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 testOnlyCurated() throws TranscriptParseException { RefSeqParser parser = new RefSeqParser(refDict, dataDirectory.getAbsolutePath(), new ArrayList<>(), curatedIniSection); ImmutableList<TranscriptModel> result = parser.run(); Assert.assertEquals(6, result.size()); SortedSet<String> values = new TreeSe... | private boolean onlyCurated() { return checkFlagInSection(iniSection.fetch("onlyCurated")); } | RefSeqParser implements TranscriptParser { private boolean onlyCurated() { return checkFlagInSection(iniSection.fetch("onlyCurated")); } } | RefSeqParser implements TranscriptParser { private boolean onlyCurated() { return checkFlagInSection(iniSection.fetch("onlyCurated")); } RefSeqParser(ReferenceDictionary refDict, String basePath, List<String> geneIdentifiers,
Section iniSection); } | RefSeqParser implements TranscriptParser { private boolean onlyCurated() { return checkFlagInSection(iniSection.fetch("onlyCurated")); } RefSeqParser(ReferenceDictionary refDict, String basePath, List<String> geneIdentifiers,
Section iniSection); @Override ImmutableList<TranscriptModel> run(); } | RefSeqParser implements TranscriptParser { private boolean onlyCurated() { return checkFlagInSection(iniSection.fetch("onlyCurated")); } RefSeqParser(ReferenceDictionary refDict, String basePath, List<String> geneIdentifiers,
Section iniSection); @Override ImmutableList<TranscriptModel> run(); } |
@Test public void testToHGVSString() { NucleotidePointLocation location1 = new NucleotidePointLocation(123, -3, false); NucleotidePointLocation location2 = new NucleotidePointLocation(123, 0, true); Assert.assertEquals("124-3", location1.toHGVSString()); Assert.assertEquals("124-3", location1.toHGVSString(AminoAcidCode... | @Override public String toHGVSString() { final int shift = (this.basePos >= 0) ? 1 : 0; final String prefix = downstreamOfCDS ? "*" : ""; if (offset == 0) return prefix + Integer.toString(this.basePos + shift); else if (offset > 0) return prefix + Joiner.on("").join(this.basePos + shift, "+", offset); else return prefi... | NucleotidePointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { final int shift = (this.basePos >= 0) ? 1 : 0; final String prefix = downstreamOfCDS ? "*" : ""; if (offset == 0) return prefix + Integer.toString(this.basePos + shift); else if (offset > 0) return prefix + Joiner.on("... | NucleotidePointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { final int shift = (this.basePos >= 0) ? 1 : 0; final String prefix = downstreamOfCDS ? "*" : ""; if (offset == 0) return prefix + Integer.toString(this.basePos + shift); else if (offset > 0) return prefix + Joiner.on("... | NucleotidePointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { final int shift = (this.basePos >= 0) ? 1 : 0; final String prefix = downstreamOfCDS ? "*" : ""; if (offset == 0) return prefix + Integer.toString(this.basePos + shift); else if (offset > 0) return prefix + Joiner.on("... | NucleotidePointLocation implements ConvertibleToHGVSString { @Override public String toHGVSString() { final int shift = (this.basePos >= 0) ? 1 : 0; final String prefix = downstreamOfCDS ? "*" : ""; if (offset == 0) return prefix + Integer.toString(this.basePos + shift); else if (offset > 0) return prefix + Joiner.on("... |
@Test public void testFactoryMethod() { Assert.assertEquals(sub1, ProteinSubstitution.build(true, "A", 123, "G")); } | public static ProteinSubstitution build(boolean onlyPredicted, String sourceAA, int pos, String targetAA) { return new ProteinSubstitution(onlyPredicted, ProteinPointLocation.build(sourceAA, pos), targetAA); } | ProteinSubstitution extends ProteinChange { public static ProteinSubstitution build(boolean onlyPredicted, String sourceAA, int pos, String targetAA) { return new ProteinSubstitution(onlyPredicted, ProteinPointLocation.build(sourceAA, pos), targetAA); } } | ProteinSubstitution extends ProteinChange { public static ProteinSubstitution build(boolean onlyPredicted, String sourceAA, int pos, String targetAA) { return new ProteinSubstitution(onlyPredicted, ProteinPointLocation.build(sourceAA, pos), targetAA); } ProteinSubstitution(boolean onlyPredicted, ProteinPointLocation lo... | ProteinSubstitution extends ProteinChange { public static ProteinSubstitution build(boolean onlyPredicted, String sourceAA, int pos, String targetAA) { return new ProteinSubstitution(onlyPredicted, ProteinPointLocation.build(sourceAA, pos), targetAA); } ProteinSubstitution(boolean onlyPredicted, ProteinPointLocation lo... | ProteinSubstitution extends ProteinChange { public static ProteinSubstitution build(boolean onlyPredicted, String sourceAA, int pos, String targetAA) { return new ProteinSubstitution(onlyPredicted, ProteinPointLocation.build(sourceAA, pos), targetAA); } ProteinSubstitution(boolean onlyPredicted, ProteinPointLocation lo... |
@Test public void testRun() throws Exception { Path dataDirectory = Paths.get("src/test/resources/build/hg19/refseq").toAbsolutePath(); Ini iniFile = new Ini(); iniFile.load(Paths.get("src/test/resources/build/default_sources.ini").toFile()); Profile.Section iniSection = iniFile.get("hg19/refseq"); ReferenceDictionary ... | @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC information to {} transcripts..", builders.s... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... |
@Test public void testBuildLtbp4() throws IOException, TranscriptParseException, ProjectionException { Path dataDirectory = Paths.get("src/test/resources/build/hg19/refseq_ltbp4") .toAbsolutePath(); Ini iniFile = new Ini(); iniFile.load( Paths.get("src/test/resources/build/hg19/refseq_ltbp4/default_sources.ini").toFile... | @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC information to {} transcripts..", builders.s... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... |
@Test public void testBuildHfm1() throws IOException, TranscriptParseException, ProjectionException { Path dataDirectory = Paths.get("src/test/resources/build/hg19/refseq_hfm1") .toAbsolutePath(); Ini iniFile = new Ini(); iniFile.load( Paths.get("src/test/resources/build/hg19/refseq_hfm1/default_sources.ini").toFile())... | @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC information to {} transcripts..", builders.s... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... |
@Test public void testBuildMyh7() throws IOException, TranscriptParseException, ProjectionException { Path dataDirectory = Paths.get("src/test/resources/build/hg19/refseq_myh7") .toAbsolutePath(); Ini iniFile = new Ini(); iniFile.load( Paths.get("src/test/resources/build/hg19/refseq_hfm1/default_sources.ini").toFile())... | @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC information to {} transcripts..", builders.s... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... | RefSeqParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGFF = PathUtil.join(basePath, getINIFileName("gff")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGFF); LOGGER.info("Assigning additional HGNC i... |
@Test public void test() throws IOException { GFFParser parser = new GFFParser(stream); ArrayList<FeatureRecord> records = new ArrayList<>(); FeatureRecord record; while ((record = parser.next()) != null) records.add(record); Assert.assertEquals(12, records.size()); Assert.assertEquals( "FeatureRecord [seqID=NC_000003.... | public FeatureRecord next() throws IOException { if (lastLine == null) return null; FeatureRecord result = recordParser.parseLine(lastLine); do { lastLine = reader.readLine(); } while (lastLine != null && lastLine.startsWith("#")); return result; } | GFFParser { public FeatureRecord next() throws IOException { if (lastLine == null) return null; FeatureRecord result = recordParser.parseLine(lastLine); do { lastLine = reader.readLine(); } while (lastLine != null && lastLine.startsWith("#")); return result; } } | GFFParser { public FeatureRecord next() throws IOException { if (lastLine == null) return null; FeatureRecord result = recordParser.parseLine(lastLine); do { lastLine = reader.readLine(); } while (lastLine != null && lastLine.startsWith("#")); return result; } GFFParser(File file); GFFParser(InputStream stream); } | GFFParser { public FeatureRecord next() throws IOException { if (lastLine == null) return null; FeatureRecord result = recordParser.parseLine(lastLine); do { lastLine = reader.readLine(); } while (lastLine != null && lastLine.startsWith("#")); return result; } GFFParser(File file); GFFParser(InputStream stream); Featu... | GFFParser { public FeatureRecord next() throws IOException { if (lastLine == null) return null; FeatureRecord result = recordParser.parseLine(lastLine); do { lastLine = reader.readLine(); } while (lastLine != null && lastLine.startsWith("#")); return result; } GFFParser(File file); GFFParser(InputStream stream); Featu... |
@Test public void testRun() throws Exception { Path dataDirectory = Paths.get("src/test/resources/build/hg19/ensembl"); Ini iniFile = new Ini(); iniFile.load(Paths.get("src/test/resources/build/default_sources.ini").toFile()); Profile.Section iniSection = iniFile.get("hg19/ensembl"); ReferenceDictionary refDict = HG19R... | @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGTF = PathUtil.join(basePath, getINIFileName("gtf")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGTF); LOGGER.info("Loading ENSEMBL to HGNC mappings..."); final Map<String, String> ensgT... | EnsemblParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGTF = PathUtil.join(basePath, getINIFileName("gtf")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGTF); LOGGER.info("Loading ENSEMBL to HGNC ma... | EnsemblParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGTF = PathUtil.join(basePath, getINIFileName("gtf")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGTF); LOGGER.info("Loading ENSEMBL to HGNC ma... | EnsemblParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGTF = PathUtil.join(basePath, getINIFileName("gtf")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGTF); LOGGER.info("Loading ENSEMBL to HGNC ma... | EnsemblParser implements TranscriptParser { @Override public ImmutableList<TranscriptModel> run() throws TranscriptParseException { final String pathGTF = PathUtil.join(basePath, getINIFileName("gtf")); Map<String, TranscriptModelBuilder> builders = loadTranscriptModels(pathGTF); LOGGER.info("Loading ENSEMBL to HGNC ma... |
