automatically adding @Override annotations

src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java

@@ -88,6 +88,7 @@ protected AbstractBAMFileIndex(final File file, final SAMSequenceDictionary dict
     /**
      * Close this index and release any associated resources.
      */
+    @Override
     public void close() {
         mIndexBuffer.close();
     }
@@ -170,6 +171,7 @@ public int getNumberOfReferences() {
      * @return The file offset of the first record in the last linear bin, or -1
      * if there are no elements in linear bins (i.e. no mapped reads).
      */
+    @Override
     public long getStartOfLastLinearBin() {
         seek(4);
 
@@ -206,6 +208,7 @@ public long getStartOfLastLinearBin() {
      * @param reference the reference of interest
      * @return meta data for the reference
      */
+    @Override
     public BAMIndexMetaData getMetaData(final int reference) {
         seek(4);
 

src/main/java/htsjdk/samtools/AsyncSAMFileWriter.java

@@ -48,11 +48,13 @@ public void setProgressLogger(final ProgressLoggerInterface progress) {
      * Adds an alignment to the queue to be written.  Will re-throw any exception that was received when
      * writing prior record(s) to the underlying SAMFileWriter.
      */
+    @Override
     public void addAlignment(final SAMRecord alignment) {
         write(alignment);
     }
 
     /** Returns the SAMFileHeader from the underlying SAMFileWriter. */
+    @Override
     public SAMFileHeader getFileHeader() {
         return this.underlyingWriter.getFileHeader();
     }

src/main/java/htsjdk/samtools/BAMFileReader.java

@@ -341,6 +341,7 @@ static long findVirtualOffsetOfFirstRecord(final File bam) throws IOException {
      * If true, writes the source of every read into the source SAMRecords.
      * @param enabled true to write source information into each SAMRecord.
      */
+    @Override
     void enableFileSource(final SamReader reader, final boolean enabled) {
         this.mReader = enabled ? reader : null;
     }
@@ -349,6 +350,7 @@ void enableFileSource(final SamReader reader, final boolean enabled) {
      * If true, uses the caching version of the index reader.
      * @param enabled true to use the caching version of the reader.
      */
+    @Override
     protected void enableIndexCaching(final boolean enabled) {
         if(mIndex != null)
             throw new SAMException("Unable to turn on index caching; index file has already been loaded.");
@@ -360,6 +362,7 @@ protected void enableIndexCaching(final boolean enabled) {
      * This is slower but more scalable when accessing large numbers of BAM files sequentially.
      * @param enabled True to use memory mapping, false to use regular I/O.
      */
+    @Override
     protected void enableIndexMemoryMapping(final boolean enabled) {
         if (mIndex != null) {
             throw new SAMException("Unable to change index memory mapping; index file has already been loaded.");
@@ -381,6 +384,7 @@ protected void enableIndexMemoryMapping(final boolean enabled) {
     /**
      * @return true if ths is a BAM file, and has an index
      */
+    @Override
     public boolean hasIndex() {
         return mIsSeekable && ((mIndexFile != null) || (mIndexStream != null));
     }
@@ -389,6 +393,7 @@ public boolean hasIndex() {
      * Retrieves the index for the given file type.  Ensure that the index is of the specified type.
      * @return An index of the given type.
      */
+    @Override
     public BAMIndex getIndex() {
         if(!hasIndex())
             throw new SAMException("No index is available for this BAM file.");
@@ -425,17 +430,20 @@ public void close() {
         mIndex = null;
     }
 
+    @Override
     public SAMFileHeader getFileHeader() {
         return mFileHeader;
     }
 
     /**
      * Set error-checking level for subsequent SAMRecord reads.
      */
+    @Override
     void setValidationStringency(final ValidationStringency validationStringency) {
         this.mValidationStringency = validationStringency;
     }
 
