Add hashCode() to classes with equals() and clean up equals()

src/main/java/htsjdk/samtools/LinearIndex.java

@@ -24,6 +24,7 @@
 package htsjdk.samtools;
 
 import java.util.Arrays;
+import java.util.Objects;
 
 /**
  * The linear index associated with a given reference in a BAM index.
@@ -103,23 +104,19 @@ public int getIndexStart() {
     }
 
     @Override
-    public boolean equals(final Object o) {
+    public boolean equals(Object o) {
         if (this == o) return true;
         if (o == null || getClass() != o.getClass()) return false;
-
-        final LinearIndex that = (LinearIndex) o;
-
-        if (mIndexStart != that.mIndexStart) return false;
-        if (mReferenceSequence != that.mReferenceSequence) return false;
-        if (!Arrays.equals(mIndexEntries, that.mIndexEntries)) return false;
-
-        return true;
+        LinearIndex that = (LinearIndex) o;
+        return mReferenceSequence == that.mReferenceSequence &&
+                mIndexStart == that.mIndexStart &&
+                Arrays.equals(mIndexEntries, that.mIndexEntries);
     }
 
     @Override
     public int hashCode() {
-        int result = mReferenceSequence;
-        result = 31 * result + mIndexStart;
+
+        int result = Objects.hash(mReferenceSequence, mIndexStart);
         result = 31 * result + Arrays.hashCode(mIndexEntries);
         return result;
     }

src/main/java/htsjdk/samtools/cram/common/Version.java

@@ -1,5 +1,7 @@
 package htsjdk.samtools.cram.common;
 
+import java.util.Objects;
+
 /**
  * A class to represent a version information, 3 number: major, minor and build number.
  */
@@ -44,20 +46,28 @@ public int compareTo(@SuppressWarnings("NullableProblems") final Version o) {
         return build - o.build;
     }
 
+    public boolean compatibleWith(final Version version) {
+        return compareTo(version) >= 0;
+    }
+
     /**
      * Check if another version is exactly the same as this one.
      *
-     * @param obj another version object
+     * @param o another version object
      * @return true if both versions are the same, false otherwise.
      */
     @Override
-    public boolean equals(final Object obj) {
-        if (obj == null || !(obj instanceof Version)) return false;
-        final Version version = (Version) obj;
-        return major == version.major && minor == version.minor;
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        Version version = (Version) o;
+        return major == version.major &&
+                minor == version.minor &&
+                build == version.build;
     }
 
-    public boolean compatibleWith(final Version version) {
-        return compareTo(version) >= 0;
+    @Override
+    public int hashCode() {
+        return Objects.hash(major, minor, build);
     }
 }

src/main/java/htsjdk/samtools/cram/encoding/huffman/codec/CanonicalHuffmanIntegerEncoding.java

@@ -28,12 +28,12 @@
 import java.nio.ByteBuffer;
 import java.util.Arrays;
 import java.util.Map;
+import java.util.Objects;
 
 public class CanonicalHuffmanIntegerEncoding implements Encoding<Integer> {
     private static final EncodingID ENCODING_ID = EncodingID.HUFFMAN;
     private int[] bitLengths;
     private int[] values;
-    private final ByteBuffer buf = ByteBuffer.allocate(1024 * 10);
 
     public CanonicalHuffmanIntegerEncoding() {
     }
@@ -45,6 +45,7 @@ public EncodingID id() {
 
     @Override
     public byte[] toByteArray() {
+        final ByteBuffer buf = ByteBuffer.allocate(1024 * 10);
         buf.clear();
         ITF8.writeUnsignedITF8(values.length, buf);
         for (final int value : values)
@@ -89,12 +90,19 @@ public static EncodingParams toParam(final int[] bfValues, final int[] bfBitLens
     }
 
     @Override
-    public boolean equals(final Object obj) {
-        if (obj instanceof CanonicalHuffmanIntegerEncoding) {
-            final CanonicalHuffmanIntegerEncoding foe = (CanonicalHuffmanIntegerEncoding) obj;
-            return Arrays.equals(bitLengths, foe.bitLengths) && Arrays.equals(values, foe.values);
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        CanonicalHuffmanIntegerEncoding that = (CanonicalHuffmanIntegerEncoding) o;
+        return Arrays.equals(bitLengths, that.bitLengths) &&
+                Arrays.equals(values, that.values);
+    }
+
+    @Override
+    public int hashCode() {
 
-        }
-        return false;
+        int result = Arrays.hashCode(bitLengths);
+        result = 31 * result + Arrays.hashCode(values);
+        return result;
     }
 }

src/main/java/htsjdk/samtools/cram/encoding/readfeatures/BaseQualityScore.java

@@ -18,6 +18,7 @@
 package htsjdk.samtools.cram.encoding.readfeatures;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 /**
  * A read feature representing a single quality score in a read.
@@ -57,21 +58,23 @@ public void setQualityScore(final byte qualityScore) {
         this.qualityScore = qualityScore;
     }
 
