals(pedFileContents.getExtraColumnHeaders().size(), 0); ImmutableList.Builder<PedPerson> individuals = ... | public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } PedFileReader(File file); } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } PedFileReader(File file); PedFileContents read(); static PedFileContents read(InputStream stream); } | PedFileReader { public PedFileContents read() throws IOException, PedParseException { return read(new FileInputStream(file)); } PedFileReader(File file); PedFileContents read(); static PedFileContents read(InputStream stream); } |
@Test public void testHashCode() { Map<Genotype, String> map = new HashMap<>(); map.put(new Genotype(Arrays.asList(1, 2)), "ONE"); map.put(new Genotype(Arrays.asList(1, 2)), "TWO"); map.put(new Genotype(Arrays.asList(1, 1)), "THREE"); Map<Genotype, String> expected = new HashMap<>(); expected.put(new Genotype(Arrays.as... | @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((alleleNumbers == null) ? 0 : alleleNumbers.hashCode()); return result; } | Genotype { @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((alleleNumbers == null) ? 0 : alleleNumbers.hashCode()); return result; } } | Genotype { @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((alleleNumbers == null) ? 0 : alleleNumbers.hashCode()); return result; } Genotype(Collection<Integer> alleleNumbers); } | Genotype { @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((alleleNumbers == null) ? 0 : alleleNumbers.hashCode()); return result; } Genotype(Collection<Integer> alleleNumbers); ImmutableList<Integer> getAlleleNumbers(); int getPloidy(); boolean isDiploid(); boolean is... | Genotype { @Override public int hashCode() { final int prime = 31; int result = 1; result = prime * result + ((alleleNumbers == null) ? 0 : alleleNumbers.hashCode()); return result; } Genotype(Collection<Integer> alleleNumbers); ImmutableList<Integer> getAlleleNumbers(); int getPloidy(); boolean isDiploid(); boolean is... |
@Test public void testEquals() { Genotype one = new Genotype(Arrays.asList(1, 2)); Genotype two = new Genotype(Arrays.asList(1, 2)); Genotype three = new Genotype(Arrays.asList(1, 1)); Genotype four = new Genotype(Collections.singletonList(1)); assertTrue(one.equals(two)); assertFalse(one.equals(three)); assertFalse(on... | @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; Genotype other = (Genotype) obj; if (alleleNumbers == null) { if (other.alleleNumbers != null) return false; } else if (!alleleNumbers.equals(other.alleleNumbers)) r... | Genotype { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; Genotype other = (Genotype) obj; if (alleleNumbers == null) { if (other.alleleNumbers != null) return false; } else if (!alleleNumbers.equals(other.allele... | Genotype { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; Genotype other = (Genotype) obj; if (alleleNumbers == null) { if (other.alleleNumbers != null) return false; } else if (!alleleNumbers.equals(other.allele... | Genotype { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; Genotype other = (Genotype) obj; if (alleleNumbers == null) { if (other.alleleNumbers != null) return false; } else if (!alleleNumbers.equals(other.allele... | Genotype { @Override public boolean equals(Object obj) { if (this == obj) return true; if (obj == null) return false; if (getClass() != obj.getClass()) return false; Genotype other = (Genotype) obj; if (alleleNumbers == null) { if (other.alleleNumbers != null) return false; } else if (!alleleNumbers.equals(other.allele... |
@Test public void testTranslationalStartSiteOverlapForward() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithTranslationalStartSite(new GenomeInterval(refDict, Strand.FWD, 1, 6640666, 6640669, PositionType.ZERO_BASED))); fo... | public boolean overlapsWithTranslationalStartSite(GenomeInterval interval) { return interval.overlapsWith(getStartCodonInterval()); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStartSite(GenomeInterval interval) { return interval.overlapsWith(getStartCodonInterval()); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStartSite(GenomeInterval interval) { return interval.overlapsWith(getStartCodonInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStartSite(GenomeInterval interval) { return interval.overlapsWith(getStartCodonInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInte... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStartSite(GenomeInterval interval) { return interval.overlapsWith(getStartCodonInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInte... |
