Develop Reference

Bit shuffling to change encoding from little endian

So in the program I need to read an number from the user which needs to be changed from little endian encoding to whatever encoding the user wants to change it to. The encoding entered by the user is just a 4 digits number which just means which byte should be where after the encoding. e.g. 4321 means put the 4th byte first followed by the 3rd and so on. the encoding can take other form such as 3214 etc.
This is my code, would really appreciate if someone point out where I am missing out.
import java.util.Scanner;
class encoding {
public static void main(String[] args) {
Scanner sc = new Scanner(System.in);
int n = sc.nextInt();
String byteOrder = sc.next();
long[] bitMask = { // little endian
Long.parseLong("11111111000000000000000000000000", 2),
Long.parseLong("00000000111111110000000000000000", 2),
Long.parseLong("00000000000000001111111100000000", 2),
Long.parseLong("00000000000000000000000011111111", 2)
};
int[] bytes = {
(int)(bitMask[0] & n),
(int)(bitMask[1] & n),
(int)(bitMask[2] & n),
(int)(bitMask[3] & n)
};
int result = 0;
shuffleBytes(bytes, byteOrder);
for (int i = 0; i < 4; i++) {
bytes[i] = bytes[i] << (i * 8);
result |= bytes[i];
}
System.out.println(result);
}
static void shuffleBytes(int[] bytes, String encoding) {
for (int i = 0; i < 4; i++) {
int index = Integer.parseInt(encoding.substring(i, i+1))-1;
int copy = bytes[i];
bytes[i] = bytes[index];
bytes[index] = copy;
}
}
}

Fixing your current solution
There are two problems:
1. Forgot to right-align bytes
In ...
int[] bytes = {
(int)(bitMask[0] & n),
(int)(bitMask[1] & n),
(int)(bitMask[2] & n),
(int)(bitMask[3] & n)
};
... you forgot to shift each "byte" to the right. As a result, you end up with a list of "bytes" of the form 0x……000000, 0x00……0000, 0x0000……00, 0x000000……. This is not a problem yet, but after shuffleBytes you shift each of these entries again using bytes[i] = bytes[i] << (i * 8);. As a result, the relevant parts (__) end up at a completely different spot or are shifted completely out of the integer.
To fix this, shift each (int)(bitMask[…] & n) to the right:
int[] bytes = {
(int)(bitMask[0] & n) >> (3*8),
(int)(bitMask[1] & n) >> (2*8),
(int)(bitMask[2] & n) >> (1*8),
(int)(bitMask[3] & n) >> (0*8)
};
2. Swapping more than once
In ...
static void shuffleBytes(int[] bytes, String encoding) {
for (int i = 0; i < 4; i++) {
int index = Integer.parseInt(encoding.substring(i, i+1))-1;
int copy = bytes[i];
bytes[i] = bytes[index];
bytes[index] = copy;
}
}
... you swap some bytes multiple times because you operate in-place. To understand what happens consider the following minimal example where we want to swap two bytes using order = "21". We inspect the variables before/after each iteration of the for loop.
The original input is bytes = {x, y} and order = "21"
We moved bytes[0] to bytes[1]. Now we have bytes = {y, x}.
But we are not finished yet. The loop continues and moves bytes[1] to bytes[0]. You assumed that bytes[1] would still be y at this point. However, because of the previous iteration this entry now holds x instead. Therefore, the result is bytes = {x, y}.
Here nothing changed, but for more entries you might also end up with something that is neither the original order nor the expected output order.
The easiest way to fix this is to write the result into a new array:
static int[] shuffleBytes(int[] bytes, String encoding) {
int[] result = new int[bytes.length];
for (int i = 0; i < 4; i++) {
int index = Integer.parseInt(encoding.substring(i, i+1))-1;
result[index] = bytes[i];
}
return result; // also adapt main() to use this return value
}
Alternative Solution
Even though you could fix your solution as described above I'm not too happy with it. Therefore, I propose this alternative solution which is cleaner, shorter, and more efficient.
import java.util.Scanner;
public class Encoding {
public static void main(String[] args) {
Scanner sc = new Scanner(System.in);
int input = sc.nextInt();
System.out.format("input = 0x%08x = %1$d%n", input);
String newOrder = sc.next();
int output = reorder(input, newOrder);
System.out.format("output = 0x%08x = %1$d%n", output);
}
/** #param newOrder permutation of "1234" */
static int reorder(int input, String newOrder) {
int output = 0;
for (char byte1Based : newOrder.toCharArray()) {
output <<= 8;
int shift = (byte1Based - '1') * 8;
output |= ((0xFF << shift) & input) >> shift;
}
return output;
}
}

