Introduced consts for prefetch levels

JetBrains-Research · Apr 27, 2018 · 6862698 · 6862698
1 parent 762ad9f
commit 6862698
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Showing 8 changed files with 29 additions and 24 deletions.
diff --git a/CHANGES b/CHANGES
@@ -27,9 +27,11 @@ Changed
 - Use `RomBufferFactory` to detect file endianness
 - Changed `prefetch` option to int value in `BigFile.read()`, 
   `BigWigFile.read()`, `BigBedFile.read()`. Supported values are:
-  * `0` : do not prefetch
-  * `1` : prefetch zoom level indexes tree, chromosomes list
-  * `2` : prefetch w/o zoom level data tree indexes up to chromosomes level
+  * `BigFile.PREFETCH_LEVEL_OFF` : do not prefetch
+  * `BigFile.PREFETCH_LEVEL_FAST` : prefetch zoom level indexes tree,
+    chromosomes list
+  * `BigFile.PREFETCH_LEVEL_DETAILED` : prefetch w/o zoom level data tree
+    indexes up to chromosomes level
   Larger prefetch values increase big file opening time and memory
   consumption but provides faster data access with fewer i/o operations
 

diff --git a/src/main/kotlin/org/jetbrains/bio/big/BigBed.kt b/src/main/kotlin/org/jetbrains/bio/big/BigBed.kt
@@ -94,7 +94,7 @@ class BigBedFile private constructor(
 
         @Throws(IOException::class)
         @JvmStatic
-        fun read(src: String, prefetch: Int = 2,
+        fun read(src: String, prefetch: Int = BigFile.PREFETCH_LEVEL_DETAILED,
                  cancelledChecker: (() -> Unit)? = null,
                  factoryProvider: RomBufferFactoryProvider = defaultFactory()
         ): BigBedFile {

diff --git a/src/main/kotlin/org/jetbrains/bio/big/BigFile.kt b/src/main/kotlin/org/jetbrains/bio/big/BigFile.kt
@@ -84,7 +84,7 @@ abstract class BigFile<out T> internal constructor(
                 bPlusTree = BPlusTree.read(input, header.chromTreeOffset)
 
                 // if do prefetch input and file not empty:
-                if (prefetch > 0) {
+                if (prefetch >= BigFile.PREFETCH_LEVEL_FAST) {
                     // stored in the beginning of file near header
                     cancelledChecker?.invoke()
                     prefetechedTotalSummary = BigSummary.read(input, header.totalSummaryOffset)
@@ -132,7 +132,7 @@ abstract class BigFile<out T> internal constructor(
                 // in buffered stream
                 cancelledChecker?.invoke()
                 rTree = RTreeIndex.read(input, header.unzoomedIndexOffset)
-                if (prefetch > 1) {
+                if (prefetch >= BigFile.PREFETCH_LEVEL_DETAILED) {
                     rTree.prefetchBlocksIndex(
                             input, false, true, header.uncompressBufSize, cancelledChecker
                     )
@@ -467,6 +467,9 @@ abstract class BigFile<out T> internal constructor(
 
     companion object {
         private val LOG = LogManager.getLogger(BigFile::class.java)
+        const val PREFETCH_LEVEL_OFF = 0
+        const val PREFETCH_LEVEL_FAST = 1
+        const val PREFETCH_LEVEL_DETAILED = 2
 
         private val lastCachedBlockInfo: ThreadLocal<Pair<RomBufferState, RomBuffer?>> = ThreadLocal.withInitial {
             RomBufferState(null, 0L, 0L, "") to null
@@ -522,7 +525,7 @@ abstract class BigFile<out T> internal constructor(
 
         @Throws(IOException::class)
         @JvmStatic
-        fun read(src: String, prefetch: Int = 2,
+        fun read(src: String, prefetch: Int = BigFile.PREFETCH_LEVEL_DETAILED,
                  cancelledChecker: (() -> Unit)? = null,
                  factoryProvider: RomBufferFactoryProvider = defaultFactory()
         ): BigFile<Comparable<*>> = factoryProvider(src, ByteOrder.LITTLE_ENDIAN).use { factory ->

diff --git a/src/main/kotlin/org/jetbrains/bio/big/BigWig.kt b/src/main/kotlin/org/jetbrains/bio/big/BigWig.kt
@@ -170,7 +170,7 @@ class BigWigFile private constructor(
 
