/*
* The MIT License
*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package htsjdk.samtools.util;
import org.testng.Assert;
import org.testng.annotations.Test;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
/*
* The Broad Institute
* SOFTWARE COPYRIGHT NOTICE AGREEMENT
* This software and its documentation are copyright Jan 9, 2009 by the
* Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. Neither
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
*/
public class BinaryCodecTest {
public final static String TEST_BASENAME = "htsjdk-BinaryCodecTest";
@Test
public void testReadAndWrite() throws IOException {
final byte[] value = new byte[2];
value[0] = 1;
value[1] = 2;
//Writing to file
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeBytes(value);
codec.close();
//Reading from file
final byte[] valuesTwo = new byte[2];
valuesTwo[0] = 1;
valuesTwo[1] = 2;
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
final byte[] bytesFromBinaryFile = new byte[2];
readCodec.readBytes(bytesFromBinaryFile);
Assert.assertEquals(valuesTwo, bytesFromBinaryFile);
readCodec.close();
outputFile.delete();
}
@Test
public void testReadAndWriteString() throws IOException {
final String value = "Test String to Write";
//Writing to file
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeString(value, true, false);
codec.close();
//Reading from file
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
final int stringLength = readCodec.readInt();
Assert.assertEquals(value.length(), stringLength);
final String s = readCodec.readString(stringLength);
Assert.assertEquals(value, s);
readCodec.close();
}
@Test
public void testReadAndWriteInt() throws IOException {
final int value = 42;
//Writing to file
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeInt(value);
codec.close();
//Reading from file
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
Assert.assertEquals(value, readCodec.readInt());
readCodec.close();
}
@Test
public void testReadAndWriteDouble() throws IOException {
final double value = 54.4;
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeDouble(value);
codec.close();
//Reading from file
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
Assert.assertEquals(value, readCodec.readDouble());
readCodec.close();
}
@Test
public void testReadAndWriteLong() throws IOException {
final long value = 42;
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeLong(value);
codec.close();
//Reading from file
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
Assert.assertEquals(value, readCodec.readLong());
readCodec.close();
}
@Test
public void testReadAndWriteFloat() throws IOException{
final float value = 42.5F;
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeFloat(value);
codec.close();
//Reading from file
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
Assert.assertEquals(value, readCodec.readFloat());
readCodec.close();
}
@Test
public void testReadAndWriteBoolean() throws IOException{
boolean values[] = {true, false};
for (boolean value : values) {
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeBoolean(value);
codec.close();
//Reading from file
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
Assert.assertEquals(value, readCodec.readBoolean());
readCodec.close();
}
}
@Test
public void testReadAndWriteMutlitpleData() throws IOException{
final float fValue = 42.5F;
final String sValue = "TestString";
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
codec.writeFloat(fValue);
codec.writeString(sValue, true, false);
codec.close();
//Reading from file
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
Assert.assertEquals(fValue, readCodec.readFloat());
final int stringLength = readCodec.readInt();
Assert.assertEquals(sValue, readCodec.readString(stringLength));
readCodec.close();
}
@Test
public void readPastEndOfFile() throws IOException{
final long startTime = System.currentTimeMillis();
int i = 0;
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
while (i<100){
codec.writeInt(i);
i++;
}
codec.close();
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
System.out.println((System.currentTimeMillis() - startTime) + "ms to write");
int z = 0;
boolean reachedStatement = false;
while (z<1000) {
try {
Assert.assertEquals(z, readCodec.readInt());
} catch (Exception e) {
Assert.assertEquals(RuntimeEOFException.class, e.getClass());
reachedStatement = true;
}
z++;
}
Assert.assertTrue(reachedStatement);
readCodec.close();
}
@Test
public void timeTest() throws IOException{
final long startTime = System.currentTimeMillis();
int i = 0;
final File outputFile = File.createTempFile(TEST_BASENAME, ".bin");
outputFile.deleteOnExit();
final DataOutputStream stream = new DataOutputStream(new FileOutputStream(outputFile));
final BinaryCodec codec = new BinaryCodec(stream);
while (i<100){
codec.writeInt(i);
i++;
}
codec.close();
final DataInputStream instream = new DataInputStream(new FileInputStream(outputFile));
final BinaryCodec readCodec = new BinaryCodec(instream);
System.out.println((System.currentTimeMillis() - startTime) + "ms to write");
int z = 0;
boolean reachedStatement = false;
while (z<1000) {
try {
Assert.assertEquals(z, readCodec.readInt());
} catch (Exception e) {
Assert.assertEquals(RuntimeEOFException.class, e.getClass());
reachedStatement = true;
}
z++;
}
Assert.assertTrue(reachedStatement);
readCodec.close();
}
}