@Test public void testToHGVSString() { Assert.assertEquals("Ala124", location1.toHGVSString()); Assert.assertEquals("A124", location1.toHGVSString(AminoAcidCode.ONE_LETTER)); Assert.assertEquals("Ala124", location1.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("Ala124", location1.toHGVSString()); Asser... | @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } | ProteinPointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } } | ProteinPointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinPointLocation(String aa, int pos, int offset, boolean downstreamOfTerminal); } | ProteinPointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinPointLocation(String aa, int pos, int offset, boolean downstreamOfTerminal); static ProteinPointLocation build(String aa, int pos); static ProteinPointLocation bui... | ProteinPointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinPointLocation(String aa, int pos, int offset, boolean downstreamOfTerminal); static ProteinPointLocation build(String aa, int pos); static ProteinPointLocation bui... |
@Test public void testTranslationalStopSiteOverlapForward() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithTranslationalStopSite(new GenomeInterval(refDict, Strand.FWD, 1, 6649266, 6649269, PositionType.ZERO_BASED))); for ... | public boolean overlapsWithTranslationalStopSite(GenomeInterval interval) { return interval.overlapsWith(getStopCodonInterval()); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStopSite(GenomeInterval interval) { return interval.overlapsWith(getStopCodonInterval()); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStopSite(GenomeInterval interval) { return interval.overlapsWith(getStopCodonInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStopSite(GenomeInterval interval) { return interval.overlapsWith(getStopCodonInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterv... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithTranslationalStopSite(GenomeInterval interval) { return interval.overlapsWith(getStopCodonInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterv... |
@Test public void testFivePrimeUTROverlapForward() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithFivePrimeUTR(new GenomeInterval(refDict, Strand.FWD, 1, 6640059, 6640062, PositionType.ZERO_BASED))); Assert.assertTrue(deco... | public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval get... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval get... |
@Test public void testThreePrimeUTROverlapForward() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithThreePrimeUTR(new GenomeInterval(refDict, Strand.FWD, 1, 6649269, 6649272, PositionType.ZERO_BASED))); Assert.assertTrue(de... | public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval g... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval g... |
@Test public void testLiesInExonForwardSuccess() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertTrue(decorator.liesInExon(new GenomeInterval(refDict, Strand.FWD, 1, 6640669, 6640672, PositionType.ZERO_BASED))); Assert.assertTrue(decorator.liesInExon(... | public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return false; return transcript.getExonRegions... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... |
@Test public void testLiesInExonForwardFailure() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.liesInExon(new GenomeInterval(refDict, Strand.FWD, 1, 6640195, 6640198, PositionType.ZERO_BASED))); } | public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return false; return transcript.getExonRegions... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... | TranscriptSequenceOntologyDecorator { public boolean liesInExon(GenomeInterval interval) { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(transcript); final int exonNo = projector.locateExon(interval.getGenomeBeginPos()); if (exonNo == TranscriptProjectionDecorator.INVALID_EXON_ID) return f... |
@Test public void testLiesInCDSExonForwardSuccess() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertTrue(decorator.liesInCDSExon(new GenomeInterval(refDict, Strand.FWD, 1, 6640669, 6640672, PositionType.ZERO_BASED))); Assert.assertTrue(decorator.liesI... | public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } } | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeI... | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeI... |
@Test public void testLiesInCDSExonForwardFailure() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.liesInCDSExon(new GenomeInterval(refDict, Strand.FWD, 1, 6640668, 6640671, PositionType.ZERO_BASED))); } | public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } } | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeI... | TranscriptSequenceOntologyDecorator { public boolean liesInCDSExon(GenomeInterval interval) { return (transcript.getCDSRegion().contains(interval) && liesInExon(interval)); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeI... |