+    @Override
     public ValidationStringency getValidationStringency() {
         return this.mValidationStringency;
     }
@@ -448,6 +456,7 @@ public ValidationStringency getValidationStringency() {
      * getIterator() begins its iteration where the last one left off.  That is the best that can be
      * done in that situation.
      */
+    @Override
     public CloseableIterator<SAMRecord> getIterator() {
         if (mStream == null) {
             throw new IllegalStateException("File reader is closed");
@@ -552,6 +561,7 @@ public SAMFileSpan getFilePointerSpanningReads() {
      * @return Iterator for the matching SAMRecords
      * @see QueryInterval#optimizeIntervals(QueryInterval[])
      */
+    @Override
     public CloseableIterator<SAMRecord> query(final QueryInterval[] intervals, final boolean contained) {
         if (mStream == null) {
             throw new IllegalStateException("File reader is closed");
@@ -582,6 +592,7 @@ public SAMFileSpan getFilePointerSpanningReads() {
      * @param start Alignment start sought.
      * @return Iterator for the matching SAMRecords.
      */
+    @Override
     public CloseableIterator<SAMRecord> queryAlignmentStart(final String sequence, final int start) {
         if (mStream == null) {
             throw new IllegalStateException("File reader is closed");
@@ -608,6 +619,7 @@ public SAMFileSpan getFilePointerSpanningReads() {
      *
      * @return Iterator for the matching SAMRecords.
      */
+    @Override
     public CloseableIterator<SAMRecord> queryUnmapped() {
         if (mStream == null) {
             throw new IllegalStateException("File reader is closed");
@@ -710,6 +722,7 @@ private static SAMSequenceRecord readSequenceRecord(final BinaryCodec stream, fi
 
         private boolean isClosed = false;
 
+        @Override
         public void close() {
             if (!isClosed) {
                 if (mCurrentIterator != null && this != mCurrentIterator) {
@@ -724,6 +737,7 @@ protected void assertOpen() {
             if (isClosed) throw new AssertionError("Iterator has been closed");
         }
 
+        @Override
         public void remove() {
             throw new UnsupportedOperationException("Not supported: remove");
         }
@@ -770,11 +784,13 @@ public SAMRecord next() {
             }
         }
 
+        @Override
         public boolean hasNext() {
             assertOpen();
             return (mNextRecord != null);
         }
 
+        @Override
         public SAMRecord next() {
             assertOpen();
             final SAMRecord result = mNextRecord;
@@ -947,6 +963,7 @@ public static BAMFileSpan getFileSpan(QueryInterval[] intervals, BAMIndex fileIn
             advance();
         }
 
+        @Override
         SAMRecord getNextRecord()
             throws IOException {
             // Advance to next file block if necessary
@@ -989,6 +1006,7 @@ public BAMQueryFilteringIterator(final CloseableIterator<SAMRecord> iterator,
         /**
          * Returns true if a next element exists; false otherwise.
          */
+        @Override
         public boolean hasNext() {
             assertOpen();
             return mNextRecord != null;
@@ -998,6 +1016,7 @@ public boolean hasNext() {
          * Gets the next record from the given iterator.
          * @return The next SAM record in the iterator.
          */
+        @Override
         public SAMRecord next() {
             if(!hasNext())
                 throw new NoSuchElementException("BAMQueryFilteringIterator: no next element available");

src/main/java/htsjdk/samtools/BAMFileSpan.java

@@ -78,6 +78,7 @@ public BAMFileSpan(final List<Chunk> chunks) {
      * Does this chunk list map to any position within the BAM file?
      * @return True iff the ChunkList points to any data within the BAM.
      */
+    @Override
     public boolean isEmpty() {
         return chunks.isEmpty();
     }
@@ -86,6 +87,7 @@ public boolean isEmpty() {
      * Deep clone the given chunk list.
      * @return A copy of the chunk list.
      */
+    @Override
     public BAMFileSpan clone() {
         final BAMFileSpan clone = new BAMFileSpan();
         for(final Chunk chunk: chunks)
@@ -100,6 +102,7 @@ public BAMFileSpan clone() {
      * @param fileSpan The filespan before which to eliminate.
      * @return A new BAMFileSpan which contains the portion of the chunk list after the given chunk.
      */
+    @Override
     public SAMFileSpan removeContentsBefore(final SAMFileSpan fileSpan) {
         if(fileSpan == null)
             return clone();
@@ -174,6 +177,7 @@ public SAMFileSpan removeContentsAfter(final SAMFileSpan fileSpan) {
      * Gets a file span over the data immediately following this span.
      * @return The a pointer to data immediately following this span.
      */
+    @Override
     public SAMFileSpan getContentsFollowing() {
         if(chunks.isEmpty())
             throw new SAMException("Unable to get the file pointer following this one: no data present.");

src/main/java/htsjdk/samtools/BAMFileWriter.java

@@ -115,6 +115,7 @@ private BAMIndexer createBamIndex(final String path) {
         }
     }
 
+    @Override
     protected void writeAlignment(final SAMRecord alignment) {
         prepareToWriteAlignments();
 
@@ -135,10 +136,12 @@ protected void writeAlignment(final SAMRecord alignment) {
         }
     }
 
+    @Override
     protected void writeHeader(final String textHeader) {
         writeHeader(outputBinaryCodec, getFileHeader(), textHeader);
     }
 
+    @Override
     protected void finish() {
         outputBinaryCodec.close();
             try {
@@ -151,6 +154,7 @@ protected void finish() {
     }
 
