From 4b947ea90c4cffe9e396afe7f14449c5508bf191 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 23 Aug 2017 10:31:05 -0500
Subject: [PATCH 1/2] NIOFileHandle: reduce calls to RandomAccessFile.setLength

---
 src/main/java/loci/common/NIOFileHandle.java | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/src/main/java/loci/common/NIOFileHandle.java b/src/main/java/loci/common/NIOFileHandle.java
index d370e588..99f527ab 100644
--- a/src/main/java/loci/common/NIOFileHandle.java
+++ b/src/main/java/loci/common/NIOFileHandle.java
@@ -105,6 +105,8 @@ public class NIOFileHandle extends AbstractNIOHandle {
   /** The original length of the file. */
   private Long defaultLength;
 
+  private long effectiveLength;
+
   // -- Constructors --
 
   /**
@@ -121,6 +123,7 @@ public NIOFileHandle(File file, String mode, int bufferSize)
       mapMode = FileChannel.MapMode.READ_WRITE;
     }
     raf = new RandomAccessFile(file, mode);
+    effectiveLength = raf.length();
     channel = raf.getChannel();
     byteBufferProvider = new NIOByteBufferProvider(channel, mapMode);
     buffer(position, 0);
@@ -199,8 +202,9 @@ public int getBufferSize() {
   @Override
   public void setLength(long length) throws IOException {
     if (raf.length() < length) {
-      raf.setLength(length);
+      raf.setLength(length + getBufferSize());
     }
+    effectiveLength = length;
     raf.seek(length - 1);
     buffer = null;
   }
@@ -210,6 +214,9 @@ public void setLength(long length) throws IOException {
   /* @see IRandomAccess.close() */
   @Override
   public void close() throws IOException {
+    if (raf.length() != length()) {
+      raf.setLength(length());
+    }
     raf.close();
   }
 
@@ -225,7 +232,7 @@ public long length() throws IOException {
     if (defaultLength != null) {
       return defaultLength;
     }
-    return raf.length();
+    return effectiveLength;
   }
 
   /* @see IRandomAccess.getOrder() */

From c2eebbdc06dbd67e056b1331bd313ae575da7bd9 Mon Sep 17 00:00:00 2001
From: Melissa Linkert <melissa@glencoesoftware.com>
Date: Wed, 23 Aug 2017 11:30:02 -0500
Subject: [PATCH 2/2] Make sure setLength is not called on a closed or
 read-only file

---
 src/main/java/loci/common/NIOFileHandle.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/main/java/loci/common/NIOFileHandle.java b/src/main/java/loci/common/NIOFileHandle.java
index 99f527ab..bf291b8b 100644
--- a/src/main/java/loci/common/NIOFileHandle.java
+++ b/src/main/java/loci/common/NIOFileHandle.java
@@ -214,7 +214,7 @@ public void setLength(long length) throws IOException {
   /* @see IRandomAccess.close() */
   @Override
   public void close() throws IOException {
-    if (raf.length() != length()) {
+    if (isReadWrite && channel.isOpen() && raf.length() != length()) {
       raf.setLength(length());
     }
     raf.close();