@Test public void testLiesInIntron() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.liesInIntron(new GenomeInterval(refDict, Strand.FWD, 1, 6640195, 6640600, PositionType.ZERO_BASED))); Assert.assertTrue(decorator.liesInIntron(new Gen... | public boolean liesInIntron(GenomePosition pos) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval intronRegion = transcript.intronRegion(i); if (intronRegion.contains(pos)) return true; } return false; } | TranscriptSequenceOntologyDecorator { public boolean liesInIntron(GenomePosition pos) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval intronRegion = transcript.intronRegion(i); if (intronRegion.contains(pos)) return true; } return false; } } | TranscriptSequenceOntologyDecorator { public boolean liesInIntron(GenomePosition pos) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval intronRegion = transcript.intronRegion(i); if (intronRegion.contains(pos)) return true; } return false; } TranscriptSequenceOntologyDecorator(Transcri... | TranscriptSequenceOntologyDecorator { public boolean liesInIntron(GenomePosition pos) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval intronRegion = transcript.intronRegion(i); if (intronRegion.contains(pos)) return true; } return false; } TranscriptSequenceOntologyDecorator(Transcri... | TranscriptSequenceOntologyDecorator { public boolean liesInIntron(GenomePosition pos) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval intronRegion = transcript.intronRegion(i); if (intronRegion.contains(pos)) return true; } return false; } TranscriptSequenceOntologyDecorator(Transcri... |
@Test public void testOverlapsWithSpliceRegion() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithSpliceRegion(new GenomeInterval(refDict, Strand.FWD, 1, 6642350, 6642356, PositionType.ZERO_BASED))); Assert.assertTrue(decora... | public boolean overlapsWithSpliceRegion(GenomeInterval interval) { for (int i = 0; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); if (i + 1 < transcript.getExonRegions().size()) { GenomeInterval spliceRegionInterval = new GenomeInterval(exonInterval.getG... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceRegion(GenomeInterval interval) { for (int i = 0; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); if (i + 1 < transcript.getExonRegions().size()) { GenomeInterval spliceRegionInterval ... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceRegion(GenomeInterval interval) { for (int i = 0; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); if (i + 1 < transcript.getExonRegions().size()) { GenomeInterval spliceRegionInterval ... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceRegion(GenomeInterval interval) { for (int i = 0; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); if (i + 1 < transcript.getExonRegions().size()) { GenomeInterval spliceRegionInterval ... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceRegion(GenomeInterval interval) { for (int i = 0; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); if (i + 1 < transcript.getExonRegions().size()) { GenomeInterval spliceRegionInterval ... |
@Test public void testOverlapsWithSpliceDonorSite() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithSpliceAcceptorSite(new GenomeInterval(refDict, Strand.FWD, 1, 6645978, 6645980, PositionType.ZERO_BASED))); Assert.assertTr... | public boolean overlapsWithSpliceDonorSite(GenomeInterval interval) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval donorInterval = new GenomeInterval(exonInterval.getGenomeEndPos(), 2); if (interval.overlapsWith(donor... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceDonorSite(GenomeInterval interval) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval donorInterval = new GenomeInterval(exonInterval.getGenomeEndPos(... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceDonorSite(GenomeInterval interval) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval donorInterval = new GenomeInterval(exonInterval.getGenomeEndPos(... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceDonorSite(GenomeInterval interval) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval donorInterval = new GenomeInterval(exonInterval.getGenomeEndPos(... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceDonorSite(GenomeInterval interval) { for (int i = 0; i + 1 < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval donorInterval = new GenomeInterval(exonInterval.getGenomeEndPos(... |