     /** @return absolute path, or null if this writer does not correspond to a file.  */
+    @Override
     protected String getFilename() {
         return outputBinaryCodec.getOutputFileName();
     }

src/main/java/htsjdk/samtools/BAMIndex.java

@@ -63,5 +63,6 @@
     /**
      * Close the index and release any associated resources.
      */
+    @Override
     void close();
 }

src/main/java/htsjdk/samtools/BAMIndexWriter.java

@@ -49,6 +49,7 @@
     /**
      * Any necessary processing at the end of the file
      */
+    @Override
     public void close();
 
 }

src/main/java/htsjdk/samtools/BAMRecord.java

@@ -113,6 +113,7 @@ protected BAMRecord(final SAMFileHeader header,
     /**
      * Force all the lazily-initialized attributes to be decoded.
      */
+    @Override
     protected void eagerDecode() {
         getReadName();
         getCigar();

src/main/java/htsjdk/samtools/BAMRecordCodec.java

@@ -49,13 +49,15 @@ public BAMRecordCodec(final SAMFileHeader header, final SAMRecordFactory factory
         this.samRecordFactory = factory;
     }
 
+    @Override
     public BAMRecordCodec clone() {
         // Do not clone the references to codecs, as they must be distinct for each instance.
         return new BAMRecordCodec(this.header, this.samRecordFactory);
     }
 
 
     /** Sets the output stream that records will be written to. */
+    @Override
     public void setOutputStream(final OutputStream os) {
         this.binaryCodec.setOutputStream(os);
     }
@@ -67,6 +69,7 @@ public void setOutputStream(final OutputStream os, final String filename) {
     }
 
     /** Sets the input stream that records will be read from. */
+    @Override
     public void setInputStream(final InputStream is) {
         this.binaryCodec.setInputStream(is);
     }
@@ -85,6 +88,7 @@ public void setInputStream(final InputStream is, final String filename) {
      *
      * @param alignment Record to be written.
      */
+    @Override
     public void encode(final SAMRecord alignment) {
         // Compute block size, as it is the first element of the file representation of SAMRecord
         final int readLength = alignment.getReadLength();
@@ -171,6 +175,7 @@ public void encode(final SAMRecord alignment) {
      * @return null if no more records.  Should throw exception if EOF is encountered in the middle of
      *         a record.
      */
+    @Override
     public SAMRecord decode() {
         int recordLength = 0;
         try {

src/main/java/htsjdk/samtools/Bin.java

@@ -105,6 +105,7 @@ public boolean containsChunks() {
      * @param other Other bin to which this bin should be compared.
      * @return -1 if this < other, 0 if this == other, 1 if this > other.
      */
+    @Override
     public int compareTo(final Bin other) {
         if(other == null)
             throw new ClassCastException("Cannot compare to a null object");

src/main/java/htsjdk/samtools/BinList.java

@@ -60,6 +60,7 @@ protected BinList(final int referenceSequence, final BitSet bins) {
      * Gets an iterator over all selected bins.
      * @return An iterator over all selected bins.
      */
+    @Override
     public Iterator<Bin> iterator() {
         return new BinIterator();
     }
@@ -95,6 +96,7 @@ public BinIterator() {
          * Are there more bins in this set, waiting to be returned?
          * @return True if more bins are remaining.
          */
+        @Override
         public boolean hasNext() {
             return nextBin >= 0;
         }
@@ -103,6 +105,7 @@ public boolean hasNext() {
          * Gets the next bin in the provided BinList.
          * @return the next available bin in the BinList.
          */
+        @Override
         public Bin next() {
             if(!hasNext())
                 throw new NoSuchElementException("This BinIterator is currently empty");
@@ -111,6 +114,7 @@ public Bin next() {
             return new Bin(referenceSequence,currentBin);
         }
 
+        @Override
         public void remove() {
             throw new UnsupportedOperationException("Unable to remove from a bin iterator");
         }

src/main/java/htsjdk/samtools/BinaryBAMIndexWriter.java

@@ -78,6 +78,7 @@ public BinaryBAMIndexWriter(final int nRef, final OutputStream output) {
     /**
      * Write this content as binary output
      */
+    @Override
     public void writeReference(final BAMIndexContent content) {
 
         if (content == null) {
@@ -147,13 +148,15 @@ public void writeReference(final BAMIndexContent content) {
      *
      * @param count
      */
+    @Override
     public void writeNoCoordinateRecordCount(final Long count) {
         codec.writeLong(count == null ? 0 : count);
     }
 
     /**
      * Any necessary processing at the end of the file
      */
+    @Override
     public void close() {
         codec.close();
     }