@Test public void testToString() { NucleotideDeletion del = NucleotideDeletion.buildWithOffsetWithLength(true, 123, 0, 124, 0, 2); System.out.println(del); } | @Override public String toString() { return "NucleotideDeletion [range=" + range + ", seq=" + seq + "]"; } | NucleotideDeletion extends NucleotideChange { @Override public String toString() { return "NucleotideDeletion [range=" + range + ", seq=" + seq + "]"; } } | NucleotideDeletion extends NucleotideChange { @Override public String toString() { return "NucleotideDeletion [range=" + range + ", seq=" + seq + "]"; } NucleotideDeletion(boolean onlyPredicted, NucleotideRange range, NucleotideSeqDescription seq); } | NucleotideDeletion extends NucleotideChange { @Override public String toString() { return "NucleotideDeletion [range=" + range + ", seq=" + seq + "]"; } NucleotideDeletion(boolean onlyPredicted, NucleotideRange range, NucleotideSeqDescription seq); static NucleotideDeletion buildWithOffset(boolean onlyPredicted, int fi... | NucleotideDeletion extends NucleotideChange { @Override public String toString() { return "NucleotideDeletion [range=" + range + ", seq=" + seq + "]"; } NucleotideDeletion(boolean onlyPredicted, NucleotideRange range, NucleotideSeqDescription seq); static NucleotideDeletion buildWithOffset(boolean onlyPredicted, int fi... |
@Test public void testToHGVSString() { Assert.assertEquals("21_24(1_2)", srr.toHGVSString()); Assert.assertEquals("21_24(3_6)", srr2.toHGVSString()); } | @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(range.toHGVSString(), "(", minCount, "_", maxCount, ")")); } | NucleotideShortSequenceRepeatVariability extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(range.toHGVSString(), "(", minCount, "_", maxCount, ")")); } } | NucleotideShortSequenceRepeatVariability extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(range.toHGVSString(), "(", minCount, "_", maxCount, ")")); } NucleotideShortSequenceRepeatVariability(boolean onlyPredicted, NucleotideRange range, int minCount,
... | NucleotideShortSequenceRepeatVariability extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(range.toHGVSString(), "(", minCount, "_", maxCount, ")")); } NucleotideShortSequenceRepeatVariability(boolean onlyPredicted, NucleotideRange range, int minCount,
... | NucleotideShortSequenceRepeatVariability extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(range.toHGVSString(), "(", minCount, "_", maxCount, ")")); } NucleotideShortSequenceRepeatVariability(boolean onlyPredicted, NucleotideRange range, int minCount,
... |
@Test public void testBuildWithOffset() { Assert.assertEquals(subWithOffset, NucleotideSubstitution.buildWithOffset(true, 10, 1, "A", "T")); } | public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } } | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } Nucleotid... | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } Nucleotid... | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } Nucleotid... |
@Test public void testBuildWithoutOffset() { Assert.assertEquals(subWithoutOffset, NucleotideSubstitution.buildWithOffset(true, 10, 0, "A", "T")); } | public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } } | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } Nucleotid... | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } Nucleotid... | NucleotideSubstitution extends NucleotideChange { public static NucleotideSubstitution buildWithOffset(boolean onlyPredicted, int basePos, int posOffset, String fromNT, String toNT) { return new NucleotideSubstitution(onlyPredicted, NucleotidePointLocation.buildWithOffset(basePos, posOffset), fromNT, toNT); } Nucleotid... |
@Test public void testToStringWithOffset() { Assert.assertEquals("(11+1A>T)", subWithOffset.toHGVSString()); } | @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } } | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } NucleotideSubstitution(boolean onlyPredicted, NucleotidePointLocation position, String fromNT, String toNT); } | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } NucleotideSubstitution(boolean onlyPredicted, NucleotidePointLocation position, String fromNT, String toNT); static NucleotideSubstitut... | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } NucleotideSubstitution(boolean onlyPredicted, NucleotidePointLocation position, String fromNT, String toNT); static NucleotideSubstitut... |
@Test public void testToStringWithoutOffset() { Assert.assertEquals("(11A>T)", subWithoutOffset.toHGVSString()); } | @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } } | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } NucleotideSubstitution(boolean onlyPredicted, NucleotidePointLocation position, String fromNT, String toNT); } | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } NucleotideSubstitution(boolean onlyPredicted, NucleotidePointLocation position, String fromNT, String toNT); static NucleotideSubstitut... | NucleotideSubstitution extends NucleotideChange { @Override public String toHGVSString() { return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(), fromNT, ">", toNT)); } NucleotideSubstitution(boolean onlyPredicted, NucleotidePointLocation position, String fromNT, String toNT); static NucleotideSubstitut... |
@Test public void testToHGVSStringSingleChange() { Assert.assertEquals("REF:c.[100A>G;301A>C]", singleAlleleVariant.toHGVSString(AminoAcidCode.ONE_LETTER)); Assert.assertEquals("REF:c.[100A>G;301A>C]", singleAlleleVariant.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("REF:c.[100A>G;301A>C]", singleAlle... | @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false; else parts.add(";"); parts.add(allele.toHGVSString()); }... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... |
@Test public void testToHGVSStringMultiChange() { Assert.assertEquals("REF:c.[100A>G;301A>C];[34T>C;301A>G]", multiAlleleVariant.toHGVSString(AminoAcidCode.ONE_LETTER)); Assert.assertEquals("REF:c.[100A>G;301A>C];[34T>C;301A>G]", multiAlleleVariant.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("REF:c.[... | @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false; else parts.add(";"); parts.add(allele.toHGVSString()); }... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... | MultiAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { ArrayList<String> parts = new ArrayList<>(); parts.add(getRefIDWithVersion()); parts.add(":"); parts.add(seqType.getPrefix()); boolean first = true; for (NucleotideChangeAllele allele : alleles) { if (first) first = false;... |
@Test public void testMultiChangeStaticFactory() { Assert.assertEquals( multiChangeAllele, NucleotideChangeAllele.build(VariantConfiguration.CHIMERIC, NucleotideSubstitution.build(false, 100, "C", "A"), NucleotideSubstitution.build(false, 99, "C", "A"))); } | public static NucleotideChangeAllele build(VariantConfiguration varConfig, NucleotideChange... changes) { return new NucleotideChangeAllele(varConfig, ImmutableList.copyOf(changes)); } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { public static NucleotideChangeAllele build(VariantConfiguration varConfig, NucleotideChange... changes) { return new NucleotideChangeAllele(varConfig, ImmutableList.copyOf(changes)); } } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { public static NucleotideChangeAllele build(VariantConfiguration varConfig, NucleotideChange... changes) { return new NucleotideChangeAllele(varConfig, ImmutableList.copyOf(changes)); } NucleotideChangeAllele(VariantConfiguration varConf... | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { public static NucleotideChangeAllele build(VariantConfiguration varConfig, NucleotideChange... changes) { return new NucleotideChangeAllele(varConfig, ImmutableList.copyOf(changes)); } NucleotideChangeAllele(VariantConfiguration varConf... | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { public static NucleotideChangeAllele build(VariantConfiguration varConfig, NucleotideChange... changes) { return new NucleotideChangeAllele(varConfig, ImmutableList.copyOf(changes)); } NucleotideChangeAllele(VariantConfiguration varConf... |
@Test public void testSingletonToHGVSString() { Assert.assertEquals("[101C>A]", singletonAllele.toHGVSString()); Assert.assertEquals("[101C>A]", singletonAllele.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("[101C>A]", singletonAllele.toHGVSString(AminoAcidCode.ONE_LETTER)); } | @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } NucleotideChangeAllele(VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes); } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } NucleotideChangeAllele(VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes); static NucleotideChangeAllele singleChan... | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } NucleotideChangeAllele(VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes); static NucleotideChangeAllele singleChan... |
@Test public void testConstructFullFrameshift() { Assert.assertEquals(fullFrameshift, ProteinFrameshift.build(false, position, "T", 23)); } | public static ProteinFrameshift build(boolean onlyPredicted, String wtAA, int position, String targetAA, int shiftLength) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, shiftLength); } | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift build(boolean onlyPredicted, String wtAA, int position, String targetAA, int shiftLength) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, shiftLength); } } | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift build(boolean onlyPredicted, String wtAA, int position, String targetAA, int shiftLength) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, shiftLength); } ProteinFrameshift(boolean onlyPredicted,... | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift build(boolean onlyPredicted, String wtAA, int position, String targetAA, int shiftLength) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, shiftLength); } ProteinFrameshift(boolean onlyPredicted,... | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift build(boolean onlyPredicted, String wtAA, int position, String targetAA, int shiftLength) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, shiftLength); } ProteinFrameshift(boolean onlyPredicted,... |
