Fix deprecation warnings from Java 11 for tests

broadinstitute · Sep 17, 2019 · 3e30784 · 3e30784
1 parent 1f8c257
commit 3e30784
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Showing 11 changed files with 34 additions and 34 deletions.
diff --git a/src/test/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtilsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/testutils/VariantContextTestUtilsUnitTest.java
@@ -88,10 +88,10 @@ public void testNormalizeScientificNotation(Object toNormalize, Object expected)
     public Object[][] getIntegerValuesToNormalize(){
         final Object aSpecificObject = new Object();
         return new Object[][] {
-                {"27", new Integer(27)},
-                {"-27", new Integer(-27)},
-                {"0", new Integer(0)},
-                {"-27014", new Integer(-27014)},
+                {"27", 27},
+                {"-27", -27},
+                {"0", 0},
+                {"-27014", -27014},
                 {1, 1},
                 {1, 1},
                 {-1, -1},

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorIntegrationTest.java
@@ -1143,10 +1143,10 @@ public void testVcfMafConcordance(final String inputVcf,
                 mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getContig).collect(Collectors.toList());
             }
             else if ( annotationsToCheckMaf.get(i).equals(MafOutputRendererConstants.FieldName_Start_Position) ) {
-                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getStart).map(x -> new Integer(x)).map(Object::toString).collect(Collectors.toList());
+                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getStart).map(Object::toString).collect(Collectors.toList());
             }
             else if ( annotationsToCheckMaf.get(i).equals(MafOutputRendererConstants.FieldName_End_Position) ) {
-                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getEnd).map(x -> new Integer(x)).map(Object::toString).collect(Collectors.toList());
+                mafFieldValues = maf.getRecords().stream().map(AnnotatedInterval::getEnd).map(Object::toString).collect(Collectors.toList());
             }
             else if ( annotationsToCheckMaf.get(i).equals(MafOutputRendererConstants.FieldName_Hugo_Symbol) ) {
                 mafFieldValues = maf.getRecords().stream().map(x -> x.getAnnotationValue(MafOutputRendererConstants.FieldName_Hugo_Symbol)).map(a -> a.isEmpty() ? "Unknown" : a).collect(Collectors.toList());

diff --git a/...t/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreIntegrationTest.java b/...t/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreIntegrationTest.java
@@ -43,11 +43,11 @@ private static Map<String, PSPathogenTaxonScore> getScores(final String[] lines)
             final PSPathogenTaxonScore score = new PSPathogenTaxonScore();
             final String taxonId = tok[0];
             score.setKingdomTaxonId(Math.abs(tok[4].hashCode()));
-            score.addSelfScore(new Double(tok[5]));
-            score.addScoreNormalized(new Double(tok[6]));
-            score.addTotalReads(new Integer(tok[7]));
-            score.addUnambiguousReads(new Integer(tok[8]));
-            score.setReferenceLength(new Long(tok[9]));
+            score.addSelfScore(Double.parseDouble(tok[5]));
+            score.addScoreNormalized(Double.parseDouble(tok[6]));
+            score.addTotalReads(Integer.parseInt(tok[7]));
+            score.addUnambiguousReads(Integer.parseInt((tok[8])));
+            score.setReferenceLength(Long.parseLong(tok[9]));
             Assert.assertFalse(scores.containsKey(taxonId), "Found more than one entry for taxon ID " + taxonId);
             scores.put(taxonId, score);
         }

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SVKmerShortUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/sv/utils/SVKmerShortUnitTest.java
@@ -104,7 +104,7 @@ public void testRandomMaskedKmers() {
             //Generate random indices to mask
             List<Byte> maskIndices = new ArrayList<>(K);
             for (int j = 0; j < K; j++) {
-                maskIndices.add(new Byte((byte) j));
+                maskIndices.add((byte) j);
             }
             Collections.shuffle(maskIndices);
             int maskSize = rand.nextInt(K - 3) + 2;

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LargeLongHopscotchSetTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LargeLongHopscotchSetTest.java
@@ -132,7 +132,7 @@ void resizeTest() {
         Assert.assertTrue(hopscotchSet.size() == hashSet.size());
         LongIterator itrL = hopscotchSet.iterator();
         while (itrL.hasNext()) {
-            Assert.assertTrue(hashSet.contains(new Long(itrL.next())));
+            Assert.assertTrue(hashSet.contains(itrL.next()));
         }
         for (Long val : hashSet) {
             Assert.assertTrue(hopscotchSet.contains(val.longValue()));
@@ -155,7 +155,7 @@ void loadRandomLongsTest() {
         for (int valNo = 0; valNo != HHASH_NVALS; ++valNo) {
             final long randLong = randomLong(rng);
             hopscotchSet.add(randLong);
-            hashSet.add(new Long(randLong));
+            hashSet.add(randLong);
         }
         Assert.assertEquals(hashSet.size(), hopscotchSet.size());
         for (final Long val : hashSet) {

