- RAFBufferFactory, RAFBuffer, RomBufferFactory moved to

`org.jetbrains.bio` package - `RAFBufferFactory` supports buffer size option for underlying random access file - By default `RAFBufferFactory` uses default Random Access File buffers size (8092 bytes) instead of 125 kb.
JetBrains-Research · Mar 30, 2018 · 489f306 · 489f306
1 parent 283a458
commit 489f306
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diff --git a/CHANGES b/CHANGES
@@ -11,6 +11,12 @@ Version 0.7.1
 Changed
 - Use maxHeapSize = "1024m" option for tests. Seems by default on
   windows heap size in about 256m and it isn't enough for tests
+- `RAFBufferFactory`, `RAFBuffer`, `RomBufferFactory` moved to
+  `org.jetbrains.bio` package
+- `RAFBufferFactory` supports buffer size option for underlying
+  random access file
+- By default `RAFBufferFactory` uses default Random Access File
+  buffers size (8092 bytes) instead of 125 kb.
 
 Version 0.7.0
 -------------

diff --git a/src/main/kotlin/org/jetbrains/bio/MMBRomBuffer.kt b/src/main/kotlin/org/jetbrains/bio/MMBRomBuffer.kt
@@ -2,7 +2,6 @@ package org.jetbrains.bio
 
 import com.google.common.primitives.*
 import com.indeed.util.mmap.MMapBuffer
-import org.jetbrains.bio.big.RomBufferFactory
 import java.nio.ByteOrder
 import java.nio.channels.FileChannel
 import java.nio.file.Path

diff --git a/...kotlin/org/jetbrains/bio/big/RAFBuffer.kt → ...ain/kotlin/org/jetbrains/bio/RAFBuffer.kt b/...kotlin/org/jetbrains/bio/big/RAFBuffer.kt → ...ain/kotlin/org/jetbrains/bio/RAFBuffer.kt
@@ -1,12 +1,16 @@
-package org.jetbrains.bio.big
+package org.jetbrains.bio
 
-import org.jetbrains.bio.RandomAccessFile
-import org.jetbrains.bio.RomBuffer
 import java.nio.ByteOrder
 import java.nio.file.Path
 
-class RAFBufferFactory(private val path: Path, private val byteOrder: ByteOrder): RomBufferFactory {
-    override fun create(): RomBuffer = RAFBuffer(path, byteOrder)
+/**
+ * @param path File path
+ * @param byteOrder Byte order
+ * @param bufferSize Random access file buffer size in bytes, use -1 for default value
+ */
+class RAFBufferFactory(private val path: Path, private val byteOrder: ByteOrder,
+                       val bufferSize: Int = -1): RomBufferFactory {
+    override fun create(): RomBuffer = RAFBuffer(path, byteOrder, bufferSize = bufferSize)
 
     override fun close() {
         // Do nothing
@@ -16,9 +20,10 @@ class RAFBufferFactory(private val path: Path, private val byteOrder: ByteOrder)
 class RAFBuffer(private val path: Path,
                 override val order: ByteOrder,
                 position: Long = 0L,
-                limit: Long = -1) : RomBuffer() {
+                limit: Long = -1,
+                val bufferSize: Int = -1) : RomBuffer() {
 
-    private val randomAccessFile = RandomAccessFile(path.toAbsolutePath().toString(), 128000).apply {
+    private val randomAccessFile = RandomAccessFile(path.toAbsolutePath().toString(), bufferSize).apply {
         order(order)
         seek(position)
     }
@@ -37,7 +42,7 @@ class RAFBuffer(private val path: Path,
         get() = randomAccessFile.filePointer
         set(position) { randomAccessFile.seek(position) }
 
-    override fun duplicate() = RAFBuffer(path, order, position, limit)
+    override fun duplicate() = RAFBuffer(path, order, position, limit, bufferSize)
 
     override fun readInts(size: Int): IntArray {
         val dst = IntArray(size)

diff --git a/src/main/kotlin/org/jetbrains/bio/RandomAccessFile.kt b/src/main/kotlin/org/jetbrains/bio/RandomAccessFile.kt
@@ -97,8 +97,9 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
 