@Test public void testMultVariantToHGVSString() { Assert.assertEquals("[101C>A Assert.assertEquals("[101C>A Assert.assertEquals("[101C>A } | @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } NucleotideChangeAllele(VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes); } | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } NucleotideChangeAllele(VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes); static NucleotideChangeAllele singleChan... | NucleotideChangeAllele implements ConvertibleToHGVSString, List<NucleotideChange> { @Override public String toHGVSString() { return toHGVSString(AminoAcidCode.THREE_LETTER); } NucleotideChangeAllele(VariantConfiguration varConfig, Collection<? extends NucleotideChange> changes); static NucleotideChangeAllele singleChan... |
@Test public void testToHGVSStringSingleChange() { Assert.assertEquals("REF:c.100A>G", singleChangeVariant.toHGVSString(AminoAcidCode.ONE_LETTER)); Assert.assertEquals("REF:c.100A>G", singleChangeVariant.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("REF:c.100A>G", singleChangeVariant.toHGVSString()); ... | @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new ArrayList<>(); parts.add(getSequenceNamePrefix()); parts.ad... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... |
@Test public void testToHGVSStringMultiChange() { Assert.assertEquals("REF:c.[100C>T;301A>G]", multiChangeVariant.toHGVSString(AminoAcidCode.ONE_LETTER)); Assert.assertEquals("REF:c.[100C>T;301A>G]", multiChangeVariant.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("REF:c.[100C>T;301A>G]", multiChangeVa... | @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new ArrayList<>(); parts.add(getSequenceNamePrefix()); parts.ad... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... | SingleAlleleNucleotideVariant extends NucleotideVariant { @Override public String toHGVSString() { if (hasOnlyOneChange()) return Joiner.on("").join(getSequenceNamePrefix(), ":", seqType.getPrefix(), getChange().toHGVSString()); final String sep = allele.getVarConfig().toHGVSSeparator(); ArrayList<String> parts = new A... |
@Test public void test() throws JannovarVarDBException { VCFHeader header = new VCFHeader(); Assert.assertEquals(0, header.getFilterLines().size()); Assert.assertEquals(0, header.getInfoHeaderLines().size()); Assert.assertEquals(0, header.getFormatHeaderLines().size()); Assert.assertEquals(0, header.getIDHeaderLines().... | @Override public void addHeaders(VCFHeader header, String prefix) { for (GnomadPopulation pop : GnomadPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(header, prefix, "", "", pop); addACHomHeader(header, p... | GnomadVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (GnomadPopulation pop : GnomadPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(he... | GnomadVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (GnomadPopulation pop : GnomadPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(he... | GnomadVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (GnomadPopulation pop : GnomadPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(he... | GnomadVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (GnomadPopulation pop : GnomadPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(he... |
@Test public void test() { VCFHeader header = new VCFHeader(); Assert.assertEquals(0, header.getFilterLines().size()); Assert.assertEquals(0, header.getInfoHeaderLines().size()); Assert.assertEquals(0, header.getFormatHeaderLines().size()); Assert.assertEquals(0, header.getIDHeaderLines().size()); Assert.assertEquals(0... | @Override public void addHeaders(VCFHeader header, String prefix) { addHeaders(header, prefix, "", ""); final String note = " (requiring no genotype match, only position overlap)"; if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeaders(header, prefix, "OVL_", note); } | ClinVarVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeaders(header, prefix, "", ""); final String note = " (requiring no genotype match, only position overlap)"; if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHead... | ClinVarVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeaders(header, prefix, "", ""); final String note = " (requiring no genotype match, only position overlap)"; if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHead... | ClinVarVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeaders(header, prefix, "", ""); final String note = " (requiring no genotype match, only position overlap)"; if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHead... | ClinVarVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeaders(header, prefix, "", ""); final String note = " (requiring no genotype match, only position overlap)"; if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHead... |
@Test public void test() { ClinVarVariantContextToRecordConverter converter = new ClinVarVariantContextToRecordConverter(); CloseableIterator<VariantContext> it = vcfReader.iterator(); VariantContext vc = null; while (vc == null || !vc.getID().equals("rs387907305")) vc = it.next(); ClinVarRecord record = converter.conv... | @Override public ClinVarRecord convert(VariantContext vc) { ClinVarRecordBuilder builder = new ClinVarRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getReference().getBaseString()); for (Allele all : vc.getAlternateAlleles()) builder.g... | ClinVarVariantContextToRecordConverter implements VariantContextToRecordConverter<ClinVarRecord> { @Override public ClinVarRecord convert(VariantContext vc) { ClinVarRecordBuilder builder = new ClinVarRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); build... | ClinVarVariantContextToRecordConverter implements VariantContextToRecordConverter<ClinVarRecord> { @Override public ClinVarRecord convert(VariantContext vc) { ClinVarRecordBuilder builder = new ClinVarRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); build... | ClinVarVariantContextToRecordConverter implements VariantContextToRecordConverter<ClinVarRecord> { @Override public ClinVarRecord convert(VariantContext vc) { ClinVarRecordBuilder builder = new ClinVarRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); build... | ClinVarVariantContextToRecordConverter implements VariantContextToRecordConverter<ClinVarRecord> { @Override public ClinVarRecord convert(VariantContext vc) { ClinVarRecordBuilder builder = new ClinVarRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); build... |
@Test public void test() { CosmicVariantContextToRecordConverter converter = new CosmicVariantContextToRecordConverter(); VariantContext vc = vcfReader.iterator().next(); CosmicRecord record = converter.convert(vc); Assert.assertEquals("CosmicRecord [chrom=1, pos=1230, id=COSM1231, ref=A, alt=[C], cnt=1, snp=false]", r... | @Override public CosmicRecord convert(VariantContext vc) { CosmicRecordBuilder builder = new CosmicRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getReference().getBaseString()); for (Allele all : vc.getAlternateAlleles()) builder.getA... | CosmicVariantContextToRecordConverter implements VariantContextToRecordConverter<CosmicRecord> { @Override public CosmicRecord convert(VariantContext vc) { CosmicRecordBuilder builder = new CosmicRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.se... | CosmicVariantContextToRecordConverter implements VariantContextToRecordConverter<CosmicRecord> { @Override public CosmicRecord convert(VariantContext vc) { CosmicRecordBuilder builder = new CosmicRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.se... | CosmicVariantContextToRecordConverter implements VariantContextToRecordConverter<CosmicRecord> { @Override public CosmicRecord convert(VariantContext vc) { CosmicRecordBuilder builder = new CosmicRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.se... | CosmicVariantContextToRecordConverter implements VariantContextToRecordConverter<CosmicRecord> { @Override public CosmicRecord convert(VariantContext vc) { CosmicRecordBuilder builder = new CosmicRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.se... |
@Test public void test() throws JannovarVarDBException { VCFHeader header = new VCFHeader(); Assert.assertEquals(0, header.getFilterLines().size()); Assert.assertEquals(0, header.getInfoHeaderLines().size()); Assert.assertEquals(0, header.getFormatHeaderLines().size()); Assert.assertEquals(0, header.getIDHeaderLines().... | @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only position overlap)"); } | CosmicVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only... | CosmicVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only... | CosmicVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only... | CosmicVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only... |
