Fix warnings under newer Java

Author: Lenbok

src/main/java/com/rtg/assembler/GraphMap.java

@@ -326,7 +326,7 @@ static void finalizeCounts(List<GraphMap> mappings, MutableGraph graph) {
       }
       for (GraphMap mapping : mappings) {
         if (mapping.mContigReadCounts.length() > i) {
-          count += mapping.mContigReadCounts.get(i);
+          count += mapping.mContigReadCounts.getInt(i);
         }
       }
       if (count > 0) {
@@ -343,7 +343,7 @@ static void finalizeCounts(List<GraphMap> mappings, MutableGraph graph) {
       }
       for (GraphMap mapping : mappings) {
         if (mapping.mPathReadCounts.length() > i) {
-          count += mapping.mPathReadCounts.get(i);
+          count += mapping.mPathReadCounts.getInt(i);
         }
       }
       if (count > 0) {

src/main/java/com/rtg/launcher/HashingRegion.java

@@ -577,7 +577,7 @@ public long longestSubSequence(final SequencesReader reader) throws IOException
         lengths[0] = (int) (mPaddedEndPosition - mPaddedStartPosition);
       } else {
         if (this.getStartClipPosition() != MISSING) {
-          lengths[0] -= mPaddedStartPosition;
+          lengths[0] -= (int) mPaddedStartPosition;
         }
         if (this.getEndClipPosition() != MISSING) {
           lengths[lengths.length - 1] = (int) mPaddedEndPosition;

src/main/java/com/rtg/metagenomics/metasnp/MetaSnpCli.java

@@ -266,7 +266,7 @@ static void outputVisualisation(List<Integer> refBytes, List<MetaSnpLine> lines,
       final int numAlleles = currentEvidence[0].length;
       for (int sample = 0; sample < currentEvidence.length; ++sample) {
         for (byte allele = 0; allele < numAlleles; ++allele) {
-          totals[sample] += currentEvidence[sample][allele];
+          totals[sample] += (int) currentEvidence[sample][allele];
         }
       }
       for (byte allele = 0; allele < numAlleles; ++allele) {

src/main/java/com/rtg/variant/BaseQualityMachineCyclePhredScaler.java

@@ -84,8 +84,8 @@ class BaseQualityMachineCyclePhredScaler implements PhredScaler {
     final int[] qualityTotals = new int[mCurve.length];
     for (int i = 0; i < qualityMismatches.length; ++i) {
       for (int j = 0; j < proc.getTotals()[i].length; ++j) {
-        qualityMismatches[i] += proc.getMismatches()[i][j];
-        qualityTotals[i] += proc.getTotals()[i][j];
+        qualityMismatches[i] += (int) proc.getMismatches()[i][j];
+        qualityTotals[i] += (int) proc.getTotals()[i][j];
       }
     }
 

src/main/java/com/rtg/variant/CalibratedMachineErrorParams.java

@@ -203,7 +203,7 @@ static double[][] histogramsToCgV1Dists(Histogram gapHistogram, Histogram overla
     //each read must have 1 and only 1 gap of between 0 and 3 (incl) long, but we can't count those with 0 long gaps
     int totSmallGaps = 0;
     for (int i = 0; i < 4 && i < gapHistogram.getLength(); ++i) {
-      totSmallGaps += gapHistogram.getValue(i);
+      totSmallGaps += (int) gapHistogram.getValue(i);
     }
     if (totSmallGaps > totalReads) {
       throw new IllegalArgumentException("invalid CG gap distribution, small gaps (1-3) has larger count than big gaps(4-8)");

src/main/java/com/rtg/variant/bayes/BinaryFactor.java

@@ -35,7 +35,7 @@
  * Factor for a binary hypothesis.
  * @param <D> description
  */
-public class BinaryFactor<D extends Description> extends AbstractFactor<D> {
+public final class BinaryFactor<D extends Description> extends AbstractFactor<D> {
 
   private final double[] mPoss;
 