     /**
      * The buffer used for reading the data.
+     * Will be set to null on file close
      */
-    protected lateinit var buffer: ByteArray
+    protected var buffer: ByteArray? = null
 
     /**
      * The offset in bytes of the start of the buffer, from the start of the file.
@@ -134,7 +135,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
      * Internal buffer size in bytes. If writing, call flush() first.
      */
     var bufferSize: Int
-        get() = buffer.size
+        get() = buffer!!.size
         set(bufferSize) {
             bufferStart = 0
             dataEnd = 0
@@ -202,6 +203,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
         // Close the underlying file object.
         randomAccessFile!!.close()
         randomAccessFile = null  // help the gc
+        buffer = null // help the gc
     }
 
     /**
@@ -230,7 +232,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
         bufferStart = pos
         filePointer = pos
 
-        dataSize = read_(pos, buffer, 0, buffer.size)
+        dataSize = read_(pos, buffer!!, 0, buffer!!.size)
 
         if (dataSize <= 0) {
             dataSize = 0
@@ -285,7 +287,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
             filePointer < dataEnd -> {
                 val pos = (filePointer - bufferStart).toInt()
                 filePointer++
-                (buffer[pos].toInt() and 0xff)
+                (buffer!![pos].toInt() and 0xff)
 
 
             }
@@ -333,7 +335,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
             len
         else
             bytesAvailable
-        System.arraycopy(buffer, (filePointer - bufferStart).toInt(), b, off, copyLength)
+        System.arraycopy(buffer!!, (filePointer - bufferStart).toInt(), b, off, copyLength)
         filePointer += copyLength.toLong()
 
         // If there is more to copy...
@@ -342,7 +344,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
 
             // If the amount remaining is more than a buffer's length, read it
             // directly from the file.
-            if (extraCopy > buffer.size) {
+            if (extraCopy > buffer!!.size) {
                 extraCopy = read_(filePointer, b, off + copyLength, len - copyLength)
 
                 // ...or read a new buffer full, and copy as much as possible...
@@ -353,7 +355,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
                         dataSize
                     else
                         extraCopy
-                    System.arraycopy(buffer, 0, b, off + copyLength, extraCopy)
+                    System.arraycopy(buffer!!, 0, b, off + copyLength, extraCopy)
                 } else {
                     extraCopy = -1
                 }
@@ -1043,7 +1045,7 @@ open class RandomAccessFile(val location: String, bufferSize: Int = defaultBuffe
 
         if (debugAccess) {
             if (logRead)
-                LOG.debug(" **read_ " + location + " = " + len + " bytes at " + pos + "; block = " + pos / buffer.size)
+                LOG.debug(" **read_ " + location + " = " + len + " bytes at " + pos + "; block = " + pos / buffer!!.size)
             seeksCounter.incrementAndGet()
             bytesReadCounter.addAndGet(len.toLong())
         }

diff --git a/...org/jetbrains/bio/big/RomBufferFactory.kt → ...lin/org/jetbrains/bio/RomBufferFactory.kt b/...org/jetbrains/bio/big/RomBufferFactory.kt → ...lin/org/jetbrains/bio/RomBufferFactory.kt
@@ -1,6 +1,4 @@
-package org.jetbrains.bio.big
-
-import org.jetbrains.bio.RomBuffer
+package org.jetbrains.bio
 
 /**
  * @author Roman.Chernyatchik

diff --git a/src/main/kotlin/org/jetbrains/bio/tdf/TdfFile.kt b/src/main/kotlin/org/jetbrains/bio/tdf/TdfFile.kt
@@ -3,8 +3,8 @@ package org.jetbrains.bio.tdf
 import com.google.common.primitives.Ints
 import org.jetbrains.bio.CompressionType
 import org.jetbrains.bio.RomBuffer
-import org.jetbrains.bio.big.RAFBufferFactory
-import org.jetbrains.bio.big.RomBufferFactory
+import org.jetbrains.bio.RAFBufferFactory
+import org.jetbrains.bio.RomBufferFactory
 import org.jetbrains.bio.divCeiling
 import org.jetbrains.bio.mapUnboxed
 import java.io.Closeable