-    @Override
-    public boolean equals(final Object obj) {
-        if (!(obj instanceof BaseQualityScore))
-            return false;
-
-        final BaseQualityScore v = (BaseQualityScore) obj;
-
-        return position == v.position && qualityScore == v.qualityScore;
-
-    }
-
     @Override
     public String toString() {
         return new StringBuilder().append((char) operator).append('@')
                 .append(position).append('#').appendCodePoint(qualityScore).toString();
     }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        BaseQualityScore that = (BaseQualityScore) o;
+        return position == that.position &&
+                qualityScore == that.qualityScore;
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(position, qualityScore);
+    }
 }

src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Bases.java

@@ -19,6 +19,7 @@
 
 import java.io.Serializable;
 import java.util.Arrays;
+import java.util.Objects;
 
 public class Bases implements Serializable, ReadFeature {
 
@@ -59,18 +60,23 @@ public void setPosition(final int position) {
     }
 
     @Override
-    public boolean equals(final Object obj) {
-        if (!(obj instanceof Bases))
-            return false;
-
-        final Bases bases = (Bases) obj;
-
-        return position == bases.position && !Arrays.equals(this.bases, bases.bases);
+    public String toString() {
+        return getClass().getSimpleName() + "[" + "position=" + position + "; bases=" + new String(bases) + "] ";
+    }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        Bases bases1 = (Bases) o;
+        return position == bases1.position &&
+                Arrays.equals(bases, bases1.bases);
     }
 
     @Override
-    public String toString() {
-        return getClass().getSimpleName() + "[" + "position=" + position + "; bases=" + new String(bases) + "] ";
+    public int hashCode() {
+        int result = Objects.hash(position);
+        result = 31 * result + Arrays.hashCode(bases);
+        return result;
     }
 }

src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Deletion.java

@@ -18,6 +18,7 @@
 package htsjdk.samtools.cram.encoding.readfeatures;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 /**
  * A read feature representing a deletion of one or more bases similar to {@link htsjdk.samtools.CigarOperator#D}.
@@ -60,18 +61,21 @@ public void setLength(final int length) {
     }
 
     @Override
-    public boolean equals(final Object obj) {
-        if (!(obj instanceof Deletion))
-            return false;
-
-        final Deletion deleteion = (Deletion) obj;
-
-        return position == deleteion.position && length == deleteion.length;
+    public String toString() {
+        return String.valueOf((char) operator) + '@' + position + '+' + length;
+    }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        Deletion deletion = (Deletion) o;
+        return position == deletion.position &&
+                length == deletion.length;
     }
 
     @Override
-    public String toString() {
-        return String.valueOf((char) operator) + '@' + position + '+' + length;
+    public int hashCode() {
+        return Objects.hash(position, length);
     }
 }

src/main/java/htsjdk/samtools/cram/encoding/readfeatures/HardClip.java

@@ -18,6 +18,7 @@
 package htsjdk.samtools.cram.encoding.readfeatures;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 /**
  * A read feature representing a hard clip similar to {@link htsjdk.samtools.CigarOperator#H}.
@@ -60,18 +61,21 @@ public void setLength(final int length) {
     }
 
     @Override
-    public boolean equals(final Object obj) {
-        if (!(obj instanceof HardClip))
-            return false;
-
-        final HardClip hardClip = (HardClip) obj;
-
-        return position == hardClip.position && length == hardClip.length;
+    public String toString() {
+        return getClass().getSimpleName() + "[" + "position=" + position + "; length=" + length + "] ";
+    }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        HardClip hardClip = (HardClip) o;
+        return position == hardClip.position &&
+                length == hardClip.length;
     }
 
     @Override
-    public String toString() {
-        return getClass().getSimpleName() + "[" + "position=" + position + "; length=" + length + "] ";
+    public int hashCode() {
+        return Objects.hash(position, length);
     }
 }

src/main/java/htsjdk/samtools/cram/encoding/readfeatures/InsertBase.java

@@ -18,6 +18,7 @@
 package htsjdk.samtools.cram.encoding.readfeatures;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 /**
  * A read feature representing a single insert base.
@@ -52,17 +53,6 @@ public void setPosition(final int position) {
         this.position = position;
     }
 
-    @Override
-    public boolean equals(final Object obj) {
-        if (!(obj instanceof InsertBase))
-            return false;
-
-        final InsertBase insertBase = (InsertBase) obj;
-
-        return position == insertBase.position && base == insertBase.base;
-
-    }
-
     @Override
     public String toString() {
         return new StringBuilder().append((char) operator).append('@')
@@ -76,4 +66,18 @@ public byte getBase() {
     public void setBase(final byte base) {
         this.base = base;
     }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        InsertBase that = (InsertBase) o;
+        return position == that.position &&
+                base == that.base;
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(position, base);
+    }
 }

src/main/java/htsjdk/samtools/cram/encoding/readfeatures/Insertion.java

@@ -19,6 +19,7 @@
 
 import java.io.Serializable;
 import java.util.Arrays;
+import java.util.Objects;
 
 /**
  * A read feature representing a multi-base insertion.
@@ -61,17 +62,23 @@ public void setSequence(final byte[] sequence) {
     }
 
     @Override
-    public boolean equals(final Object obj) {
-        if (!(obj instanceof Insertion))
-            return false;
-
-        final Insertion insertion = (Insertion) obj;
+    public String toString() {
+        return getClass().getSimpleName() + "[" + "position=" + position + "; sequence=" + new String(sequence) + "] ";
+    }
 
-        return position == insertion.position && Arrays.equals(sequence, insertion.sequence);
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        final Insertion insertion = (Insertion) o;
+        return position == insertion.position &&
+                Arrays.equals(sequence, insertion.sequence);
     }
 
     @Override
-    public String toString() {
-        return getClass().getSimpleName() + "[" + "position=" + position + "; sequence=" + new String(sequence) + "] ";
+    public int hashCode() {
+        int result = Objects.hash(position);
+        result = 31 * result + Arrays.hashCode(sequence);
+        return result;
     }
 }