         @Throws(IOException::class)
         @JvmStatic
-        fun read(src: String, prefetch: Int = 2,
+        fun read(src: String, prefetch: Int = BigFile.PREFETCH_LEVEL_DETAILED,
                  cancelledChecker: (() -> Unit)? = null,
                  factoryProvider: RomBufferFactoryProvider = defaultFactory()
         ): BigWigFile {

diff --git a/src/test/kotlin/org/jetbrains/bio/TestSupport.kt b/src/test/kotlin/org/jetbrains/bio/TestSupport.kt
@@ -89,7 +89,7 @@ fun threadSafeRomFactoryProvidersAndPrefetchParams(): List<Array<Any>> {
         })
     }
     return providers.flatMap { fp ->
-        intArrayOf(0, 1, 2).map { prefetch ->
+        intArrayOf(BigFile.PREFETCH_LEVEL_OFF, BigFile.PREFETCH_LEVEL_FAST, BigFile.PREFETCH_LEVEL_DETAILED).map { prefetch ->
             arrayOf(fp, prefetch)
         }
     }
@@ -98,7 +98,7 @@ fun threadSafeRomFactoryProvidersAndPrefetchParams(): List<Array<Any>> {
 fun romFactoryProviderParams(): List<Array<Any>> = romFactoryProviders().map { arrayOf<Any>(it) }
 
 fun romFactoryProviderAndPrefetchParams(): List<Array<Any>> = romFactoryProviders().flatMap { fp ->
-    intArrayOf(0, 1, 2).map { prefetch ->
+    intArrayOf(BigFile.PREFETCH_LEVEL_OFF, BigFile.PREFETCH_LEVEL_FAST, BigFile.PREFETCH_LEVEL_DETAILED).map { prefetch ->
         arrayOf(fp, prefetch)
     }
 }
@@ -132,7 +132,7 @@ fun romFactoryByteOrderCompressionParamsSets(): Iterable<Array<Any>> {
 }
 
 fun allBigFileParams(): List<Array<Any>> = romFactoryByteOrderCompressionParamsSets().flatMap {
-    intArrayOf(0, 1, 2).map { prefetch ->
+    intArrayOf(BigFile.PREFETCH_LEVEL_OFF, BigFile.PREFETCH_LEVEL_FAST, BigFile.PREFETCH_LEVEL_DETAILED).map { prefetch ->
         it + prefetch
     }
 }
diff --git a/src/test/kotlin/org/jetbrains/bio/big/BigBedFileTest.kt b/src/test/kotlin/org/jetbrains/bio/big/BigBedFileTest.kt
@@ -26,8 +26,8 @@ class BigBedFileTest(
         BigBedFile.read(Examples["example1.bb"], bfProvider, prefetch).use { bf ->
             assertEquals(5, bf.zoomLevels.size)
             assertEquals(39110000, bf.zoomLevels[4].reduction)
-            assertEquals(prefetch > 0, bf.prefetchedLevel2RTreeIndex != null)
-            if (prefetch > 0) {
+            assertEquals(prefetch == BigFile.PREFETCH_LEVEL_OFF, bf.prefetchedLevel2RTreeIndex == null)
+            if (prefetch >= BigFile.PREFETCH_LEVEL_FAST) {
                 assertEquals(5, bf.prefetchedLevel2RTreeIndex!!.size)
 
                 val zRTree0 = bf.prefetchedLevel2RTreeIndex!![bf.zoomLevels[0]]!!
@@ -41,8 +41,8 @@ class BigBedFileTest(
                              (zRTree4.rootNode!! as RTReeNodeLeaf).leaves[0].interval.toString())
             }
 
-            assertEquals(prefetch > 0, bf.prefetchedChr2Leaf != null)
-            if (prefetch > 0) {
+            assertEquals(prefetch == BigFile.PREFETCH_LEVEL_OFF, bf.prefetchedChr2Leaf == null)
+            if (prefetch >= BigFile.PREFETCH_LEVEL_FAST) {
                 assertEquals(1, bf.prefetchedChr2Leaf!!.size)
                 assertEquals("chr21", bf.prefetchedChr2Leaf!!["chr21"]!!.key)
                 assertEquals(0, bf.prefetchedChr2Leaf!!["chr21"]!!.id)
@@ -58,7 +58,7 @@ class BigBedFileTest(
 