Converting integer to byte hex in java

I am trying to developing a java card application. There will a dynamic input string which will contain a phone number in a byte array like:
byte[] number =new byte[] {1,2,3,4,5,6,7,8,9,5};
I want this array to be changed into following array:
byte[] changed num = {(byte)0x0C, (byte)0x91, (byte)0x19, (byte)0x21, (byte)0x43, (byte)0x65, (byte)0x87, (byte)0x59}
Where first three bytes will be same always and remaining 5 will be update from the incoming array.
I have tried the following:
public static void main(String args[]){
byte[] number =new byte[] {1,2,3,4,5,6,7,8,9,5};
byte[] changednum = new byte[8];
changednum[0] = (byte)0x0C;
changednum[1] = (byte)0x91;
changednum[2] = (byte)0x19;
changednum[3] = (byte)0x(number[0] + number[1]*10);
changednum[4] = (byte)0x(number[2] + number[3]*10);
changednum[5] = (byte)0x(number[4] + number[5]*10);
changednum[6] = (byte)0x(number[6] + number[7]*10);
changednum[7] = (byte)0x(number[8] + number[9]*10);
System.out.println(Arrays.toString(changednum));
}
}
But the last 5 values are not being converted to byte value
s.

This line
changednum[3] = (byte)0x(number[0] + number[1]*10);
could be done with a complicate set of String manipulation how simple maths will do what you want.
changednum[3] = (byte)(number[0] + number[1]*16);
The *16 is needed because you appear to be assuming the number is in hexadecimal.
You could use a loop
for (int i = 0; i < 4; i++)
changednum[i+3] = (byte)(number[i*2] + number[i*2+1]*16);
or using += to avoid the cast
for (int i = 0; i < 4; i++)
changednum[i+3] += number[i*2] + number[i*2+1] * 16;
or you can write
for (int i = 0; i < 4; i++)
changednum[i+3] += number[i*2] + (number[i*2+1] << 4);

Although it is not very important in the standard edition of Java in this case, performance is often crucial in Java Card. This solution is slightly faster than the accepted answer thanks to bitwise operators and it is a valid Java Card code without 32-bit integers:
for (short i = 3, j = 0; i < 7; i++, j += 2) {
changednum[i] = (byte) ((number[j+1] << 4) | (number[j] & 0x0F));
}

You can use the method Integer.toHexString, that will do the convertion,
you need to carefully note that casting explicity integer to byte will truncate its value in a range between -128 to 127
final int f = -2211;
System.out.println(f);
System.out.println((byte) f);
System.out.println(Integer.toHexString((byte) f));