@Test public void testMultiChangeStaticFactory() { Assert.assertEquals(multiChangeAllele, ProteinChangeAllele.build(VariantConfiguration.CHIMERIC, ProteinSubstitution.build(false, "L", 100, "R"), ProteinSubstitution.build(false, "A", 99, "G"))); } | public static ProteinChangeAllele build(VariantConfiguration varConfig, ProteinChange... changes) { return new ProteinChangeAllele(varConfig, ImmutableList.copyOf(changes)); } | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { public static ProteinChangeAllele build(VariantConfiguration varConfig, ProteinChange... changes) { return new ProteinChangeAllele(varConfig, ImmutableList.copyOf(changes)); } } | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { public static ProteinChangeAllele build(VariantConfiguration varConfig, ProteinChange... changes) { return new ProteinChangeAllele(varConfig, ImmutableList.copyOf(changes)); } ProteinChangeAllele(VariantConfiguration varConfig, Collection<? e... | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { public static ProteinChangeAllele build(VariantConfiguration varConfig, ProteinChange... changes) { return new ProteinChangeAllele(varConfig, ImmutableList.copyOf(changes)); } ProteinChangeAllele(VariantConfiguration varConfig, Collection<? e... | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { public static ProteinChangeAllele build(VariantConfiguration varConfig, ProteinChange... changes) { return new ProteinChangeAllele(varConfig, ImmutableList.copyOf(changes)); } ProteinChangeAllele(VariantConfiguration varConfig, Collection<? e... |
@Test public void testOverlapsWithSpliceAcceptorSite() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithSpliceAcceptorSite(new GenomeInterval(refDict, Strand.FWD, 1, 6642117, 6642119, PositionType.ZERO_BASED))); Assert.asser... | public boolean overlapsWithSpliceAcceptorSite(GenomeInterval interval) { for (int i = 1; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval acceptorInterval = new GenomeInterval(exonInterval.getGenomeBeginPos().shifted(-2), 2); if (interval.ov... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceAcceptorSite(GenomeInterval interval) { for (int i = 1; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval acceptorInterval = new GenomeInterval(exonInterval.getGenomeBegin... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceAcceptorSite(GenomeInterval interval) { for (int i = 1; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval acceptorInterval = new GenomeInterval(exonInterval.getGenomeBegin... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceAcceptorSite(GenomeInterval interval) { for (int i = 1; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval acceptorInterval = new GenomeInterval(exonInterval.getGenomeBegin... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithSpliceAcceptorSite(GenomeInterval interval) { for (int i = 1; i < transcript.getExonRegions().size(); ++i) { GenomeInterval exonInterval = transcript.getExonRegions().get(i); GenomeInterval acceptorInterval = new GenomeInterval(exonInterval.getGenomeBegin... |
@Test public void testOverlapsWithUpstreamRegion() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithUpstreamRegion(new GenomeInterval(refDict, Strand.FWD, 1, 6640062, 6640064, PositionType.ZERO_BASED))); Assert.assertTrue(de... | public boolean overlapsWithUpstreamRegion(GenomeInterval interval) { GenomeInterval upstream = getUpstreamInterval(); return interval.overlapsWith(upstream); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithUpstreamRegion(GenomeInterval interval) { GenomeInterval upstream = getUpstreamInterval(); return interval.overlapsWith(upstream); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithUpstreamRegion(GenomeInterval interval) { GenomeInterval upstream = getUpstreamInterval(); return interval.overlapsWith(upstream); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithUpstreamRegion(GenomeInterval interval) { GenomeInterval upstream = getUpstreamInterval(); return interval.overlapsWith(upstream); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartC... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithUpstreamRegion(GenomeInterval interval) { GenomeInterval upstream = getUpstreamInterval(); return interval.overlapsWith(upstream); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartC... |
@Test public void testOverlapsWithDownstreamRegion() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithDownstreamRegion(new GenomeInterval(refDict, Strand.FWD, 1, 6649339, 6649340, PositionType.ZERO_BASED))); Assert.assertTru... | public boolean overlapsWithDownstreamRegion(GenomeInterval interval) { GenomeInterval downstream = getDownstreamInterval(); return interval.overlapsWith(downstream); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithDownstreamRegion(GenomeInterval interval) { GenomeInterval downstream = getDownstreamInterval(); return interval.overlapsWith(downstream); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithDownstreamRegion(GenomeInterval interval) { GenomeInterval downstream = getDownstreamInterval(); return interval.overlapsWith(downstream); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithDownstreamRegion(GenomeInterval interval) { GenomeInterval downstream = getDownstreamInterval(); return interval.overlapsWith(downstream); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval g... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithDownstreamRegion(GenomeInterval interval) { GenomeInterval downstream = getDownstreamInterval(); return interval.overlapsWith(downstream); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval g... |
@Test public void testOverlapsWithFivePrimeUTR() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithFivePrimeUTR(new GenomeInterval(refDict, Strand.FWD, 1, 6640669, 6640670, PositionType.ZERO_BASED))); Assert.assertTrue(decora... | public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval get... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithFivePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getFivePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval get... |
@Test public void testOverlapsWithThreePrimeUTR() { TranscriptSequenceOntologyDecorator decorator = new TranscriptSequenceOntologyDecorator(infoForward); Assert.assertFalse(decorator.overlapsWithThreePrimeUTR(new GenomeInterval(refDict, Strand.FWD, 1, 6649270, 6649272, PositionType.ZERO_BASED))); Assert.assertTrue(deco... | public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); } | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval g... | TranscriptSequenceOntologyDecorator { public boolean overlapsWithThreePrimeUTR(GenomeInterval interval) { return interval.overlapsWith(getThreePrimeUTRInterval()); } TranscriptSequenceOntologyDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); GenomeInterval getStartCodonInterval(); GenomeInterval g... |
@Test public void testGetCodonAt() throws Exception { TranscriptSequenceDecorator decorator = new TranscriptSequenceDecorator(MODEL); Assert.assertEquals(CODONS[CODONS.length - 1], decorator.getCodonAt(tx(START_LAST_CODON), cds(START_LAST_CODON))); Assert.assertEquals(CODONS[0], decorator.getCodonAt(tx(0), cds(0))); } | public String getCodonAt(TranscriptPosition txPos, CDSPosition cdsPos) throws InvalidCodonException { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3; if (transcript.getTrimmedSequence().length() < endPos) throw new InvalidCodonException("Could not access ... | TranscriptSequenceDecorator { public String getCodonAt(TranscriptPosition txPos, CDSPosition cdsPos) throws InvalidCodonException { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3; if (transcript.getTrimmedSequence().length() < endPos) throw new InvalidCod... | TranscriptSequenceDecorator { public String getCodonAt(TranscriptPosition txPos, CDSPosition cdsPos) throws InvalidCodonException { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3; if (transcript.getTrimmedSequence().length() < endPos) throw new InvalidCod... | TranscriptSequenceDecorator { public String getCodonAt(TranscriptPosition txPos, CDSPosition cdsPos) throws InvalidCodonException { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3; if (transcript.getTrimmedSequence().length() < endPos) throw new InvalidCod... | TranscriptSequenceDecorator { public String getCodonAt(TranscriptPosition txPos, CDSPosition cdsPos) throws InvalidCodonException { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3; if (transcript.getTrimmedSequence().length() < endPos) throw new InvalidCod... |
@Test public void testGetCodonsStartingFrom() throws Exception { TranscriptSequenceDecorator decorator = new TranscriptSequenceDecorator(MODEL); Assert.assertEquals(CODONS[0] + CODONS[1], decorator.getCodonsStartingFrom(tx(0), cds(0), 2)); Assert.assertEquals(CODONS[CODONS.length - 2] + CODONS[CODONS.length - 1], decor... | public String getCodonsStartingFrom(TranscriptPosition txPos, CDSPosition cdsPos, int count) { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3 * count; if (endPos > transcript.getTrimmedSequence().length()) endPos = transcript.getTrimmedSequence().length()... | TranscriptSequenceDecorator { public String getCodonsStartingFrom(TranscriptPosition txPos, CDSPosition cdsPos, int count) { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3 * count; if (endPos > transcript.getTrimmedSequence().length()) endPos = transcript... | TranscriptSequenceDecorator { public String getCodonsStartingFrom(TranscriptPosition txPos, CDSPosition cdsPos, int count) { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3 * count; if (endPos > transcript.getTrimmedSequence().length()) endPos = transcript... | TranscriptSequenceDecorator { public String getCodonsStartingFrom(TranscriptPosition txPos, CDSPosition cdsPos, int count) { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3 * count; if (endPos > transcript.getTrimmedSequence().length()) endPos = transcript... | TranscriptSequenceDecorator { public String getCodonsStartingFrom(TranscriptPosition txPos, CDSPosition cdsPos, int count) { int frameShift = cdsPos.getPos() % 3; int codonStart = txPos.getPos() - frameShift; int endPos = codonStart + 3 * count; if (endPos > transcript.getTrimmedSequence().length()) endPos = transcript... |