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LongBloomFilterTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LongBloomFilterTest.java
@@ -84,7 +84,7 @@ void testRandomLongs() {
         final LongBloomFilter bloomFilter = new LongBloomFilter(HHASH_NVALS, FPP);
         for (int valNo = 0; valNo != HHASH_NVALS; ++valNo) {
             final long randLong = randomLong(rng);
-            hashSet.add(new Long(randLong));
+            hashSet.add(randLong);
             bloomFilter.add(randLong);
         }
         for (final Long val : hashSet) {
@@ -94,7 +94,7 @@ void testRandomLongs() {
         int num_total = 0;
         for (int valNo = 0; valNo != FPR_NVALS; ++valNo) {
             final long randLong = randomLong(rng);
-            if (!hashSet.contains(new Long(randLong))) {
+            if (!hashSet.contains(randLong)) {
                 num_total++;
                 if (bloomFilter.contains(randLong)) {
                     num_false_pos++;

diff --git a/src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LongHopscotchSetTest.java b/src/test/java/org/broadinstitute/hellbender/tools/spark/utils/LongHopscotchSetTest.java
@@ -72,7 +72,7 @@ void capacityTest() {
             Assert.assertTrue(capacity >= size);
             Assert.assertTrue(capacity < 2 * size);
             final List<Integer> legalSizes = IntStream.of(SetSizeUtils.legalSizes).boxed().collect(Collectors.toList());
-            Assert.assertTrue(legalSizes.contains(new Integer((int) capacity)));
+            Assert.assertTrue(legalSizes.contains((int) capacity));
         }
     }
 
@@ -106,7 +106,7 @@ void iteratorTest() {
         final List<Long> filteredVals = new LinkedList<>();
         for (long testVal : testVals) {
             if (KEY_TO_REMOVE == testVal) {
-                filteredVals.add(new Long(testVal));
+                filteredVals.add(testVal);
             }
         }
         final int onesCount = filteredVals.size();
@@ -186,7 +186,7 @@ void loadRandomLongsTest() {
             for (int valNo = 0; valNo != HHASH_NVALS; ++valNo) {
                 final long randLong = randomLong(rng);
                 hopscotchSet.add(randLong);
-                hashSet.add(new Long(randLong));
+                hashSet.add(randLong);
             }
             Assert.assertEquals(hashSet.size(), hopscotchSet.size(), trialMsg);
             for (final Long val : hashSet) {

diff --git a/src/test/java/org/broadinstitute/hellbender/utils/HistogramUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/HistogramUnitTest.java
@@ -16,8 +16,8 @@ public void testAdd() throws Exception {
         for (int i = 0; i <= 100; i++) {
             bimodalHist.add(1 + i / 1000.0);
         }
-        Assert.assertEquals(bimodalHist.get(1.0), new Integer(100), "");
-        Assert.assertEquals(bimodalHist.get(1.1), new Integer(1), "");
+        Assert.assertEquals(bimodalHist.get(1.0), Integer.valueOf(100), "");
+        Assert.assertEquals(bimodalHist.get(1.1), Integer.valueOf(1), "");
     }
 
     @Test
@@ -26,7 +26,7 @@ public void testAddingQuantizedValues() throws Exception {
         for (int i = 0; i < 100; i++) {
             hist.add(1.2);
         }
-        Assert.assertEquals(hist.get(1.2), new Integer(100));
+        Assert.assertEquals(hist.get(1.2), Integer.valueOf(100));
         Assert.assertEquals(hist.median(), 1.2, EPSILON);
     }
 
@@ -36,8 +36,8 @@ public void testBulkAdd() throws Exception {
         for (int i = 0; i <= 100; i++) {
             bimodalHist.add(1 + i / 1000.0, 2);
         }
-        Assert.assertEquals(bimodalHist.get(1.0), new Integer(200), "");
-        Assert.assertEquals(bimodalHist.get(1.1), new Integer(2), "");
+        Assert.assertEquals(bimodalHist.get(1.0), Integer.valueOf(200), "");
+        Assert.assertEquals(bimodalHist.get(1.1), Integer.valueOf(2), "");
     }
 