The other answers lack readability, in my opinion.
This solution uses separate methods and a ByteBuffer to make the methods work without passing an offset and other plumbing. It has weird things like constants and well thought out identifiers, exceptions, JavaDoc and other scary concepts from the book of maintainability.
package nl.owlstead.stackoverflow;
import java.nio.BufferOverflowException;
import java.nio.ByteBuffer;
/**
* Helper class to create telephone numbers with headers for Java card using
* reverse packed BCD format.
*
* #param buffer
* a buffer with enough space for the 3 byte header
*/
public final class OverlyDesignedTelephoneNumberHelper {
private static final int TELEPHONE_NUMBER_SIZE = 10;
private static final int NIBBLE_SIZE = 4;
private static final byte[] HEADER = { (byte) 0x0C, (byte) 0x91,
(byte) 0x19 };
/**
* Adds the header for the telephone number to the given buffer.
*
* #param buffer
* a buffer with enough space for the 3 byte header
* #throws NullPointerException
* if the buffer is null
* #throws BufferOverflowException
* if the buffer doesn't have enough space for the header
*/
private static void addTelephoneNumberHeader(final ByteBuffer buffer) {
buffer.put(HEADER);
}
/**
* Adds the telephone number to the given buffer.
*
* #param buffer
* a buffer with enough space for the 3 byte header
* #param number
* the number in BCD format, should be 10 bytes in size
* #throws IllegalArgumentException
* if the number is null or doesn't contain 10 BCD digits
* #throws NullPointerException
* if the buffer is null
* #throws BufferOverflowException
* if the buffer doesn't have enough space for the telephone
* number
*/
private static void addTelephoneNumber(final ByteBuffer buffer,
final byte[] number) {
if (number == null || number.length != TELEPHONE_NUMBER_SIZE) {
throw new IllegalArgumentException("Expecting 10 digit number");
}
for (int i = 0; i < number.length; i += 2) {
final byte lowDigit = number[i];
validateUnpackedBCDDigit(lowDigit);
final byte highDigit = number[i + 1];
validateUnpackedBCDDigit(highDigit);
buffer.put((byte) ((highDigit << NIBBLE_SIZE) | lowDigit));
}
}
/**
* Tests if the given unpacked BCD digit is within range.
*
* #param b
* the byte to test
* #throws IllegalArgumentException
* if it isn't
*/
private static void validateUnpackedBCDDigit(final byte b) {
if (b < 0 || b > 9) {
throw new IllegalArgumentException(
"Telefonenumber isn't all bytes representing digits in BCD");
}
}
public static void main(final String... args) {
final byte[] number = new byte[] { 1, 2, 3, 4, 5, 6, 7, 8, 9, 5 };
final ByteBuffer buf = ByteBuffer.allocate(HEADER.length
+ TELEPHONE_NUMBER_SIZE);
addTelephoneNumberHeader(buf);
addTelephoneNumber(buf, number);
buf.flip();
while (buf.hasRemaining()) {
System.out.printf("%02X", buf.get());
}
System.out.println();
}
private OverlyDesignedTelephoneNumberHelper() {
// avoid instantiation
}
}

Store binary sequence in byte array?

I need to store a couple binary sequences that are 16 bits in length into a byte array (of length 2). The one or two binary numbers don't change, so a function that does conversion might be overkill. Say for example the 16 bit binary sequence is 1111000011110001. How do I store that in a byte array of length two?

String val = "1111000011110001";
byte[] bval = new BigInteger(val, 2).toByteArray();
There are other options, but I found it best to use BigInteger class, that has conversion to byte array, for this kind of problems. I prefer if, because I can instantiate class from String, that can represent various bases like 8, 16, etc. and also output it as such.
Edit: Mondays ... :P
public static byte[] getRoger(String val) throws NumberFormatException,
NullPointerException {
byte[] result = new byte[2];
byte[] holder = new BigInteger(val, 2).toByteArray();
if (holder.length == 1) result[0] = holder[0];
else if (holder.length > 1) {
result[1] = holder[holder.length - 2];
result[0] = holder[holder.length - 1];
}
return result;
}
Example:
int bitarray = 12321;
String val = Integer.toString(bitarray, 2);
System.out.println(new StringBuilder().append(bitarray).append(':').append(val)
.append(':').append(Arrays.toString(getRoger(val))).append('\n'));

