Merge pull request #239 from samtools/dr_make_variant_headers_seriali…

…zable

Make VCFHeader Serializable

src/java/htsjdk/variant/vcf/VCFCompoundHeaderLine.java

@@ -249,16 +249,34 @@ protected String toStringEncoding() {
     }
 
     /**
-     * returns true if we're equal to another compounder header line
+     * returns true if we're equal to another compound header line
      * @param o a compound header line
      * @return true if equal
      */
-    public boolean equals(Object o) {
-        if (!(o instanceof VCFCompoundHeaderLine))
+    @Override
+    public boolean equals(final Object o) {
+        if ( this == o ) {
+            return true;
+        }
+        if ( o == null || getClass() != o.getClass() || ! super.equals(o) ) {
             return false;
-        VCFCompoundHeaderLine other = (VCFCompoundHeaderLine) o;
-        return equalsExcludingDescription(other) &&
-                description.equals(other.description);
+        }
+
+        final VCFCompoundHeaderLine that = (VCFCompoundHeaderLine) o;
+        return equalsExcludingDescription(that) &&
+               description.equals(that.description);
+    }
+
+    @Override
+    public int hashCode() {
+        int result = super.hashCode();
+        result = 31 * result + name.hashCode();
+        result = 31 * result + count;
+        result = 31 * result + (countType != null ? countType.hashCode() : 0);  // only nullable field according to validate()
+        result = 31 * result + description.hashCode();
+        result = 31 * result + type.hashCode();
+        result = 31 * result + lineType.hashCode();
+        return result;
     }
 
     public boolean equalsExcludingDescription(VCFCompoundHeaderLine other) {

src/java/htsjdk/variant/vcf/VCFContigHeaderLine.java

@@ -34,6 +34,8 @@
 /**
  * A special class representing a contig VCF header line.  Knows the true contig order and sorts on that
  *
+ * Note: this class has a natural ordering that is inconsistent with equals()
+ *
  * @author mdepristo
  */
 public class VCFContigHeaderLine extends VCFSimpleHeaderLine {
@@ -82,6 +84,26 @@ public SAMSequenceRecord getSAMSequenceRecord() {
 		return record;
 	}
 
+    @Override
+    public boolean equals(final Object o) {
+        if ( this == o ) {
+            return true;
+        }
+        if ( o == null || getClass() != o.getClass() || ! super.equals(o) ) {
+            return false;
+        }
+
+        final VCFContigHeaderLine that = (VCFContigHeaderLine) o;
+        return contigIndex.equals(that.contigIndex);
+    }
+
+    @Override
+    public int hashCode() {
+        int result = super.hashCode();
+        result = 31 * result + contigIndex.hashCode();
+        return result;
+    }
+
     /**
      * IT IS CRITICAL THAT THIS BE OVERRIDDEN SO WE SORT THE CONTIGS IN THE CORRECT ORDER
      */

src/java/htsjdk/variant/vcf/VCFHeader.java

@@ -32,6 +32,7 @@
 import htsjdk.variant.utils.GeneralUtils;
 import htsjdk.variant.variantcontext.VariantContextComparator;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -57,7 +58,8 @@
  *         <p/>
  *         A class representing the VCF header
  */
-public class VCFHeader {
+public class VCFHeader implements Serializable {
+    public static final long serialVersionUID = 1L;
 
     // the mandatory header fields
     public enum HEADER_FIELDS {

src/java/htsjdk/variant/vcf/VCFHeaderLine.java

@@ -27,6 +27,7 @@
 
 import htsjdk.tribble.TribbleException;
 
+import java.io.Serializable;
 import java.util.Map;
 
 
@@ -37,7 +38,9 @@
  *         <p/>
  *         A class representing a key=value entry in the VCF header
  */
-public class VCFHeaderLine implements Comparable {
+public class VCFHeaderLine implements Comparable, Serializable {
+    public static final long serialVersionUID = 1L;
+
     protected static final boolean ALLOW_UNBOUND_DESCRIPTIONS = true;
     protected static final String UNBOUND_DESCRIPTION = "Not provided in original VCF header";
 
@@ -101,10 +104,25 @@ protected String toStringEncoding() {
         return mKey + "=" + mValue;
     }
 
-    public boolean equals(Object o) {
-        if ( !(o instanceof VCFHeaderLine) )
+    @Override
+    public boolean equals(final Object o) {
+        if ( this == o ) {
+            return true;
+        }
+        if ( o == null || getClass() != o.getClass() ) {
             return false;
-        return mKey.equals(((VCFHeaderLine)o).getKey()) && mValue.equals(((VCFHeaderLine)o).getValue());
+        }
+
+        final VCFHeaderLine that = (VCFHeaderLine) o;
+        return mKey.equals(that.mKey) &&                                             // key not nullable
+               (mValue != null ? mValue.equals(that.mValue) : that.mValue == null);  // value is nullable
+    }
+
+    @Override
+    public int hashCode() {
+        int result = mKey.hashCode();
+        result = 31 * result + (mValue != null ? mValue.hashCode() : 0);
+        return result;
     }
 
     public int compareTo(Object other) {

src/java/htsjdk/variant/vcf/VCFSimpleHeaderLine.java

@@ -98,18 +98,26 @@ protected String toStringEncoding() {
         return getKey() + "=" + VCFHeaderLine.toStringEncoding(map);
     }
 