@Test public void testProjectionTranscriptToGenomeForwardSuccess() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoForward); Assert.assertEquals("1:g.6640063", projector.transcriptToGenomePos(new TranscriptPosition(infoForward, 1, PositionType.ONE_BASED)) .to... | public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLength(transcript.getSeqAlignment().... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... |
@Test public void testProjectionTranscriptToGenomeReverseSuccess() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoReverse); Assert.assertEquals("1:g.23696357", projector.transcriptToGenomePos(new TranscriptPosition(infoReverse, 1, PositionType.ONE_BASED)) .t... | public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLength(transcript.getSeqAlignment().... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... |
@Test(expected = ProjectionException.class) public void testProjectionTranscriptToGenomeThrowsLeft() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoForward); projector.transcriptToGenomePos(new TranscriptPosition(infoForward, 0, PositionType.ONE_BASED)); } | public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLength(transcript.getSeqAlignment().... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... |
@Test public void testSingletonToHGVSString() { Assert.assertEquals("[Leu101Arg]", singletonAllele.toHGVSString()); Assert.assertEquals("[Leu101Arg]", singletonAllele.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("[L101R]", singletonAllele.toHGVSString(AminoAcidCode.ONE_LETTER)); } | @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } } | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinChangeAllele(VariantConfiguration varConfig, Collection<? extends ProteinChange> changes); } | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinChangeAllele(VariantConfiguration varConfig, Collection<? extends ProteinChange> changes); static ProteinChangeAllele singleChangeAllele(Protei... | ProteinChangeAllele implements ConvertibleToHGVSString, List<ProteinChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } ProteinChangeAllele(VariantConfiguration varConfig, Collection<? extends ProteinChange> changes); static ProteinChangeAllele singleChangeAllele(Protei... |
@Test public void testToHGVSString() { Assert.assertEquals("(A124G)", sub1.toHGVSString(AminoAcidCode.ONE_LETTER)); Assert.assertEquals("(Ala124Gly)", sub1.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("(A124G)", sub1.toHGVSString()); } | @Override public String toHGVSString(AminoAcidCode code) { if (code == AminoAcidCode.THREE_LETTER) return wrapIfOnlyPredicted(location.toHGVSString(code) + Translator.getTranslator().toLong(targetAA)); else return wrapIfOnlyPredicted(location.toHGVSString(code) + targetAA); } | ProteinSubstitution extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { if (code == AminoAcidCode.THREE_LETTER) return wrapIfOnlyPredicted(location.toHGVSString(code) + Translator.getTranslator().toLong(targetAA)); else return wrapIfOnlyPredicted(location.toHGVSString(code) + targetAA); }... | ProteinSubstitution extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { if (code == AminoAcidCode.THREE_LETTER) return wrapIfOnlyPredicted(location.toHGVSString(code) + Translator.getTranslator().toLong(targetAA)); else return wrapIfOnlyPredicted(location.toHGVSString(code) + targetAA); }... | ProteinSubstitution extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { if (code == AminoAcidCode.THREE_LETTER) return wrapIfOnlyPredicted(location.toHGVSString(code) + Translator.getTranslator().toLong(targetAA)); else return wrapIfOnlyPredicted(location.toHGVSString(code) + targetAA); }... | ProteinSubstitution extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { if (code == AminoAcidCode.THREE_LETTER) return wrapIfOnlyPredicted(location.toHGVSString(code) + Translator.getTranslator().toLong(targetAA)); else return wrapIfOnlyPredicted(location.toHGVSString(code) + targetAA); }... |
@Test(expected = ProjectionException.class) public void testProjectionTranscriptToGenomeThrowsRight() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoForward); projector.transcriptToGenomePos(new TranscriptPosition(infoForward, 2350, PositionType.ONE_BASED));... | public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLength(transcript.getSeqAlignment().... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... | TranscriptProjectionDecorator { public GenomePosition transcriptToGenomePos(TranscriptPosition pos) throws ProjectionException { final int targetSeqPos = pos.getPos(); if (targetSeqPos < 0) { throw new ProjectionException("Invalid transcript sequence position " + targetSeqPos); } else if (targetSeqPos > Anchors.seqLeng... |