@Test public void test() { ExacVariantContextToRecordConverter converter = new ExacVariantContextToRecordConverter(); VariantContext vc = vcfReader.iterator().next(); ExacRecord record = converter.convert(vc); Assert.assertEquals( "ExacRecord [chrom=1, pos=13371, id=., ref=G, alt=[C], filter=[], " + "alleleCounts={AFR=... | @Override public ExacRecord convert(VariantContext vc) { ExacRecordBuilder builder = new ExacRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getReference().getBaseString()); for (Allele all : vc.getAlternateAlleles()) builder.getAlt().a... | ExacVariantContextToRecordConverter implements VariantContextToRecordConverter<ExacRecord> { @Override public ExacRecord convert(VariantContext vc) { ExacRecordBuilder builder = new ExacRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.ge... | ExacVariantContextToRecordConverter implements VariantContextToRecordConverter<ExacRecord> { @Override public ExacRecord convert(VariantContext vc) { ExacRecordBuilder builder = new ExacRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.ge... | ExacVariantContextToRecordConverter implements VariantContextToRecordConverter<ExacRecord> { @Override public ExacRecord convert(VariantContext vc) { ExacRecordBuilder builder = new ExacRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.ge... | ExacVariantContextToRecordConverter implements VariantContextToRecordConverter<ExacRecord> { @Override public ExacRecord convert(VariantContext vc) { ExacRecordBuilder builder = new ExacRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.ge... |
@Test public void test() throws JannovarVarDBException { VCFHeader header = new VCFHeader(); Assert.assertEquals(0, header.getFilterLines().size()); Assert.assertEquals(0, header.getInfoHeaderLines().size()); Assert.assertEquals(0, header.getFormatHeaderLines().size()); Assert.assertEquals(0, header.getIDHeaderLines().... | @Override public void addHeaders(VCFHeader header, String prefix) { for (ExacPopulation pop : ExacPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(header, prefix, "", "", pop); addACHomHeader(header, prefi... | ExacVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (ExacPopulation pop : ExacPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(header, ... | ExacVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (ExacPopulation pop : ExacPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(header, ... | ExacVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (ExacPopulation pop : ExacPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(header, ... | ExacVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { for (ExacPopulation pop : ExacPopulation.values()) { addACHeader(header, prefix, "", "", pop); addANHeader(header, prefix, "", "", pop); addAFHeader(header, prefix, "", "", pop); addACHetHeader(header, ... |
@Test public void testConstructNoTerFrameshift() { Assert.assertEquals(noTerFrameshift, ProteinFrameshift.buildWithoutTerminal(false, position, "T")); } | public static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted, String wtAA, int position, String targetAA) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, LEN_NO_TER); } | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted, String wtAA, int position, String targetAA) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, LEN_NO_TER); } } | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted, String wtAA, int position, String targetAA) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, LEN_NO_TER); } ProteinFrameshift(boolean onlyPredicted, Pr... | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted, String wtAA, int position, String targetAA) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, LEN_NO_TER); } ProteinFrameshift(boolean onlyPredicted, Pr... | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildWithoutTerminal(boolean onlyPredicted, String wtAA, int position, String targetAA) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), targetAA, LEN_NO_TER); } ProteinFrameshift(boolean onlyPredicted, Pr... |
@Test public void test() throws JannovarVarDBException { DBVariantContextAnnotator annotator = new DBVariantContextAnnotatorFactory().constructDBSNP(pathDBVCF, pathRefFASTA, options); VariantContextWriter writer = new VariantContextWriterBuilder().setOutputStream(outStream) .unsetOption(Options.INDEX_ON_THE_FLY).build(... | public DBVariantContextAnnotator constructDBSNP(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException { return new DBVariantContextAnnotator( new DBSNPAnnotationDriver(vcfDBPath, fastaRefPath, options), options); } | DBVariantContextAnnotatorFactory { public DBVariantContextAnnotator constructDBSNP(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException { return new DBVariantContextAnnotator( new DBSNPAnnotationDriver(vcfDBPath, fastaRefPath, options), options); } } | DBVariantContextAnnotatorFactory { public DBVariantContextAnnotator constructDBSNP(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException { return new DBVariantContextAnnotator( new DBSNPAnnotationDriver(vcfDBPath, fastaRefPath, options), options); } } | DBVariantContextAnnotatorFactory { public DBVariantContextAnnotator constructDBSNP(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException { return new DBVariantContextAnnotator( new DBSNPAnnotationDriver(vcfDBPath, fastaRefPath, options), options); } DBVariantContextAnnotator... | DBVariantContextAnnotatorFactory { public DBVariantContextAnnotator constructDBSNP(String vcfDBPath, String fastaRefPath, DBAnnotationOptions options) throws JannovarVarDBException { return new DBVariantContextAnnotator( new DBSNPAnnotationDriver(vcfDBPath, fastaRefPath, options), options); } DBVariantContextAnnotator... |
@Test public void test() { UK10KVariantContextToRecordConverter converter = new UK10KVariantContextToRecordConverter(); VariantContext vc = vcfReader.iterator().next(); UK10KRecord record = converter.convert(vc); Assert.assertEquals( "UK10KRecord [chrom=1, pos=28589, id=., ref=T, alt=[TTGG], filter=[], " + "altAlleleCo... | @Override public UK10KRecord convert(VariantContext vc) { UK10KRecordBuilder builder = new UK10KRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getReference().getBaseString()); for (Allele all : vc.getAlternateAlleles()) builder.getAlt(... | UK10KVariantContextToRecordConverter implements VariantContextToRecordConverter<UK10KRecord> { @Override public UK10KRecord convert(VariantContext vc) { UK10KRecordBuilder builder = new UK10KRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(... | UK10KVariantContextToRecordConverter implements VariantContextToRecordConverter<UK10KRecord> { @Override public UK10KRecord convert(VariantContext vc) { UK10KRecordBuilder builder = new UK10KRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(... | UK10KVariantContextToRecordConverter implements VariantContextToRecordConverter<UK10KRecord> { @Override public UK10KRecord convert(VariantContext vc) { UK10KRecordBuilder builder = new UK10KRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(... | UK10KVariantContextToRecordConverter implements VariantContextToRecordConverter<UK10KRecord> { @Override public UK10KRecord convert(VariantContext vc) { UK10KRecordBuilder builder = new UK10KRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(... |
@Test public void test() throws JannovarVarDBException { VCFHeader header = new VCFHeader(); Assert.assertEquals(0, header.getFilterLines().size()); Assert.assertEquals(0, header.getInfoHeaderLines().size()); Assert.assertEquals(0, header.getFormatHeaderLines().size()); Assert.assertEquals(0, header.getIDHeaderLines().... | @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only position overlap)"); } | UK10KVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... | UK10KVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... | UK10KVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... | UK10KVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... |
@Test public void test() { DBSNPVariantContextToRecordConverter converter = new DBSNPVariantContextToRecordConverter(); VariantContext vc = vcfReader.iterator().next(); DBSNPRecord record = converter.convert(vc); Assert.assertEquals("DBSNPRecord [chrom=1, pos=10018, id=rs775809821, ref=TA, alt=[T], " + "filter=[], rsID... | public DBSNPRecord convert(VariantContext vc) { DBSNPRecordBuilder builder = new DBSNPRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getReference().getBaseString()); for (Allele all : vc.getAlternateAlleles()) builder.getAlt().add(all.... | DBSNPVariantContextToRecordConverter implements VariantContextToRecordConverter<DBSNPRecord> { public DBSNPRecord convert(VariantContext vc) { DBSNPRecordBuilder builder = new DBSNPRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getRefe... | DBSNPVariantContextToRecordConverter implements VariantContextToRecordConverter<DBSNPRecord> { public DBSNPRecord convert(VariantContext vc) { DBSNPRecordBuilder builder = new DBSNPRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getRefe... | DBSNPVariantContextToRecordConverter implements VariantContextToRecordConverter<DBSNPRecord> { public DBSNPRecord convert(VariantContext vc) { DBSNPRecordBuilder builder = new DBSNPRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getRefe... | DBSNPVariantContextToRecordConverter implements VariantContextToRecordConverter<DBSNPRecord> { public DBSNPRecord convert(VariantContext vc) { DBSNPRecordBuilder builder = new DBSNPRecordBuilder(); builder.setContig(vc.getContig()); builder.setPos(vc.getStart() - 1); builder.setID(vc.getID()); builder.setRef(vc.getRefe... |
@Test public void test() throws JannovarVarDBException { VCFHeader header = new VCFHeader(); Assert.assertEquals(0, header.getFilterLines().size()); Assert.assertEquals(0, header.getInfoHeaderLines().size()); Assert.assertEquals(0, header.getFormatHeaderLines().size()); Assert.assertEquals(0, header.getIDHeaderLines().... | @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only position overlap)"); } | DBSNPVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... | DBSNPVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... | DBSNPVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... | DBSNPVCFHeaderExtender extends VCFHeaderExtender { @Override public void addHeaders(VCFHeader header, String prefix) { addHeadersInfixes(header, prefix, "", ""); if (options.isReportOverlapping() && !options.isReportOverlappingAsMatching()) addHeadersInfixes(header, prefix, "OVL_", " (requiring no genotype match, only ... |