             assertEquals(192819, bf.rTree.header.rootOffset)
             assertEquals(14810, bf.rTree.header.itemCount)
-            if (prefetch > 1) {
+            if (prefetch >= BigFile.PREFETCH_LEVEL_DETAILED) {
                 assertNotNull(bf.rTree.rootNode)
                 assertTrue(bf.rTree.rootNode!! is RTReeNodeLeaf)
                 assertEquals(232, (bf.rTree.rootNode!! as RTReeNodeLeaf).leaves.size)

diff --git a/src/test/kotlin/org/jetbrains/bio/big/BigWigFileTest.kt b/src/test/kotlin/org/jetbrains/bio/big/BigWigFileTest.kt
@@ -23,8 +23,8 @@ class BigWigFileTest(
         BigWigFile.read(Examples["example2.bw"], bfProvider, prefetch).use { bf ->
             assertEquals(10, bf.zoomLevels.size)
             assertEquals(25600, bf.zoomLevels[4].reduction)
-            assertEquals(prefetch > 0, bf.prefetchedLevel2RTreeIndex != null)
-            if (prefetch > 0) {
+            assertEquals(prefetch == BigFile.PREFETCH_LEVEL_OFF, bf.prefetchedLevel2RTreeIndex == null)
+            if (prefetch >= BigFile.PREFETCH_LEVEL_FAST) {
                 assertEquals(10, bf.prefetchedLevel2RTreeIndex!!.size)
 
                 val zRTree0 = bf.prefetchedLevel2RTreeIndex!![bf.zoomLevels[0]]!!
@@ -42,8 +42,8 @@ class BigWigFileTest(
                              (zRTree4.rootNode!! as RTReeNodeLeaf).leaves[1].interval)
             }
 
-            assertEquals(prefetch > 0, bf.prefetchedChr2Leaf != null)
-            if (prefetch > 0) {
+            assertEquals(prefetch == BigFile.PREFETCH_LEVEL_OFF, bf.prefetchedChr2Leaf == null)
+            if (prefetch >= BigFile.PREFETCH_LEVEL_FAST) {
                 assertEquals(1, bf.prefetchedChr2Leaf!!.size)
                 assertEquals("chr21", bf.prefetchedChr2Leaf!!["chr21"]!!.key)
                 assertEquals(0, bf.prefetchedChr2Leaf!!["chr21"]!!.id)
@@ -59,7 +59,7 @@ class BigWigFileTest(
 
             assertEquals(15751097, bf.rTree.header.rootOffset)
             assertEquals(6857, bf.rTree.header.itemCount)
-            if (prefetch > 1) {
+            if (prefetch >= BigFile.PREFETCH_LEVEL_DETAILED) {
                 assertNotNull(bf.rTree.rootNode)
                 assertTrue(bf.rTree.rootNode!! is RTReeNodeIntermediate)
                 assertEquals(27, (bf.rTree.rootNode!! as RTReeNodeIntermediate).children.size)

diff --git a/src/test/kotlin/org/jetbrains/bio/big/RTreeIndexTest.kt b/src/test/kotlin/org/jetbrains/bio/big/RTreeIndexTest.kt
@@ -24,7 +24,7 @@ class RTreeIndexTest(
             assertEquals(192771L, rti.header.endDataOffset)
             assertEquals(64, rti.header.itemsPerSlot)
             assertEquals(192819L, rti.header.rootOffset)
-            if (prefetch > 1) {
+            if (prefetch >= BigFile.PREFETCH_LEVEL_DETAILED) {
                 assertNotNull(bbf.rTree.rootNode)
                 assertTrue(bbf.rTree.rootNode is RTReeNodeLeaf)
                 assertEquals(232, (bbf.rTree.rootNode as RTReeNodeLeaf).leaves.size)
@@ -49,7 +49,7 @@ class RTreeIndexTest(
                 f.create().use { input ->
 
                     val rti = RTreeIndex.read(input, 0L)
-                    if (prefetch > 0) {
+                    if (prefetch >= BigFile.PREFETCH_LEVEL_FAST) {
                         rti.prefetchBlocksIndex(input, true, false, 0, null)
                     }
 
@@ -108,7 +108,7 @@ class RTreeIndexTest(
             bfProvider(path.toString(), ByteOrder.nativeOrder()).use { f ->
                 f.create().use { input ->
                     val rti = RTreeIndex.read(input, 0)
-                    if (prefetch > 0) {
+                    if (prefetch >= BigFile.PREFETCH_LEVEL_FAST) {
                         rti.prefetchBlocksIndex(input, true, false, 0, null)
                     }
                     for (leaf in leaves) {