From 7960934d22f271fb5a77dc8ecd9a9afe4e7ef64d Mon Sep 17 00:00:00 2001
From: Sebastian Bittrich <bittrich@hs-mittweida.de>
Date: Mon, 29 Jul 2019 14:17:52 -0700
Subject: [PATCH] buffering of InputStream during reading

---
 .../src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java    | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/mmtf-codec/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java b/mmtf-codec/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java
index 2da3ff9..cbef80b 100644
--- a/mmtf-codec/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java
+++ b/mmtf-codec/src/main/java/org/rcsb/mmtf/decoder/ReaderUtils.java
@@ -1,5 +1,6 @@
 package org.rcsb.mmtf.decoder;
 
+import java.io.BufferedInputStream;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
@@ -158,6 +159,11 @@ private static byte[] readFile(Path path) throws IOException {
 	 */
 	public static MmtfStructure getDataFromInputStream(InputStream inStream)
 		throws IOException {
+		// ensure that InputStream is buffered if needed  (i.e. not externally buffered e.g. via GZIPInputStream)
+		if (!(inStream instanceof BufferedInputStream)) {
+			inStream = new BufferedInputStream(inStream, 65536);
+		}
+
 		MessagePackSerialization mmtfBeanSeDeMessagePackImpl
 			= new MessagePackSerialization();
 		return mmtfBeanSeDeMessagePackImpl.deserialize(inStream);