@Test public void test() { DBSNPInfoFactory factory = new DBSNPInfoFactory(); DBSNPInfo info = factory.build(vcfReader.getFileHeader()); Assert.assertEquals("20160408", info.getFileDate()); Assert.assertEquals("dbSNP", info.getSource()); Assert.assertEquals(147, info.getDbSNPBuildID()); Assert.assertEquals("GRCh37.p13"... | public DBSNPInfo build(VCFHeader vcfHeader) { String fileDate = vcfHeader.getMetaDataLine("fileDate").getValue(); String source = vcfHeader.getMetaDataLine("source").getValue(); int dbSNPBuildID = Integer.parseInt(vcfHeader.getMetaDataLine("dbSNP_BUILD_ID").getValue()); String reference = vcfHeader.getMetaDataLine("ref... | DBSNPInfoFactory { public DBSNPInfo build(VCFHeader vcfHeader) { String fileDate = vcfHeader.getMetaDataLine("fileDate").getValue(); String source = vcfHeader.getMetaDataLine("source").getValue(); int dbSNPBuildID = Integer.parseInt(vcfHeader.getMetaDataLine("dbSNP_BUILD_ID").getValue()); String reference = vcfHeader.g... | DBSNPInfoFactory { public DBSNPInfo build(VCFHeader vcfHeader) { String fileDate = vcfHeader.getMetaDataLine("fileDate").getValue(); String source = vcfHeader.getMetaDataLine("source").getValue(); int dbSNPBuildID = Integer.parseInt(vcfHeader.getMetaDataLine("dbSNP_BUILD_ID").getValue()); String reference = vcfHeader.g... | DBSNPInfoFactory { public DBSNPInfo build(VCFHeader vcfHeader) { String fileDate = vcfHeader.getMetaDataLine("fileDate").getValue(); String source = vcfHeader.getMetaDataLine("source").getValue(); int dbSNPBuildID = Integer.parseInt(vcfHeader.getMetaDataLine("dbSNP_BUILD_ID").getValue()); String reference = vcfHeader.g... | DBSNPInfoFactory { public DBSNPInfo build(VCFHeader vcfHeader) { String fileDate = vcfHeader.getMetaDataLine("fileDate").getValue(); String source = vcfHeader.getMetaDataLine("source").getValue(); int dbSNPBuildID = Integer.parseInt(vcfHeader.getMetaDataLine("dbSNP_BUILD_ID").getValue()); String reference = vcfHeader.g... |
@Test public void testMatchSingle() throws JannovarVarDBException { AlleleMatcher matcher = new AlleleMatcher(fastaPath); Collection<GenotypeMatch> matches = matcher.matchGenotypes(vcSingle, vcSingle); assertEquals(1, matches.size()); GenotypeMatch first = (GenotypeMatch) matches.toArray()[0]; Assert.assertSame(vcSingl... | public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsVar : obsVars) { ... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... |
@Test public void testMatchSingleToMultiple() throws JannovarVarDBException { AlleleMatcher matcher = new AlleleMatcher(fastaPath); Collection<GenotypeMatch> matches = matcher.matchGenotypes(vcSingle, vcMultiple); assertEquals(1, matches.size()); GenotypeMatch first = (GenotypeMatch) matches.toArray()[0]; Assert.assert... | public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsVar : obsVars) { ... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... |
@Test public void testMatchMultipleToSingle() throws JannovarVarDBException { AlleleMatcher matcher = new AlleleMatcher(fastaPath); Collection<GenotypeMatch> matches = matcher.matchGenotypes(vcMultiple, vcSingle); assertEquals(1, matches.size()); GenotypeMatch first = (GenotypeMatch) matches.toArray()[0]; Assert.assert... | public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsVar : obsVars) { ... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... |
@Test public void testMatchMultipleToMultiple() throws JannovarVarDBException { AlleleMatcher matcher = new AlleleMatcher(fastaPath); Collection<GenotypeMatch> matches = matcher.matchGenotypes(vcMultiple, vcMultiple); assertEquals(2, matches.size()); GenotypeMatch first = (GenotypeMatch) matches.toArray()[0]; Assert.as... | public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsVar : obsVars) { ... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... | AlleleMatcher { public Collection<GenotypeMatch> matchGenotypes(VariantContext obsVC, VariantContext dbVC) { List<GenotypeMatch> result = new ArrayList<>(); Collection<VariantDescription> obsVars = ctxToVariants(obsVC); Collection<VariantDescription> dbVars = ctxToVariants(dbVC); int i = 1; for (VariantDescription obsV... |
@Test public void testConstructShortFrameshift() { Assert.assertEquals(shortFrameshift, ProteinFrameshift.buildShort(false, position)); } | public static ProteinFrameshift buildShort(boolean onlyPredicted, String wtAA, int position) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), null, LEN_SHORT); } | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildShort(boolean onlyPredicted, String wtAA, int position) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), null, LEN_SHORT); } } | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildShort(boolean onlyPredicted, String wtAA, int position) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), null, LEN_SHORT); } ProteinFrameshift(boolean onlyPredicted, ProteinPointLocation position, Str... | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildShort(boolean onlyPredicted, String wtAA, int position) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), null, LEN_SHORT); } ProteinFrameshift(boolean onlyPredicted, ProteinPointLocation position, Str... | ProteinFrameshift extends ProteinChange { public static ProteinFrameshift buildShort(boolean onlyPredicted, String wtAA, int position) { return new ProteinFrameshift(onlyPredicted, ProteinPointLocation.build(wtAA, position), null, LEN_SHORT); } ProteinFrameshift(boolean onlyPredicted, ProteinPointLocation position, Str... |
@Test public void testSNV() { VariantDescription descIn = new VariantDescription("braf", 19, "G", "C"); VariantDescription descOut = normalizer.normalizeVariant(descIn); Assert.assertEquals("braf", descOut.getChrom()); Assert.assertEquals(19, descOut.getPos()); Assert.assertEquals("G", descOut.getRef()); Assert.assertE... | public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... |
@Test public void testOnNormalInsertion() { VariantDescription descIn = new VariantDescription("braf", 19, "G", "GCT"); VariantDescription descOut = normalizer.normalizeVariant(descIn); Assert.assertEquals("braf", descOut.getChrom()); Assert.assertEquals(19, descOut.getPos()); Assert.assertEquals("", descOut.getRef());... | public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... |
@Test public void testShiftDeletionLeft() { VariantDescription descIn = new VariantDescription("braf", 180, "TGT", "T"); VariantDescription descOut = normalizer.normalizeVariant(descIn); Assert.assertEquals("braf", descOut.getChrom()); Assert.assertEquals(175, descOut.getPos()); Assert.assertEquals("TG", descOut.getRef... | public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... |
@Test public void testShiftInsertionLeft() { VariantDescription descIn = new VariantDescription("braf", 180, "T", "TGT"); VariantDescription descOut = normalizer.normalizeVariant(descIn); Assert.assertEquals("braf", descOut.getChrom()); Assert.assertEquals(175, descOut.getPos()); Assert.assertEquals("", descOut.getRef(... | public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); } | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... | VariantNormalizer { public VariantDescription normalizeVariant(VariantDescription desc) { final VariantDescription shifted = shiftLeft(desc); return trimBasesLeft(shifted, 0); } VariantNormalizer(String fastaPath); VariantDescription normalizeVariant(VariantDescription desc); VariantDescription normalizeInsertion(Varia... |
@Test public void testLoadGenomeInterval() { GenomeRegionSequenceExtractor extractor = new GenomeRegionSequenceExtractor(jannovarData, this.indexedFile); GenomeInterval region = new GenomeInterval(new GenomePosition(jannovarData.getRefDict(), Strand.FWD, 1, 99), 51); String seq = extractor.load(region); Assert.assertEq... | public String load(GenomeInterval region) { region = region.withStrand(Strand.FWD); String contigName = region.getRefDict().getContigIDToName().get(region.getChr()); contigName = mapContigToFasta(contigName); ReferenceSequence seq = indexedFile.getSubsequenceAt(contigName, region.getBeginPos() + 1, region.getEndPos());... | GenomeRegionSequenceExtractor { public String load(GenomeInterval region) { region = region.withStrand(Strand.FWD); String contigName = region.getRefDict().getContigIDToName().get(region.getChr()); contigName = mapContigToFasta(contigName); ReferenceSequence seq = indexedFile.getSubsequenceAt(contigName, region.getBegi... | GenomeRegionSequenceExtractor { public String load(GenomeInterval region) { region = region.withStrand(Strand.FWD); String contigName = region.getRefDict().getContigIDToName().get(region.getChr()); contigName = mapContigToFasta(contigName); ReferenceSequence seq = indexedFile.getSubsequenceAt(contigName, region.getBegi... | GenomeRegionSequenceExtractor { public String load(GenomeInterval region) { region = region.withStrand(Strand.FWD); String contigName = region.getRefDict().getContigIDToName().get(region.getChr()); contigName = mapContigToFasta(contigName); ReferenceSequence seq = indexedFile.getSubsequenceAt(contigName, region.getBegi... | GenomeRegionSequenceExtractor { public String load(GenomeInterval region) { region = region.withStrand(Strand.FWD); String contigName = region.getRefDict().getContigIDToName().get(region.getChr()); contigName = mapContigToFasta(contigName); ReferenceSequence seq = indexedFile.getSubsequenceAt(contigName, region.getBegi... |