@Test public void testLocateIntronFromGenomePosForward() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoForward); this.builderForward = TranscriptModelFactory.parseKnownGenesLine(refDict, "uc001anx.3\tchr1\t+\t6640062\t6649340\t6640669\t6649272\t11" + "\t664... | public int locateIntron(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_INTRON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos)) return INVALID_INTRON_ID; i... | TranscriptProjectionDecorator { public int locateIntron(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_INTRON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(p... | TranscriptProjectionDecorator { public int locateIntron(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_INTRON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(p... | TranscriptProjectionDecorator { public int locateIntron(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_INTRON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(p... | TranscriptProjectionDecorator { public int locateIntron(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_INTRON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(p... |
@Test public void testLocateExonFromGenomePosForward() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoForward); Assert.assertEquals(0, projector.locateExon(new GenomePosition(refDict, Strand.FWD, 1, 6640063, PositionType.ONE_BASED))); Assert.assertEquals(0, ... | public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos)) return INVALID_EXON_ID; GenomeI... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... |
@Test public void testLocateExonFromGenomePosReverse() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoReverse); Assert.assertEquals(3, projector.locateExon(new GenomePosition(refDict, Strand.FWD, 1, 23685941, PositionType.ONE_BASED))); Assert.assertEquals(3,... | public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos)) return INVALID_EXON_ID; GenomeI... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... |
@Test public void testLocateExonFromTranscriptPosForward() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoForward); Assert.assertEquals(0, projector.locateExon(new TranscriptPosition(infoForward, 1, PositionType.ONE_BASED))); Assert.assertEquals(0, projector... | public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos)) return INVALID_EXON_ID; GenomeI... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... |
@Test public void testLocateExonFromTranscriptPosReverse() throws ProjectionException { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoReverse); Assert.assertEquals(3, projector.locateExon(new TranscriptPosition(infoReverse, 723, PositionType.ONE_BASED))); Assert.assertEquals(3, project... | public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos)) return INVALID_EXON_ID; GenomeI... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... | TranscriptProjectionDecorator { public int locateExon(GenomePosition pos) { if (pos.getChr() != transcript.getChr()) return INVALID_EXON_ID; if (pos.getStrand() != transcript.getStrand()) pos = pos.withStrand(transcript.getStrand()); if (transcript.getTXRegion().isLeftOf(pos) || transcript.getTXRegion().isRightOf(pos))... |
@Test public void testExonIDInReferenceOrderForward() { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoForward); for (int i = 0; i < 11; ++i) Assert.assertEquals(i, projector.exonIDInReferenceOrder(i)); } | public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } } | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } TranscriptProjectionDecorator(TranscriptModel transcript); } | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } TranscriptProjectionDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); String getCDSTranscript(); Str... | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } TranscriptProjectionDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); String getCDSTranscript(); Str... |
@Test public void testExonIDInReferenceOrderReverse() { TranscriptProjectionDecorator projector = new TranscriptProjectionDecorator(infoReverse); for (int i = 0; i < 4; ++i) Assert.assertEquals(3 - i, projector.exonIDInReferenceOrder(i)); } | public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } } | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } TranscriptProjectionDecorator(TranscriptModel transcript); } | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } TranscriptProjectionDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); String getCDSTranscript(); Str... | TranscriptProjectionDecorator { public int exonIDInReferenceOrder(int exonID) { if (transcript.getStrand().isForward()) return exonID; else return transcript.getExonRegions().size() - exonID - 1; } TranscriptProjectionDecorator(TranscriptModel transcript); TranscriptModel getTranscript(); String getCDSTranscript(); Str... |
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