-    public boolean equals(Object o) {
-        if ( !(o instanceof VCFSimpleHeaderLine) )
-            return false;
-        VCFSimpleHeaderLine other = (VCFSimpleHeaderLine)o;
-        if ( !name.equals(other.name) || genericFields.size() != other.genericFields.size() )
+    @Override
+    public boolean equals( final Object o ) {
+        if ( this == o ) {
+            return true;
+        }
+        if ( o == null || getClass() != o.getClass() || ! super.equals(o) ) {
             return false;
-        for ( Map.Entry<String, String> entry : genericFields.entrySet() ) {
-            if ( !entry.getValue().equals(other.genericFields.get(entry.getKey())) )
-                return false;
         }
-
-        return true;       
+
+        final VCFSimpleHeaderLine that = (VCFSimpleHeaderLine) o;
+        return name.equals(that.name) &&
+               genericFields.equals(that.genericFields);
+    }
+
+    @Override
+    public int hashCode() {
+        int result = super.hashCode();
+        result = 31 * result + name.hashCode();
+        result = 31 * result + genericFields.hashCode();
+        return result;
     }
 
     public String getID() {

src/tests/java/htsjdk/variant/vcf/VCFHeaderUnitTest.java

@@ -38,11 +38,15 @@
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.io.InputStream;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
 import java.io.PrintWriter;
 import java.io.StringReader;
 import java.math.BigInteger;
@@ -51,6 +55,7 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Set;
 
 /**
  * Created by IntelliJ IDEA.
@@ -192,6 +197,35 @@ public void testVCFHeaderAddDuplicateHeaderLine() {
         Assert.assertEquals(numHeaderLinesBefore, numHeaderLinesAfter);
     }
 
+    @Test
+    public void testVCFHeaderSerialization() throws Exception {
+        final VCFFileReader reader = new VCFFileReader(new File("testdata/htsjdk/variant/HiSeq.10000.vcf"), false);
+        final VCFHeader originalHeader = reader.getFileHeader();
+        reader.close();
+
+        final ByteArrayOutputStream byteArrayStream = new ByteArrayOutputStream();
+        final ObjectOutputStream out = new ObjectOutputStream(byteArrayStream);
+        out.writeObject(originalHeader);
+        out.close();
+
+        final ObjectInputStream in = new ObjectInputStream(new ByteArrayInputStream(byteArrayStream.toByteArray()));
+        final VCFHeader deserializedHeader = (VCFHeader)in.readObject();
+        in.close();
+
+        Assert.assertEquals(deserializedHeader.getMetaDataInInputOrder(), originalHeader.getMetaDataInInputOrder(), "Header metadata does not match before/after serialization");
+        Assert.assertEquals(deserializedHeader.getContigLines(), originalHeader.getContigLines(), "Contig header lines do not match before/after serialization");
+        Assert.assertEquals(deserializedHeader.getFilterLines(), originalHeader.getFilterLines(), "Filter header lines do not match before/after serialization");
+        Assert.assertEquals(deserializedHeader.getFormatHeaderLines(), originalHeader.getFormatHeaderLines(), "Format header lines do not match before/after serialization");
+        Assert.assertEquals(deserializedHeader.getIDHeaderLines(), originalHeader.getIDHeaderLines(), "ID header lines do not match before/after serialization");
+        Assert.assertEquals(deserializedHeader.getInfoHeaderLines(), originalHeader.getInfoHeaderLines(), "Info header lines do not match before/after serialization");
+        Assert.assertEquals(deserializedHeader.getOtherHeaderLines(), originalHeader.getOtherHeaderLines(), "Other header lines do not match before/after serialization");
+        Assert.assertEquals(deserializedHeader.getGenotypeSamples(), originalHeader.getGenotypeSamples(), "Genotype samples not the same before/after serialization");
+        Assert.assertEquals(deserializedHeader.samplesWereAlreadySorted(), originalHeader.samplesWereAlreadySorted(), "Sortedness of samples not the same before/after serialization");
+        Assert.assertEquals(deserializedHeader.getSampleNamesInOrder(), originalHeader.getSampleNamesInOrder(), "Sorted list of sample names in header not the same before/after serialization");
+        Assert.assertEquals(deserializedHeader.getSampleNameToOffset(), originalHeader.getSampleNameToOffset(), "Sample name to offset map not the same before/after serialization");
+        Assert.assertEquals(deserializedHeader.toString(), originalHeader.toString(), "String representation of header not the same before/after serialization");
+    }
+
     /**
      * a little utility function for all tests to md5sum a file
      * Shameless taken from: