/** Try and convert an object to a List. */ private List<?> toList(Object o) { Class<?> c = o.getClass(); if (!c.isArray()) { return null; } if (c.getComponentType().isPrimitive()) { if (o instanceof boolean[]) { return Arrays.asList(ArrayUtils.toObject((boolean[]) o)); } else if (o instanceof byte[]) { return Arrays.asList(ArrayUtils.toObject((byte[]) o)); } else if (o instanceof short[]) { return Arrays.asList(ArrayUtils.toObject((short[]) o)); } else if (o instanceof int[]) { return Arrays.asList(ArrayUtils.toObject((int[]) o)); } else if (o instanceof long[]) { return Arrays.asList(ArrayUtils.toObject((long[]) o)); } else if (o instanceof float[]) { return Arrays.asList(ArrayUtils.toObject((float[]) o)); } else if (o instanceof double[]) { return Arrays.asList(ArrayUtils.toObject((double[]) o)); } else if (o instanceof char[]) { return Arrays.asList(ArrayUtils.toObject((char[]) o)); } else { throw new RuntimeException("Unhandled primitive type"); } } else { return Arrays.asList((Object[]) o); } }
public void deleteFile( String user, String password, String file, String recursive, int... status) { getMock("WEBHDFS") .expect() .method("DELETE") .pathInfo("/v1" + file) .queryParam("user.name", user) .queryParam("op", "DELETE") .queryParam("recursive", recursive) .respond() .status(status[0]); given() // .log().all() .auth() .preemptive() .basic(user, password) .header("X-XSRF-Header", "jksdhfkhdsf") .queryParam("op", "DELETE") .queryParam("recursive", recursive) .expect() // .log().all() .statusCode(isIn(ArrayUtils.toObject(status))) .when() .delete(getUrl("WEBHDFS") + "/v1" + file + (isUseGateway() ? "" : "?user.name=" + user)); assertComplete(); }
@Test public void testPrimitiveArray() { final int[] beast = {6, 6, 6}; assertEquals( Arrays.asList(ArrayUtils.toObject(beast)), therianContext.eval( Convert.to(new TypeLiteral<List<Integer>>() {}, Positions.readOnly(beast)))); }
/** {@inheritDoc} */ @Override public Integer[] getFromFile() { if (getPropertiesFile().containsKey(getKey())) { return ArrayUtils.toObject(getPropertiesFile().getIntArray(getKey(), getSpacer())); } else { return new Integer[0]; } }
@Override public Loader<Cursor> onCreateLoader(int arg0, Bundle arg1) { if (getActivity() == null) { return null; } String selection = KEY_PARENTID + " is null AND " + KEY_ROWID + " NOT IN (" + Joiner.on(',').join(ArrayUtils.toObject(getArguments().getLongArray(KEY_EXCLUDED_ID))) + ")"; CursorLoader cursorLoader = new CursorLoader( getActivity(), TransactionProvider.CATEGORIES_URI, projection, selection, null, null); return cursorLoader; }
public String submitPig( String user, String password, String group, String file, String arg, String statusDir, int... status) { getMock("WEBHCAT") .expect() .method("POST") .pathInfo("/v1/pig") .respond() .status(status[0]) .contentType("application/json") .content("{\"id\":\"job_201210301335_0086\"}".getBytes()); String json = given() // .log().all() .auth() .preemptive() .basic(user, password) .header("X-XSRF-Header", "jksdhfkhdsf") // BUG: The identity asserter needs to check for this too. .formParam("user.name", user) .formParam("group", group) .formParam("file", file) .formParam("arg", arg) .formParam("statusdir", statusDir) .expect() // .log().all(); .statusCode(isIn(ArrayUtils.toObject(status))) .contentType("application/json") // .content( "boolean", equalTo( true ) ) .when() .post(getUrl("WEBHCAT") + "/v1/pig" + (isUseGateway() ? "" : "?user.name=" + user)) .asString(); log.trace("JSON=" + json); String job = from(json).getString("id"); log.debug("JOB=" + job); assertComplete(); return job; }
@Override public DocScoreList mostSimilar(String phrase, int maxResults, TIntSet validIds) throws IOException { final TIntDoubleHashMap scores = getConceptVector(phrase, validIds); Integer luceneIds[] = ArrayUtils.toObject(scores.keys()); Arrays.sort( luceneIds, new Comparator<Integer>() { @Override public int compare(Integer id1, Integer id2) { return -1 * new Double(scores.get(id1)).compareTo(scores.get(id2)); } }); DocScoreList result = new DocScoreList(Math.min(luceneIds.length, maxResults)); for (int i = 0; i < result.numDocs(); i++) { result.set(i, esaHelper.luceneIdToWpId(luceneIds[i]), scores.get(luceneIds[i])); } return normalize(result); }
@Test public void testPerReadAlleleLikelihoodMap() { final PerReadAlleleLikelihoodMap map = new PerReadAlleleLikelihoodMap(); final Allele alleleA = Allele.create("A"); final double lik = -1.0; // ignored final int[] MQs = {1, 2, 3, 4, 5, 6, 7, 8, 9, 10, QualityUtils.MAPPING_QUALITY_UNAVAILABLE}; final List<Integer> MQsList = Arrays.asList(ArrayUtils.toObject(MQs)); // MQ 255 are excluded from the calculations, we test it here. final List<Integer> MQsListOK = new ArrayList<>(MQsList); // NOTE: if we just call remove(i), Java thinks i is an index. // A workaround for this overloading bogosity to to call removeAll and pass a collection // (casting i to (Object) would work too but it's more error prone) MQsListOK.removeAll(Collections.singleton(QualityUtils.MAPPING_QUALITY_UNAVAILABLE)); final int n1A = MQs.length; for (int i = 0; i < n1A; i++) { final GATKRead read = ArtificialReadUtils.createArtificialRead(TextCigarCodec.decode("10M")); read.setMappingQuality(MQs[i]); map.add(read, alleleA, lik); } final Map<String, PerReadAlleleLikelihoodMap> perReadAlleleLikelihoodMap = Collections.singletonMap("sample1", map); final VariantContext vc = makeVC(); final ReferenceContext referenceContext = null; final Map<String, Object> annotate = new RMSMappingQuality().annotate(referenceContext, vc, perReadAlleleLikelihoodMap); Assert.assertEquals(annotate.size(), 1, "size"); Assert.assertEquals( annotate.keySet(), Collections.singleton(VCFConstants.RMS_MAPPING_QUALITY_KEY), "annots"); final double rms = MathUtils.rms(MQsListOK); // only those are MQ0 Assert.assertEquals( annotate.get(VCFConstants.RMS_MAPPING_QUALITY_KEY), String.format("%.2f", rms)); }