I have been disappointed with all of the solutions I have found to converting strings of bits to byte arrays and vice versa -- all have been buggy (even the BigInteger solution above), and very few are as efficient as they should be.
I realize the OP was only concerned with a bit string to an array of two bytes, which the BitInteger approach seems to work fine for. However, since this post is currently the first search result when searching "bit string to byte array java" in Google, I am going to post my general solution here for people dealing with huge strings and/or huge byte arrays.
Note that my solution below is the only solution I have ran that passes all of my test cases -- many online solutions to this relatively simple problem simply do not work.
Code
/**
* Zips (compresses) bit strings to byte arrays and unzips (decompresses)
* byte arrays to bit strings.
*
* #author ryan
*
*/
public class BitZip {
private static final byte[] BIT_MASKS = new byte[] {1, 2, 4, 8, 16, 32, 64, -128};
private static final int BITS_PER_BYTE = 8;
private static final int MAX_BIT_INDEX_IN_BYTE = BITS_PER_BYTE - 1;
/**
* Decompress the specified byte array to a string.
* <p>
* This function does not pad with zeros for any bit-string result
* with a length indivisible by 8.
*
* #param bytes The bytes to convert into a string of bits, with byte[0]
* consisting of the least significant bits in the byte array.
* #return The string of bits representing the byte array.
*/
public static final String unzip(final byte[] bytes) {
int byteCount = bytes.length;
int bitCount = byteCount * BITS_PER_BYTE;
char[] bits = new char[bitCount];
{
int bytesIndex = 0;
int iLeft = Math.max(bitCount - BITS_PER_BYTE, 0);
while (bytesIndex < byteCount) {
byte value = bytes[bytesIndex];
for (int b = MAX_BIT_INDEX_IN_BYTE; b >= 0; --b) {
bits[iLeft + b] = ((value % 2) == 0 ? '0' : '1');
value >>= 1;
}
iLeft = Math.max(iLeft - BITS_PER_BYTE, 0);
++bytesIndex;
}
}
return new String(bits).replaceFirst("^0+(?!$)", "");
}
/**
* Compresses the specified bit string to a byte array, ignoring trailing
* zeros past the most significant set bit.
*
* #param bits The string of bits (composed strictly of '0' and '1' characters)
* to convert into an array of bytes.
* #return The bits, as a byte array with byte[0] containing the least
* significant bits.
*/
public static final byte[] zip(final String bits) {
if ((bits == null) || bits.isEmpty()) {
// No observations -- return nothing.
return new byte[0];
}
char[] bitChars = bits.toCharArray();
int bitCount = bitChars.length;
int left;
for (left = 0; left < bitCount; ++left) {
// Ignore leading zeros.
if (bitChars[left] == '1') {
break;
}
}
if (bitCount == left) {
// Only '0's in the string.
return new byte[] {0};
}
int cBits = bitCount - left;
byte[] bytes = new byte[((cBits) / BITS_PER_BYTE) + (((cBits % BITS_PER_BYTE) > 0) ? 1 : 0)];
{
int iRight = bitCount - 1;
int iLeft = Math.max(bitCount - BITS_PER_BYTE, left);
int bytesIndex = 0;
byte _byte = 0;
while (bytesIndex < bytes.length) {
while (iLeft <= iRight) {
if (bitChars[iLeft] == '1') {
_byte |= BIT_MASKS[iRight - iLeft];
}
++iLeft;
}
bytes[bytesIndex++] = _byte;
iRight = Math.max(iRight - BITS_PER_BYTE, left);
iLeft = Math.max((1 + iRight) - BITS_PER_BYTE, left);
_byte = 0;
}
}
return bytes;
}
}
Performance
I was bored at work so I did some performance testing comparing against the accepted answer here for when N is large. (Pretending to ignore the fact that the BigInteger approach posted above doesn't even work properly as a general approach.)
This is running with a random bit string of size 5M and a random byte array of size 1M:
String -> byte[] -- BigInteger result: 39098ms
String -> byte[] -- BitZip result: 29ms
byte[] -> String -- Integer result: 138ms
byte[] -> String -- BitZip result: 71ms
And the code:
public static void main(String[] argv) {
int testByteLength = 1000000;
int testStringLength = 5000000;
// Independently random.
final byte[] randomBytes = new byte[testByteLength];
final String randomBitString;
{
StringBuilder sb = new StringBuilder();
Random rand = new Random();
for (int i = 0; i < testStringLength; ++i) {
int value = rand.nextInt(1 + i);
sb.append((value % 2) == 0 ? '0' : '1');
randomBytes[i % testByteLength] = (byte) value;
}
randomBitString = sb.toString();
}
byte[] resultCompress;
String resultDecompress;
{
Stopwatch s = new Stopwatch();
TimeUnit ms = TimeUnit.MILLISECONDS;
{
s.start();
{
resultCompress = compressFromBigIntegerToByteArray(randomBitString);
}
s.stop();
{
System.out.println("String -> byte[] -- BigInteger result: " + s.elapsed(ms) + "ms");
}
s.reset();
}
{
s.start();
{
resultCompress = zip(randomBitString);
}
s.stop();
{
System.out.println("String -> byte[] -- BitZip result: " + s.elapsed(ms) + "ms");
}
s.reset();
}
{
s.start();
{
resultDecompress = decompressFromIntegerParseInt(randomBytes);
}
s.stop();
{
System.out.println("byte[] -> String -- Integer result: " + s.elapsed(ms) + "ms");
}
s.reset();
}
{
s.start();
{
resultDecompress = unzip(randomBytes);
}
s.stop();
{
System.out.println("byte[] -> String -- BitZip result: " + s.elapsed(ms) + "ms");
}
s.reset();
}
}
}

