Description: Using nio instead of the JNI to avoid unaligned access memory
Author: Bernd Rinn <brinn@ethz.ch>
Origin: upstream
Forwarded: not-needed
Reviewed-by: Pierre Gruet <pgt@debian.org>
Last-Update: 2020-12-15

--- a/source/java/ch/systemsx/cisd/base/convert/NativeData.java
+++ b/source/java/ch/systemsx/cisd/base/convert/NativeData.java
@@ -15,8 +15,6 @@
 
 import java.nio.ByteBuffer;
 
-import ch.systemsx.cisd.base.utilities.NativeLibraryUtilities;
-
 /**
  * This class encapsulates native methods to deal with arrays of numbers, converting from numbers to
  * bytes and bytes to numbers.
@@ -28,27 +26,10 @@
  * primitive numbers (int, short, ...)
  * <p>
  * Variant interfaces convert only a sub-array.
- * <p>
- * The class has optimized methods using jni-libraries for some common platforms and a pure-java
- * implementation (called <i>javamode</i> if the jni-libraries are not available). If you want to
- * enforce <i>javamode</i>, you need to pass the property <code>nativedata.javamode=true</code> to
- * the JRE.
  */
 public class NativeData
 {
-    private static final boolean useNativeLib;
-
-    static
-    {
-        if (Boolean.getBoolean("nativedata.javamode"))
-        {
-            useNativeLib = false;
-        } else
-        {
-	    System.loadLibrary("cisd_nativedata");
-	    useNativeLib = true;
-        }
-    }
+    private static final boolean useNativeLib = false;
 
     /** Size of a <code>short</code> value in <code>byte</code>s. */
     public final static int SHORT_SIZE = 2;
--- a/sourceTest/java/ch/systemsx/cisd/base/convert/NativeDataTests.java
+++ b/sourceTest/java/ch/systemsx/cisd/base/convert/NativeDataTests.java
@@ -162,7 +162,6 @@
     @Test(dataProvider = "getOfs")
     public void testLongToByteToLong(int sourceOfs, int targetOfs)
     {
-        assertTrue(NativeData.isUseNativeLib());
         final int sizeOfTarget = 8;
         final long[] orignalArr = new long[]
             { -1, 17, 100000, -1000000 };
@@ -180,7 +179,6 @@
     @Test(dataProvider = "getOfs")
     public void testShortToByteToShort(int sourceOfs, int targetOfs)
     {
-        assertTrue(NativeData.isUseNativeLib());
         final int sizeOfTarget = 2;
         final short[] orignalArr = new short[]
             { -1, 17, 20000, (short) -50000 };
@@ -198,7 +196,6 @@
     @Test(dataProvider = "getOfs")
     public void testCharToByteToChar(int sourceOfs, int targetOfs)
     {
-        assertTrue(NativeData.isUseNativeLib());
         final int sizeOfTarget = 2;
         final char[] orignalArr = new char[]
             { 'c', ';', '\u0222', '\u1000' };
@@ -216,7 +213,6 @@
     @Test(dataProvider = "getOfs")
     public void testFloatToByteToFloat(int sourceOfs, int targetOfs)
     {
-        assertTrue(NativeData.isUseNativeLib());
         final int sizeOfTarget = 4;
         final float[] orignalArr = new float[]
             { -1, 17, 3.14159f, -1e6f };
@@ -234,7 +230,6 @@
     @Test(dataProvider = "getOfs")
     public void testDoubleToByteToDouble(int sourceOfs, int targetOfs)
     {
-        assertTrue(NativeData.isUseNativeLib());
         final int sizeOfTarget = 8;
         final double[] orignalArr = new double[]
             { -1, 17, 3.14159, -1e42 };
@@ -252,7 +247,6 @@
     @Test
     public void testShortEndianConversion()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final short[] values = new short[]
             { 1, 2, 4, 8, 16, 256, 512 };
         final short[] convertedValuesExpected = new short[]
@@ -266,7 +260,6 @@
     @Test
     public void testIntEndianConversion()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final int[] values = new int[]
             { 1, 2, 4, 8, 16, 256, 1 << 16 };
         final int[] convertedValuesExpected = new int[]
@@ -280,7 +273,6 @@
     @Test
     public void testLongEndianConversion()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final long[] values = new long[]
             { 1, 2, 4, 8, 16, 256, 1L << 16, 1L << 24 };
         final long[] convertedValuesExpected = new long[]
@@ -294,7 +286,6 @@
     @Test
     public void testFloatLittleEndianRoundtrip()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final float[] values = new float[]
             { 1.1f, 2.2f, 3.3f, 1e-25f, 1e25f };
         final float[] convertedValuesFound =
@@ -306,7 +297,6 @@
     @Test
     public void testFloatBigEndianRoundtrip()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final float[] values = new float[]
             { 1.1f, 2.2f, 3.3f, 1e-25f, 1e25f };
         final float[] convertedValuesFound =
@@ -318,7 +308,6 @@
     @Test
     public void testDoubleLittleEndianRoundtrip()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final double[] values = new double[]
             { 1.1f, 2.2f, 3.3f, 1e-25f, 1e25f };
         final double[] convertedValuesFound =
@@ -330,7 +319,6 @@
     @Test
     public void testDoubleBigEndianRoundtrip()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final double[] values = new double[]
             { 1.1, 2.2, 3.3, 1e-25, 1e25 };
         final double[] convertedValuesFound =
@@ -342,28 +330,24 @@
     @Test(expectedExceptions = NullPointerException.class)
     public void testNPE()
     {
-        assertTrue(NativeData.isUseNativeLib());
         NativeData.copyByteToLong(null, 0, null, 0, 0, ByteOrder.NATIVE);
     }
 
     @Test(expectedExceptions = IndexOutOfBoundsException.class)
     public void testIOOB()
     {
-        assertTrue(NativeData.isUseNativeLib());
         NativeData.copyByteToLong(new byte[] {}, -1, new long[] {}, 0, 0, ByteOrder.NATIVE);
     }
 
     @Test(expectedExceptions = IndexOutOfBoundsException.class)
     public void testIOOB2()
     {
-        assertTrue(NativeData.isUseNativeLib());
         NativeData.copyByteToLong(new byte[] {}, 0, new long[] {}, 10, 0, ByteOrder.NATIVE);
     }
 
     @Test
     public void testPlatformEndiness()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final double[] values = new double[]
             { 1.1, 2.2, 3.3, 1e-200, 1e200 };
         final double[] valuesLE =
@@ -387,7 +371,6 @@
     @Test
     public void testFloatToByteNonNativeByteOrderPartialOutputArray()
     {
-        assertTrue(NativeData.isUseNativeLib());
         final int sizeOfTarget = 4;
         final ByteOrder nonNativeByteOrder =
                 (NativeData.getNativeByteOrder() == ByteOrder.LITTLE_ENDIAN) ? ByteOrder.BIG_ENDIAN