src/main/java/com/rtg/variant/bayes/UnitFactor.java

@@ -35,7 +35,7 @@
  * Unit factor.
  * @param <D> description
  */
-public class UnitFactor<D extends Description> extends AbstractFactor<D> {
+public final class UnitFactor<D extends Description> extends AbstractFactor<D> {
 
   private final double mUnit;
 

src/main/java/com/rtg/variant/bayes/complex/ComplexTemplate.java

@@ -31,8 +31,6 @@
 
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
-import java.security.AccessController;
-import java.security.PrivilegedAction;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -77,12 +75,7 @@ public class ComplexTemplate extends SequenceNameLocusSimple {
   private static final Constructor<Environment> ENVIRONMENT_COMBINED_CONSTRUCTOR;
   static {
     Diagnostic.developerLog("Classloading hack = " + HOTSPOT_HACK);
-    final SeparateClassLoader loader = AccessController.doPrivileged(new PrivilegedAction<SeparateClassLoader>() {
-      @Override
-      public SeparateClassLoader run() {
-        return new SeparateClassLoader(ScoreFastUnderflow.class, ScoreMatrix.class, AbstractAllPaths.class, EnvironmentCombined.class);
-      }
-    });
+    final SeparateClassLoader loader =  new SeparateClassLoader(ScoreFastUnderflow.class, ScoreMatrix.class, AbstractAllPaths.class, EnvironmentCombined.class);
     try {
       @SuppressWarnings("unchecked")
       final Class<AllPaths> sfClazz = (Class<AllPaths>) loader.loadClass(ScoreFastUnderflow.class.getName());

src/main/java/com/rtg/variant/bayes/complex/EvidenceComplex.java

@@ -62,7 +62,7 @@
  * Provides evidence for a complex hypothesis by performing an all-paths alignment
  * from an alignment record to each hypothesis.
  */
-public class EvidenceComplex extends Evidence {
+public final class EvidenceComplex extends Evidence {
 
   /** Print complex evidence scores into the developer log for debugging. */
   private static final boolean PRINT_EVIDENCE_DETAILS = GlobalFlags.isSet(CoreGlobalFlags.COMPLEX_EVIDENCE_DETAILS);

src/main/java/com/rtg/variant/bayes/multisample/Complexities.java

@@ -249,11 +249,11 @@ final SynchronizedLinkedList<ComplexRegion> filter(Deque<ComplexRegion> regions)
     return ret;
   }
 
-  boolean joinInteresting(int positionA, int positionB) {
+  final boolean joinInteresting(int positionA, int positionB) {
     return joinInteresting(positionA, positionB, 0, 0);
   }
 
-  boolean joinInteresting(int positionA, int positionB, int indelA, int indelB) {
+  final boolean joinInteresting(int positionA, int positionB, int indelA, int indelB) {
     final int indelHint = Math.max(indelA, indelB);
     final int posA = positionA + indelA / 2;
     final int posB = positionB - indelB / 2;
@@ -270,7 +270,7 @@ final ComplexRegion computeEndDangle(Deque<ComplexRegion> regions) {
     return regions.peekLast();
   }
 
-  void addRegion(final Deque<ComplexRegion> regions, int firstInteresting, int endInteresting, boolean forceComplex, int firstIndel, int endIndel) {
+  final void addRegion(final Deque<ComplexRegion> regions, int firstInteresting, int endInteresting, boolean forceComplex, int firstIndel, int endIndel) {
     if (firstInteresting != -1) {
       assert endInteresting >= firstInteresting : endInteresting + ":" + firstInteresting;
       final ComplexRegion.RegionType regionType;
@@ -286,7 +286,7 @@ void addRegion(final Deque<ComplexRegion> regions, int firstInteresting, int end
     }
   }
 
-  void addOverflowRegion(final Deque<ComplexRegion> regions, final VariantLocus locus) {
+  final void addOverflowRegion(final Deque<ComplexRegion> regions, final VariantLocus locus) {
     final ComplexRegion com = new ComplexRegion(mReferenceName, locus.getStart(), locus.getEnd(), RegionType.OVERFLOW);
     regions.add(com);
   }