     @Test

diff --git a/src/test/java/org/broadinstitute/hellbender/utils/hmm/HMMUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/hmm/HMMUnitTest.java
@@ -261,7 +261,7 @@ public void testBackward(final TestHMM model, final List<TestHMM.Datum> sequence
         for (int position = positions.size() - 1; position >= 0; position--) {
             for (final TestHMM.State state : TestHMM.State.values()) {
                 final double expectedValue = expected.get(position)[state.ordinal()];
-                final double observedValue = forwardBackwardResult.logBackwardProbability(new Integer(position), state);
+                final double observedValue = forwardBackwardResult.logBackwardProbability(Integer.valueOf(position), state);
                 final double observedValueUsingIndex = forwardBackwardResult.logBackwardProbability(position, state);
                 Assert.assertEquals(observedValueUsingIndex, observedValue);
                 final double epsilon = 0.001 * Math.min(Math.abs(expectedValue),
@@ -500,7 +500,7 @@ public void testLogProbabilityWithNullStateUsingPositionObject() {
 
         }
         Assert.assertNotNull(result);
-        result.logProbability(new Integer(2), (TestHMM.State)null);
+        result.logProbability(Integer.valueOf(2), (TestHMM.State)null);
     }
 
 
@@ -529,7 +529,7 @@ public void testLogDataLikelihoodWithWrongTargetUsingPositionObject() {
             Assert.fail("this part of the test must not fail");
 
         }
-        result.logDataLikelihood(new Integer(14));
+        result.logDataLikelihood(Integer.valueOf(14));
     }
 
     @Test(expectedExceptions = IllegalArgumentException.class)
@@ -559,7 +559,7 @@ public void testLogBackProbabilityWithNullStateUsingPositionObject() {
 
         }
         Assert.assertNotNull(result);
-        result.logBackwardProbability(new Integer(2), null);
+        result.logBackwardProbability(Integer.valueOf(2), null);
     }
 
     @Test(expectedExceptions = IllegalArgumentException.class)
@@ -589,7 +589,7 @@ public void testLogForwardProbabilityWithNullStateUsingPositionObject() {
 
         }
         Assert.assertNotNull(result);
-        result.logForwardProbability(new Integer(2), null);
+        result.logForwardProbability(Integer.valueOf(2), null);
     }
 
     @Test(expectedExceptions = IllegalArgumentException.class)
@@ -649,7 +649,7 @@ public void testLogProbabilityWithMadeUpPositionObject() {
 
         }
         Assert.assertNotNull(result);
-        result.logProbability(new Integer(14), TestHMM.State.A);
+        result.logProbability(Integer.valueOf(14), TestHMM.State.A);
     }
 
     @Test(expectedExceptions = IllegalArgumentException.class)
@@ -679,7 +679,7 @@ public void testLogProbabilityWithASequenceThatIsTwoLongUsingPositionObject() {
 
         }
         Assert.assertNotNull(result);
-        result.logProbability(new Integer(2), Arrays.asList(TestHMM.State.A, TestHMM.State.A, TestHMM.State.B));
+        result.logProbability(Integer.valueOf(2), Arrays.asList(TestHMM.State.A, TestHMM.State.A, TestHMM.State.B));
     }
 
     @Test(expectedExceptions = IllegalArgumentException.class)
@@ -769,7 +769,7 @@ public void testLogProbabilityWithNonExistentPositionObject() {
 
         }
         Assert.assertNotNull(result);
-        result.logProbability(new Integer(4), TestHMM.State.A);
+        result.logProbability(Integer.valueOf(4), TestHMM.State.A);
     }
 
     @Test(expectedExceptions = IllegalArgumentException.class)

diff --git a/src/test/java/org/broadinstitute/hellbender/utils/pairhmm/VectorPairHMMUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/pairhmm/VectorPairHMMUnitTest.java
@@ -42,7 +42,7 @@ private List<Pair<PairHMM, Boolean> > getHMMs() {
                 loaded = false;
             }
 
-            final Pair<PairHMM, Boolean> hmm_load = new ImmutablePair<PairHMM, Boolean>(avxPairHMM, new Boolean(loaded));
+            final Pair<PairHMM, Boolean> hmm_load = new ImmutablePair<PairHMM, Boolean>(avxPairHMM, loaded);
             list.add(hmm_load);
         }
 

diff --git a/src/test/java/org/broadinstitute/hellbender/utils/recalibration/RecalDatumUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/recalibration/RecalDatumUnitTest.java
@@ -217,7 +217,7 @@ public void testlog10QempLikelihood() {
             }
         }
 
-        long bigNum = new Long((long) Integer.MAX_VALUE);
+        long bigNum = Integer.MAX_VALUE;
         bigNum *= 2L;
         final double log10likelihood = RecalDatum.log10QempLikelihood(30, bigNum, 100000);
         Assert.assertTrue(log10likelihood < 0.0);