Sending a Java UUID to C++ as bytes and back over TCP

I'm trying to send a Java UUID to C++, where it will be used as a GUID, then send it back and see it as a UUID, and I'm hoping to send it across as just 16 bytes.
Any suggestions on an easy way to do this?
I've got a complicated way of doing it, sending from Java to C++, where I ask the UUID for its least and most significant bits, write this into a ByteBuffer, and then read it out as bytes.
Here is my silly-complicated way of getting 2 longs out of a UUID, sending them to C++:
Java
public static byte[] asByteArray(UUID uuid)
{
long msb = uuid.getMostSignificantBits();
long lsb = uuid.getLeastSignificantBits();
byte[] buffer = new byte[16];
for (int i = 0; i < 8; i++) {
buffer[i] = (byte) (msb >>> 8 * (7 - i));
}
for (int i = 8; i < 16; i++) {
buffer[i] = (byte) (lsb >>> 8 * (7 - i));
}
return buffer;
}
byte[] bytesOriginal = asByteArray(uuid);
byte[] bytes = new byte[16];
// Reverse the first 4 bytes
bytes[0] = bytesOriginal[3];
bytes[1] = bytesOriginal[2];
bytes[2] = bytesOriginal[1];
bytes[3] = bytesOriginal[0];
// Reverse 6th and 7th
bytes[4] = bytesOriginal[5];
bytes[5] = bytesOriginal[4];
// Reverse 8th and 9th
bytes[6] = bytesOriginal[7];
bytes[7] = bytesOriginal[6];
// Copy the rest straight up
for ( int i = 8; i < 16; i++ )
{
bytes[i] = bytesOriginal[i];
}
// Use a ByteBuffer to switch our ENDIAN-ness
java.nio.ByteBuffer buffer = java.nio.ByteBuffer.allocate(16);
buffer.order(java.nio.ByteOrder.BIG_ENDIAN);
buffer.put(bytes);
buffer.order(java.nio.ByteOrder.LITTLE_ENDIAN);
buffer.position(0);
UUIDComponents x = new UUIDComponents();
x.id1 = buffer.getLong();
x.id2 = buffer.getLong();
C++
google::protobuf::int64 id1 = id.id1();
google::protobuf::int64 id2 = id.id2();
char* pGuid = (char*) &guid;
char* pGuidLast8Bytes = pGuid + 8;
memcpy(pGuid, &id1, 8);
memcpy(pGuidLast8Bytes, &id2, 8);
This works, but seems way too complex, and I can't yet get it working in the other direction.
(I'm using google protocol buffers to send the two longs back and forth)
Alex