@Test public void testExonicOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946660), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_145243.3(1:g.589... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testIntronicFivePrimeOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58957157), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_14524... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testExonicThreerimeOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946502), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_145243.... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testExonicFivePrimeOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012403), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_145243.... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testIntronicThreePrimeOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012355), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_1452... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testFullFrameshiftToHGVSString() { Assert.assertEquals("A124Tfs*23", fullFrameshift.toHGVSString()); Assert.assertEquals("Ala124Thrfs*23", fullFrameshift.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("A124Tfs*23", fullFrameshift.toHGVSString(AminoAcidCode.ONE_LETTER)); } | @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(code), "fs")); else if (shiftLength... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... |
@Test public void testUpstreamOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012449), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_145243.3(1:g.5... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testDownstreamOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58942733), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_145243.3(1:g... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testIntergenicOma1() { final SVInsertion svIns = new SVInsertion( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017449), 0, 0 ); final SVAnnotation anno = new SVInsertionAnnotationBuilder(oma1, svIns).build(); Assert.assertEquals(anno.getTranscript().toString(), "NM_145243.3(1:g... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion())) { return buildIntronAnnotation(changeInterval); } else ... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... | SVInsertionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svIns.getGenomeInterval(); if (so.overlapsWithExon(changeInterval)) { return buildExonOverlapAnnotation(changeInterval); } else if (changeInterval.overlapsWith(transcript.getTXRegion(... |
@Test public void testTranscriptAblationOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(om... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testExonLossOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(oma1, svDel)... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testExonOverlapStartLostOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testExonOverlapStopLostOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(o... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testExonOverlapFrameshiftOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testExonOverlapNoFrameshiftOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuild... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testIntronicOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(oma1, svDel)... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testNoTerFrameshiftToHGVSString() { Assert.assertEquals("A124Tfs*?", noTerFrameshift.toHGVSString()); Assert.assertEquals("Ala124Thrfs*?", noTerFrameshift.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("A124Tfs*?", noTerFrameshift.toHGVSString(AminoAcidCode.ONE_LETTER)); } | @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(code), "fs")); else if (shiftLength... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... |
@Test public void testUpstreamOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(oma1, svDel)... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testDownstreamOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(oma1, svDe... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testIntergenicOma1() { final SVDeletion svDel = new SVDeletion( 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 SVDeletionAnnotationBuilder(oma1, svDe... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval)) { return buildExonLossAnnotation(changeInterval); } els... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... | SVDeletionAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svDel.getGenomeInterval(); if (changeInterval.contains(transcript.getTXRegion())) { return buildAnnotation(VariantEffect.TRANSCRIPT_ABLATION); } else if (so.containsExon(changeInterval... |
@Test public void testExonicOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946660), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new SVBreakendAn... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testIntronicFivePrimeOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58957157), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new S... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testExonicFivePrimeOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58946502), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new SVB... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testExonicThreePrimeOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012403), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new SV... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testIntronicThreePrimeOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012355), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new ... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testUpstreamOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59012449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new SVBreakend... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testDownstreamOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 58941393), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new SVBreake... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testShortFrameshiftToHGVSString() { Assert.assertEquals("A124fs", shortFrameshift.toHGVSString()); Assert.assertEquals("Ala124fs", shortFrameshift.toHGVSString(AminoAcidCode.THREE_LETTER)); Assert.assertEquals("A124fs", shortFrameshift.toHGVSString(AminoAcidCode.ONE_LETTER)); } | @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVSString(code), "fs")); else if (shiftLength... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... | ProteinFrameshift extends ProteinChange { @Override public String toHGVSString(AminoAcidCode code) { String targetAA = this.targetAA; if (!isShort() && code == AminoAcidCode.THREE_LETTER) targetAA = Translator.getTranslator().toLong(targetAA); if (isShort()) return wrapIfOnlyPredicted(Joiner.on("").join(position.toHGVS... |
@Test public void testIntergenicOma1() { final SVBreakend svBnd = new SVBreakend( new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 59017449), new GenomePosition(jvData.getRefDict(), Strand.FWD, oma1.getChr(), 42), 0, 0, 0, 0, "A", "T", SVBreakend.Side.LEFT_END ); final SVAnnotation anno = new SVBreake... | @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildForInterval(new GenomeInterval( svBND.getGenomePos2().shift... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... | SVBreakendAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final SVAnnotation annoLeft = buildForInterval(new GenomeInterval( svBND.getGenomePos().shifted(svBND.getPosCILowerBound()), svBND.getPosCIUpperBound() - svBND.getPosCILowerBound() )); final SVAnnotation annoRight = buildF... |
@Test public void testTranscriptDuplicationOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopyNum... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testExonDuplicationOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopyNumberVar... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testExonOverlapStartDuplicatedOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCo... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testExonOverlapStopDuplicatedOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopy... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testExonOverlapDuplicationOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopyNu... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testExonOverlapNoFrameshiftOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopyN... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testIntronicOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopyNumberVariantAnn... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testUpstreamOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopyNumberVariantAnn... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testDownstreamOma1() { final SVCopyNumberVariant svCNV = new SVCopyNumberVariant( 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 SVCopyNumberVariantA... | @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( VariantEffect.COPY_NUMBER_CHANGE, VariantEffect.STRUCTURAL_VARIANT ))); }... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... | SVCopyNumberVariantAnnotationBuilder extends SVAnnotationBuilder { @Override public SVAnnotation build() { final GenomeInterval changeInterval = svCNV.getGenomeInterval(); if (changeInterval.overlapsWith(transcript.getTXRegion())) { return new SVAnnotation(svCNV, transcript, buildEffectSet(Sets.immutableEnumSet( Varian... |
@Test public void testBuildNormalExtension() { Assert.assertEquals(normalExtension, ProteinExtension.build(false, position, "T", 23)); } | public static ProteinExtension build(boolean onlyPredicted, String wtAA, int pos, String targetAA, int shift) { return build(onlyPredicted, ProteinPointLocation.build(wtAA, pos), targetAA, shift); } | ProteinExtension extends ProteinChange { public static ProteinExtension build(boolean onlyPredicted, String wtAA, int pos, String targetAA, int shift) { return build(onlyPredicted, ProteinPointLocation.build(wtAA, pos), targetAA, shift); } } | ProteinExtension extends ProteinChange { public static ProteinExtension build(boolean onlyPredicted, String wtAA, int pos, String targetAA, int shift) { return build(onlyPredicted, ProteinPointLocation.build(wtAA, pos), targetAA, shift); } ProteinExtension(boolean onlyPredicted, ProteinPointLocation position, String ta... | ProteinExtension extends ProteinChange { public static ProteinExtension build(boolean onlyPredicted, String wtAA, int pos, String targetAA, int shift) { return build(onlyPredicted, ProteinPointLocation.build(wtAA, pos), targetAA, shift); } ProteinExtension(boolean onlyPredicted, ProteinPointLocation position, String ta... | ProteinExtension extends ProteinChange { public static ProteinExtension build(boolean onlyPredicted, String wtAA, int pos, String targetAA, int shift) { return build(onlyPredicted, ProteinPointLocation.build(wtAA, pos), targetAA, shift); } ProteinExtension(boolean onlyPredicted, ProteinPointLocation position, String ta... |
