From a40a73834cd9a1aeb28225845187a49569f4d5db Mon Sep 17 00:00:00 2001
From: Pavel Silin <pavel_silin@epam.com>
Date: Wed, 21 Jun 2017 17:29:00 +0300
Subject: [PATCH] rename AbstractCompressedOutputStream to
 AbstractBlockCompressedOutputStream

---
 src/main/java/htsjdk/samtools/BAMFileWriter.java            | 4 ++--
 ...Stream.java => AbstractBlockCompressedOutputStream.java} | 6 +++---
 .../htsjdk/samtools/util/BlockCompressedOutputStream.java   | 6 +++---
 .../samtools/util/ParallelBlockCompressedOutputStream.java  | 4 ++--
 4 files changed, 10 insertions(+), 10 deletions(-)
 rename src/main/java/htsjdk/samtools/util/{AbstractCompressedOutputStream.java => AbstractBlockCompressedOutputStream.java} (97%)

diff --git a/src/main/java/htsjdk/samtools/BAMFileWriter.java b/src/main/java/htsjdk/samtools/BAMFileWriter.java
index 4d678f3ee5..cf2fdbf86c 100644
--- a/src/main/java/htsjdk/samtools/BAMFileWriter.java
+++ b/src/main/java/htsjdk/samtools/BAMFileWriter.java
@@ -23,7 +23,7 @@
  */
 package htsjdk.samtools;
 
-import htsjdk.samtools.util.AbstractCompressedOutputStream;
+import htsjdk.samtools.util.AbstractBlockCompressedOutputStream;
 import htsjdk.samtools.util.BinaryCodec;
 import htsjdk.samtools.util.BlockCompressedOutputStream;
 import htsjdk.samtools.util.ParallelBlockCompressedOutputStream;
@@ -44,7 +44,7 @@ class BAMFileWriter extends SAMFileWriterImpl {
 
     private final BinaryCodec outputBinaryCodec;
     private BAMRecordCodec bamRecordCodec = null;
-    private final AbstractCompressedOutputStream blockCompressedOutputStream;
+    private final AbstractBlockCompressedOutputStream blockCompressedOutputStream;
     private BAMIndexer bamIndexer = null;
 
     protected BAMFileWriter(final File path, boolean createIndex) {
diff --git a/src/main/java/htsjdk/samtools/util/AbstractCompressedOutputStream.java b/src/main/java/htsjdk/samtools/util/AbstractBlockCompressedOutputStream.java
similarity index 97%
rename from src/main/java/htsjdk/samtools/util/AbstractCompressedOutputStream.java
rename to src/main/java/htsjdk/samtools/util/AbstractBlockCompressedOutputStream.java
index ea36d080e2..027dd11c8a 100644
--- a/src/main/java/htsjdk/samtools/util/AbstractCompressedOutputStream.java
+++ b/src/main/java/htsjdk/samtools/util/AbstractBlockCompressedOutputStream.java
@@ -46,7 +46,7 @@
  *
  * c.f. http://samtools.sourceforge.net/SAM1.pdf for details of BGZF file format.
  */
-public abstract class AbstractCompressedOutputStream extends OutputStream implements LocationAware {
+public abstract class AbstractBlockCompressedOutputStream extends OutputStream implements LocationAware {
 
     protected static DeflaterFactory defaultDeflaterFactory = new DeflaterFactory();
     protected static int defaultCompressionLevel = BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL;
@@ -97,13 +97,13 @@ public static int getDefaultCompressionLevel() {
      * Prepare to compress at the given compression level
      * @param file file to output
      */
-    public AbstractCompressedOutputStream(final File file) {
+    public AbstractBlockCompressedOutputStream(final File file) {
         this.file = file;
         codec = new BinaryCodec(file, true);
     }
 
 
-    public AbstractCompressedOutputStream(final OutputStream os, final File file) {
+    public AbstractBlockCompressedOutputStream(final OutputStream os, final File file) {
         this.file = file;
         codec = new BinaryCodec(os);
         if (file != null) {
diff --git a/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java b/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
index 7442788af8..b79054f705 100644
--- a/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
+++ b/src/main/java/htsjdk/samtools/util/BlockCompressedOutputStream.java
@@ -31,13 +31,13 @@
 import java.util.zip.Deflater;
 
 /**
- * Single threaded realisation of {@link AbstractCompressedOutputStream}
+ * Single threaded realisation of {@link AbstractBlockCompressedOutputStream}
  * Each block compressed one-by-one synchronously.
  *
- * @see AbstractCompressedOutputStream
+ * @see AbstractBlockCompressedOutputStream
  */
 public class BlockCompressedOutputStream
-        extends AbstractCompressedOutputStream {
+        extends AbstractBlockCompressedOutputStream {
 
     private final byte[] compressedBuffer =
             new byte[BlockCompressedStreamConstants.MAX_COMPRESSED_BLOCK_SIZE -
diff --git a/src/main/java/htsjdk/samtools/util/ParallelBlockCompressedOutputStream.java b/src/main/java/htsjdk/samtools/util/ParallelBlockCompressedOutputStream.java
index c87dc1b395..2c9ea18f1f 100644
--- a/src/main/java/htsjdk/samtools/util/ParallelBlockCompressedOutputStream.java
+++ b/src/main/java/htsjdk/samtools/util/ParallelBlockCompressedOutputStream.java
@@ -47,9 +47,9 @@
  * After compressing each thread save compressed block to the disk in input order.
  * <p>
  *
- * @see AbstractCompressedOutputStream
+ * @see AbstractBlockCompressedOutputStream
  */
-public class ParallelBlockCompressedOutputStream extends AbstractCompressedOutputStream {
+public class ParallelBlockCompressedOutputStream extends AbstractBlockCompressedOutputStream {
 
     private static final ExecutorService gzipExecutorService = createThreadPoolBlockingExecutor();
     private static final Void NOTHING = null;