I got something working.
Instead of sending it across as two longs, I send it across as bytes, here is the Java code:
public static UUID fromBytes( ByteString byteString)
{
byte[] bytesOriginal = byteString.toByteArray();
byte[] bytes = new byte[16];
// Reverse the first 4 bytes
bytes[0] = bytesOriginal[3];
bytes[1] = bytesOriginal[2];
bytes[2] = bytesOriginal[1];
bytes[3] = bytesOriginal[0];
// Reverse 6th and 7th
bytes[4] = bytesOriginal[5];
bytes[5] = bytesOriginal[4];
// Reverse 8th and 9th
bytes[6] = bytesOriginal[7];
bytes[7] = bytesOriginal[6];
// Copy the rest straight up
for ( int i = 8; i < 16; i++ )
{
bytes[i] = bytesOriginal[i];
}
return toUUID(bytes);
}
public static ByteString toBytes( UUID uuid )
{
byte[] bytesOriginal = asByteArray(uuid);
byte[] bytes = new byte[16];
// Reverse the first 4 bytes
bytes[0] = bytesOriginal[3];
bytes[1] = bytesOriginal[2];
bytes[2] = bytesOriginal[1];
bytes[3] = bytesOriginal[0];
// Reverse 6th and 7th
bytes[4] = bytesOriginal[5];
bytes[5] = bytesOriginal[4];
// Reverse 8th and 9th
bytes[6] = bytesOriginal[7];
bytes[7] = bytesOriginal[6];
// Copy the rest straight up
for ( int i = 8; i < 16; i++ )
{
bytes[i] = bytesOriginal[i];
}
return ByteString.copyFrom(bytes);
}
private static byte[] asByteArray(UUID uuid)
{
long msb = uuid.getMostSignificantBits();
long lsb = uuid.getLeastSignificantBits();
byte[] buffer = new byte[16];
for (int i = 0; i < 8; i++) {
buffer[i] = (byte) (msb >>> 8 * (7 - i));
}
for (int i = 8; i < 16; i++) {
buffer[i] = (byte) (lsb >>> 8 * (7 - i));
}
return buffer;
}
private static UUID toUUID(byte[] byteArray) {
long msb = 0;
long lsb = 0;
for (int i = 0; i < 8; i++)
msb = (msb << 8) | (byteArray[i] & 0xff);
for (int i = 8; i < 16; i++)
lsb = (lsb << 8) | (byteArray[i] & 0xff);
UUID result = new UUID(msb, lsb);
return result;
}
Doing it this way, the bytes can be used straight up on the C++ side. I suppose the switching around of the order of the bytes could be done on either end.
C++
memcpy(&guid, data, 16);

It's possibly easiest to use getMostSignificantBits and getLeastSignificant bits to get long values, and send those. Likewise you can reconstruct the UUID from those two longs using the appropriate constructor.
It's a shame there isn't a toByteArray/fromByteArray pair of methods :(

Your current way is fine, nothing wrong about doing it that way.
Another approace is yo just communicate with the string representation of the uuid, send the string, parse it in c++.
Btw, bytes do not have endianess, Unless you're casting a byte/char array or similar to an integer type, you just determine the endianess by assigning the bytes back in the approprate order.