@Test public void hiddenMiddlePhoneNum() throws Exception { String hiddenPhoneNumber = PhoneUtil.hiddenMiddlePhoneNum("13634429866"); Assert.assertEquals("", "136****9866", hiddenPhoneNumber); } | public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } } | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } } | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } @SuppressLint("HardwareIds") static String getIMEI(Context context); @... | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } @SuppressLint("HardwareIds") static String getIMEI(Context context); @... |
@Test(expected = IOException.class) public void testErrorPhoneNumber() throws Exception { String hiddenPhoneNumber = PhoneUtil.hiddenMiddlePhoneNum("1363442986"); Assert.assertEquals("", "136****986", hiddenPhoneNumber); } | public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } } | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } } | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } @SuppressLint("HardwareIds") static String getIMEI(Context context); @... | PhoneUtil { public static String hiddenMiddlePhoneNum(String phoneNumber) throws IOException { if (!isPhoneNumber(phoneNumber)) { throw new IOException("phoneNumber invalid"); } return phoneNumber.replaceAll("(\\d{3})\\d{4}(\\d{4})", "$1****$2"); } @SuppressLint("HardwareIds") static String getIMEI(Context context); @... |
@Test public void isPhoneNumber() throws Exception { boolean phoneNumber = PhoneUtil.isPhoneNumber("13634429866"); Assert.assertTrue(phoneNumber); } | public static boolean isPhoneNumber(String phoneNumber) { if (phoneNumber == null || phoneNumber.trim().length() != 11) { return false; } Pattern p = Pattern.compile("^[1][0-9]{10}$"); Matcher m = p.matcher(phoneNumber); return m.matches(); } | PhoneUtil { public static boolean isPhoneNumber(String phoneNumber) { if (phoneNumber == null || phoneNumber.trim().length() != 11) { return false; } Pattern p = Pattern.compile("^[1][0-9]{10}$"); Matcher m = p.matcher(phoneNumber); return m.matches(); } } | PhoneUtil { public static boolean isPhoneNumber(String phoneNumber) { if (phoneNumber == null || phoneNumber.trim().length() != 11) { return false; } Pattern p = Pattern.compile("^[1][0-9]{10}$"); Matcher m = p.matcher(phoneNumber); return m.matches(); } } | PhoneUtil { public static boolean isPhoneNumber(String phoneNumber) { if (phoneNumber == null || phoneNumber.trim().length() != 11) { return false; } Pattern p = Pattern.compile("^[1][0-9]{10}$"); Matcher m = p.matcher(phoneNumber); return m.matches(); } @SuppressLint("HardwareIds") static String getIMEI(Context conte... | PhoneUtil { public static boolean isPhoneNumber(String phoneNumber) { if (phoneNumber == null || phoneNumber.trim().length() != 11) { return false; } Pattern p = Pattern.compile("^[1][0-9]{10}$"); Matcher m = p.matcher(phoneNumber); return m.matches(); } @SuppressLint("HardwareIds") static String getIMEI(Context conte... |
@Test public void shouldCallCustomerService() throws JSONException { JSONObject json = new JSONObject(); json.put("customerId", 101); json.put("name", "Fred"); json.put("creditLimit", "12.34"); String expectedResponse = json.toString(); stubFor(get(urlEqualTo("/customers/101")) .willReturn(aResponse() .withStatus(200) ... | public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMono(GetCustomerResponse.... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... |
@Test(expected = CallNotPermittedException.class) public void shouldTimeoutAndTripCircuitBreaker() { String expectedResponse = "{}"; stubFor(get(urlEqualTo("/customers/99")) .willReturn(aResponse() .withStatus(500) .withHeader("Content-Type", "application/json") .withBody(expectedResponse))); IntStream.range(0, 100).fo... | public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMono(GetCustomerResponse.... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... | CustomerServiceProxy { public Mono<Optional<GetCustomerResponse>> findCustomerById(String customerId) { Mono<ClientResponse> response = client .get() .uri(customerServiceUrl + "/customers/{customerId}", customerId) .exchange(); return response.flatMap(resp -> { switch (resp.statusCode()) { case OK: return resp.bodyToMo... |
@Test public void testToFile() throws IOException { final String oldFile = System.getProperty("user.dir") + "/src/test/resources/images/lion2.jpg"; final String newFile = System.getProperty("user.dir") + "/src/test/resources/images/lion2_watermark"; final String warterFile = System.getProperty("user.dir") + "/src/test/... | public static void toFile(String oldFile, String newFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile) || StringUtils.isBlank(newFile)) { logger.error("原文件名或目标文件名为空"); return; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (null == builde... | ImageUtil { public static void toFile(String oldFile, String newFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile) || StringUtils.isBlank(newFile)) { logger.error("原文件名或目标文件名为空"); return; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (nu... | ImageUtil { public static void toFile(String oldFile, String newFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile) || StringUtils.isBlank(newFile)) { logger.error("原文件名或目标文件名为空"); return; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (nu... | ImageUtil { public static void toFile(String oldFile, String newFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile) || StringUtils.isBlank(newFile)) { logger.error("原文件名或目标文件名为空"); return; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (nu... | ImageUtil { public static void toFile(String oldFile, String newFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile) || StringUtils.isBlank(newFile)) { logger.error("原文件名或目标文件名为空"); return; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (nu... |
@Test public void testToBufferedImage() throws IOException { final String oldFile = System.getProperty("user.dir") + "/src/test/resources/images/lion2.jpg"; ImageParamDTO params = new ImageParamDTO(); params.setWidth(64); params.setHeight(64); BufferedImage bufferedImage = ImageUtil.toBufferedImage(oldFile, params); As... | public static BufferedImage toBufferedImage(String oldFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile)) { logger.error("原文件名或目标文件名为空"); return null; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (null == builder) { return null; } retur... | ImageUtil { public static BufferedImage toBufferedImage(String oldFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile)) { logger.error("原文件名或目标文件名为空"); return null; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (null == builder) { return n... | ImageUtil { public static BufferedImage toBufferedImage(String oldFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile)) { logger.error("原文件名或目标文件名为空"); return null; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (null == builder) { return n... | ImageUtil { public static BufferedImage toBufferedImage(String oldFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile)) { logger.error("原文件名或目标文件名为空"); return null; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (null == builder) { return n... | ImageUtil { public static BufferedImage toBufferedImage(String oldFile, ImageParamDTO params) throws IOException { if (StringUtils.isBlank(oldFile)) { logger.error("原文件名或目标文件名为空"); return null; } Thumbnails.Builder builder = Thumbnails.of(oldFile); fillBuilderWithParams(builder, params); if (null == builder) { return n... |
@Test public void testGetContentType() throws MagicParseException, MagicException, MagicMatchNotFoundException, IOException { final String oldFile = System.getProperty("user.dir") + "/src/test/resources/images/lion2.jpg"; byte[] bytes = toBytes(new File(oldFile)); String type = ImageUtil.getContentType(bytes); Assert.a... | public static String getContentType(byte[] content) throws MagicParseException, MagicException, MagicMatchNotFoundException { MagicMatch match = Magic.getMagicMatch(content); return match.getMimeType(); } | ImageUtil { public static String getContentType(byte[] content) throws MagicParseException, MagicException, MagicMatchNotFoundException { MagicMatch match = Magic.getMagicMatch(content); return match.getMimeType(); } } | ImageUtil { public static String getContentType(byte[] content) throws MagicParseException, MagicException, MagicMatchNotFoundException { MagicMatch match = Magic.getMagicMatch(content); return match.getMimeType(); } } | ImageUtil { public static String getContentType(byte[] content) throws MagicParseException, MagicException, MagicMatchNotFoundException { MagicMatch match = Magic.getMagicMatch(content); return match.getMimeType(); } static void toFile(String oldFile, String newFile, ImageParamDTO params); static BufferedImage toBuffe... | ImageUtil { public static String getContentType(byte[] content) throws MagicParseException, MagicException, MagicMatchNotFoundException { MagicMatch match = Magic.getMagicMatch(content); return match.getMimeType(); } static void toFile(String oldFile, String newFile, ImageParamDTO params); static BufferedImage toBuffe... |
