rename AbstractCompressedOutputStream to AbstractBlockCompressedOutpu…

…tStream
EpamLifeSciencesTeam · Jun 21, 2017 · a40a738 · a40a738
1 parent d0919d5
commit a40a738
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Showing 4 changed files with 10 additions and 10 deletions.
diff --git 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/.../util/AbstractCompressedOutputStream.java → .../AbstractBlockCompressedOutputStream.java b/.../util/AbstractCompressedOutputStream.java → .../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
@@ -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
@@ -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;