Here is what I do to convert a C++ GUID to a Java UUID. On the C++ side, the GUID struct is just converted to bytes. The conversion to C++ can then just go along the same lines.
public static UUID cppGuidBytesToUuid(byte[] cppGuid) {
ByteBuffer b = ByteBuffer.wrap(cppGuid);
b.order(ByteOrder.LITTLE_ENDIAN);
java.nio.ByteBuffer out = java.nio.ByteBuffer.allocate(16);
out.order(ByteOrder.BIG_ENDIAN);
out.putInt(b.getInt());
out.putShort(b.getShort());
out.putShort(b.getShort());
out.put(b);
out.position(0);
return new UUID(out.getLong(), out.getLong());
}
// Here is the JNI code ;-)
jbyteArray GUID2ByteArray(JNIEnv *env,GUID* guid)
{
if (guid == NULL)
return NULL;
jbyteArray jGUID = env->NewByteArray(sizeof(GUID));
if (jGUID == NULL)
return NULL;
env->SetByteArrayRegion(jGUID,0,sizeof(GUID),(signed char*)(guid));
if (env->ExceptionOccurred() != NULL)
return NULL;
return jGUID;
}

Perhaps you could explain why you are not just doing.
UUID uuid =
x.id1 = uuid.getMostSignificantBits();
x.id2 = uuid.getLeastSignificantBits();
P.S. As I read #Jon Skeet's post again, I think this is much the same advice. ;)

Bit manipulation and output in Java

If you have binary strings (literally String objects that contain only 1's and 0's), how would you output them as bits into a file?
This is for a text compressor I was working on; it's still bugging me, and it'd be nice to finally get it working. Thanks!

Easiest is to simply take 8 consecutive characters, turn them into a byte and output that byte. Pad with zeros at the end if you can recognize the end-of-stream, or add a header with length (in bits) at the beginning of the file.
The inner loop would look something like:
byte[] buffer = new byte[ ( string.length + 7 ) / 8 ];
for ( int i = 0; i < buffer.length; ++i ) {
byte current = 0;
for ( int j = 7; j >= 0; --j )
if ( string[ i * 8 + j ] == '1' )
current |= 1 << j;
output( current );
}
You'll need to make some adjustments, but that's the general idea.

If you're lucky, java.math.BigInteger may do everything for you.
String s = "11001010001010101110101001001110";
byte[] bytes = (new java.math.BigInteger(s, 2)).toByteArray();
This does depend on the byte order (big-endian) and right-aligning (if the number of bits is not a multiple of 8) being what you want but it may be simpler to modify the array afterwards than to do the character conversion yourself.

public class BitOutputStream extends FilterOutputStream
{
private int buffer = 0;
private int bitCount = 0;
public BitOutputStream(OutputStream out)
{
super(out);
}
public void writeBits(int value, int numBits) throws IOException
{
while(numBits>0)
{
numBits--;
int mix = ((value&1)<<bitCount++);
buffer|=mix;
value>>=1;
if(bitCount==8)
align8();
}
}
#Override
public void close() throws IOException
{
align8(); /* Flush any remaining partial bytes */
super.close();
}
public void align8() throws IOException
{
if(bitCount > 0)
{
bitCount=0;
write(buffer);
buffer=0;
}
}
}
And then...
if (nextChar == '0')
{
bos.writeBits(0, 1);
}
else
{
bos.writeBits(1, 1);
}

Assuming the String has a multiple of eight bits, (you can pad it otherwise), take advantage of Java's built in parsing in the Integer.valueOf method to do something like this:
String s = "11001010001010101110101001001110";
byte[] data = new byte[s.length() / 8];
for (int i = 0; i < data.length; i++) {
data[i] = (byte) Integer.parseInt(s.substring(i * 8, (i + 1) * 8), 2);
}
Then you should be able to write the bytes to a FileOutputStream pretty simply.
On the other hand, if you looking for effeciency, you should consider not using a String to store the bits to begin with, but build up the bytes directly in your compressor.