@Test public void test01() throws IOException, WriterException { QRCodeUtil.encode(jsonContent, paramDTO); File f = new File(qrcodeFile); Assert.assertTrue(f.exists()); } | public static void encode(String content, BarcodeParamDTO paramDTO) throws WriterException, IOException { BitMatrix bitMatrix = new MultiFormatWriter().encode(content, paramDTO.getBarcodeFormat(), paramDTO.getWidth(), paramDTO.getHeight(), paramDTO.getEncodeHints()); Path path = FileSystems.getDefault().getPath(paramDT... | QRCodeUtil { public static void encode(String content, BarcodeParamDTO paramDTO) throws WriterException, IOException { BitMatrix bitMatrix = new MultiFormatWriter().encode(content, paramDTO.getBarcodeFormat(), paramDTO.getWidth(), paramDTO.getHeight(), paramDTO.getEncodeHints()); Path path = FileSystems.getDefault().ge... | QRCodeUtil { public static void encode(String content, BarcodeParamDTO paramDTO) throws WriterException, IOException { BitMatrix bitMatrix = new MultiFormatWriter().encode(content, paramDTO.getBarcodeFormat(), paramDTO.getWidth(), paramDTO.getHeight(), paramDTO.getEncodeHints()); Path path = FileSystems.getDefault().ge... | QRCodeUtil { public static void encode(String content, BarcodeParamDTO paramDTO) throws WriterException, IOException { BitMatrix bitMatrix = new MultiFormatWriter().encode(content, paramDTO.getBarcodeFormat(), paramDTO.getWidth(), paramDTO.getHeight(), paramDTO.getEncodeHints()); Path path = FileSystems.getDefault().ge... | QRCodeUtil { public static void encode(String content, BarcodeParamDTO paramDTO) throws WriterException, IOException { BitMatrix bitMatrix = new MultiFormatWriter().encode(content, paramDTO.getBarcodeFormat(), paramDTO.getWidth(), paramDTO.getHeight(), paramDTO.getEncodeHints()); Path path = FileSystems.getDefault().ge... |
@Test public void test02() { String expect = "{\"gender\":\"MALE\",\"name\":{\"last\":\"Zhang\",\"first\":\"Peng\"},\"email\":\"aaa@163.com\"}"; String content = QRCodeUtil.decode(paramDTO); Assert.assertEquals(expect, content); } | public static String decode(BarcodeParamDTO paramDTO) { try { BufferedImage bufferedImage = ImageIO.read(new FileInputStream(paramDTO.getFilepath())); LuminanceSource source = new BufferedImageLuminanceSource(bufferedImage); Binarizer binarizer = new HybridBinarizer(source); BinaryBitmap bitmap = new BinaryBitmap(binar... | QRCodeUtil { public static String decode(BarcodeParamDTO paramDTO) { try { BufferedImage bufferedImage = ImageIO.read(new FileInputStream(paramDTO.getFilepath())); LuminanceSource source = new BufferedImageLuminanceSource(bufferedImage); Binarizer binarizer = new HybridBinarizer(source); BinaryBitmap bitmap = new Binar... | QRCodeUtil { public static String decode(BarcodeParamDTO paramDTO) { try { BufferedImage bufferedImage = ImageIO.read(new FileInputStream(paramDTO.getFilepath())); LuminanceSource source = new BufferedImageLuminanceSource(bufferedImage); Binarizer binarizer = new HybridBinarizer(source); BinaryBitmap bitmap = new Binar... | QRCodeUtil { public static String decode(BarcodeParamDTO paramDTO) { try { BufferedImage bufferedImage = ImageIO.read(new FileInputStream(paramDTO.getFilepath())); LuminanceSource source = new BufferedImageLuminanceSource(bufferedImage); Binarizer binarizer = new HybridBinarizer(source); BinaryBitmap bitmap = new Binar... | QRCodeUtil { public static String decode(BarcodeParamDTO paramDTO) { try { BufferedImage bufferedImage = ImageIO.read(new FileInputStream(paramDTO.getFilepath())); LuminanceSource source = new BufferedImageLuminanceSource(bufferedImage); Binarizer binarizer = new HybridBinarizer(source); BinaryBitmap bitmap = new Binar... |
@Test public void test() { VelocityContext context = new VelocityContext(); context.put("name", "Victor Zhang"); context.put("project", "Velocity"); System.out.println(VelocityUtil.getMergeOutput(context, "template/hello.vm")); } | public static String getMergeOutput(VelocityContext context, String templateName) { Template template = velocityEngine.getTemplate(templateName); StringWriter sw = new StringWriter(); template.merge(context, sw); String output = sw.toString(); try { sw.close(); } catch (IOException e) { e.printStackTrace(); } return ou... | VelocityUtil { public static String getMergeOutput(VelocityContext context, String templateName) { Template template = velocityEngine.getTemplate(templateName); StringWriter sw = new StringWriter(); template.merge(context, sw); String output = sw.toString(); try { sw.close(); } catch (IOException e) { e.printStackTrace... | VelocityUtil { public static String getMergeOutput(VelocityContext context, String templateName) { Template template = velocityEngine.getTemplate(templateName); StringWriter sw = new StringWriter(); template.merge(context, sw); String output = sw.toString(); try { sw.close(); } catch (IOException e) { e.printStackTrace... | VelocityUtil { public static String getMergeOutput(VelocityContext context, String templateName) { Template template = velocityEngine.getTemplate(templateName); StringWriter sw = new StringWriter(); template.merge(context, sw); String output = sw.toString(); try { sw.close(); } catch (IOException e) { e.printStackTrace... | VelocityUtil { public static String getMergeOutput(VelocityContext context, String templateName) { Template template = velocityEngine.getTemplate(templateName); StringWriter sw = new StringWriter(); template.merge(context, sw); String output = sw.toString(); try { sw.close(); } catch (IOException e) { e.printStackTrace... |
@Test public void testJoin() throws Exception { String result = StringUtils.join(", ", asList(1, 2, 3, 4, 5)); Assert.assertEquals(result, "1, 2, 3, 4, 5"); } | public static String join(CharSequence delimiter, Iterable values) { StringBuilder sb = new StringBuilder(); Iterator<?> it = values.iterator(); if (it.hasNext()) { sb.append(it.next()); while (it.hasNext()) { sb.append(delimiter); sb.append(it.next()); } } return sb.toString(); } | StringUtils { public static String join(CharSequence delimiter, Iterable values) { StringBuilder sb = new StringBuilder(); Iterator<?> it = values.iterator(); if (it.hasNext()) { sb.append(it.next()); while (it.hasNext()) { sb.append(delimiter); sb.append(it.next()); } } return sb.toString(); } } | StringUtils { public static String join(CharSequence delimiter, Iterable values) { StringBuilder sb = new StringBuilder(); Iterator<?> it = values.iterator(); if (it.hasNext()) { sb.append(it.next()); while (it.hasNext()) { sb.append(delimiter); sb.append(it.next()); } } return sb.toString(); } } | StringUtils { public static String join(CharSequence delimiter, Iterable values) { StringBuilder sb = new StringBuilder(); Iterator<?> it = values.iterator(); if (it.hasNext()) { sb.append(it.next()); while (it.hasNext()) { sb.append(delimiter); sb.append(it.next()); } } return sb.toString(); } static String join(Char... | StringUtils { public static String join(CharSequence delimiter, Iterable values) { StringBuilder sb = new StringBuilder(); Iterator<?> it = values.iterator(); if (it.hasNext()) { sb.append(it.next()); while (it.hasNext()) { sb.append(delimiter); sb.append(it.next()); } } return sb.toString(); } static String join(Char... |
@Test public void isLegacyDevice() throws Exception { given(cameraCharacteristics.get(CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL)) .willReturn(CameraMetadata.INFO_SUPPORTED_HARDWARE_LEVEL_LEGACY); boolean isLegacyDevice = testee.isLegacyDevice(); assertTrue(isLegacyDevice); } | public boolean isLegacyDevice() { int hardwareLevel = cameraCharacteristics .get(CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL); return hardwareLevel == CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL_LEGACY; } | Characteristics { public boolean isLegacyDevice() { int hardwareLevel = cameraCharacteristics .get(CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL); return hardwareLevel == CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL_LEGACY; } } | Characteristics { public boolean isLegacyDevice() { int hardwareLevel = cameraCharacteristics .get(CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL); return hardwareLevel == CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL_LEGACY; } Characteristics(CameraCharacteristics cameraCharacteristics); } | Characteristics { public boolean isLegacyDevice() { int hardwareLevel = cameraCharacteristics .get(CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL); return hardwareLevel == CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL_LEGACY; } Characteristics(CameraCharacteristics cameraCharacteristics); boolean isFrontFaci... | Characteristics { public boolean isLegacyDevice() { int hardwareLevel = cameraCharacteristics .get(CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL); return hardwareLevel == CameraCharacteristics.INFO_SUPPORTED_HARDWARE_LEVEL_LEGACY; } Characteristics(CameraCharacteristics cameraCharacteristics); boolean isFrontFaci... |
@Test public void sensorOrientation() throws Exception { given(cameraCharacteristics.get(CameraCharacteristics.SENSOR_ORIENTATION)) .willReturn(90); int sensorOrientation = testee.getSensorOrientation(); assertEquals(90, sensorOrientation); } | public int getSensorOrientation() { return cameraCharacteristics.get(CameraCharacteristics.SENSOR_ORIENTATION); } | Characteristics { public int getSensorOrientation() { return cameraCharacteristics.get(CameraCharacteristics.SENSOR_ORIENTATION); } } | Characteristics { public int getSensorOrientation() { return cameraCharacteristics.get(CameraCharacteristics.SENSOR_ORIENTATION); } Characteristics(CameraCharacteristics cameraCharacteristics); } | Characteristics { public int getSensorOrientation() { return cameraCharacteristics.get(CameraCharacteristics.SENSOR_ORIENTATION); } Characteristics(CameraCharacteristics cameraCharacteristics); boolean isFrontFacingLens(); boolean isFlashAvailable(); boolean isFixedFocusLens(); boolean isLegacyDevice(); int getSensorOr... | Characteristics { public int getSensorOrientation() { return cameraCharacteristics.get(CameraCharacteristics.SENSOR_ORIENTATION); } Characteristics(CameraCharacteristics cameraCharacteristics); boolean isFrontFacingLens(); boolean isFlashAvailable(); boolean isFixedFocusLens(); boolean isLegacyDevice(); int getSensorOr... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.