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How to update part of the encrypted data with newly encrypted data?

I need to encrypt an audio file while it is being generated. I am encrypting header with dummy data(because I don't know the actual size of audio data) at the starting and encrypting the audio data on the fly. My plan is to update the header at the end with actual data size of audio file.
But, When I tried to overwrite the encrypted header data with newly encrypted header data of same size by using same key and IV and try to decrypt later, I am getting junk data generated.
Why is this happening even though I am using same key and IV? In the below code I tried to simulate what I am doing. Encrypted file of size 64 bytes generated and decrypted file of size 50 bytes generated.
Without updation: abcdabcdab0123456789012345678901234567890123456789
With header updation: ABCDABCDAB÷‹þ#óMCKL­ZƒÖ^Ô234567890123456789
Expected output: ABCDABCDAB0123456789012345678901234567890123456789
Is this the right approach to achieve partial update of already encrypted data?
protected void Encrypt()
{
byte[] numBytes = {'0','1','2','3','4','5','6','7','8','9','0','1','2','3','4','5','6','7','8','9', '0','1','2','3','4','5','6','7','8','9', '0','1','2','3','4','5','6','7','8','9'};
byte[] smallCase = {'a','b','c','d','a','b','c','d','a','b','c','d','a','b','c','d'};
byte[] capitalCase = {'A','B','C','D','A','B','C','D','A','B','C','D','A','B','C','D'};
try {
SecretKeyFactory factory = SecretKeyFactory.getInstance("PBKDF2withHmacSHA1And8BIT");
KeySpec spec = new PBEKeySpec("junglebook".toCharArray(), "Salt".getBytes(), 65536, 256);
SecretKey tmp = null;
tmp = factory.generateSecret(spec);
SecretKey secret = new SecretKeySpec(tmp.getEncoded(), "AES");
/* Encryption cipher initialization. */
Cipher cipher = Cipher.getInstance("AES/CBC/PKCS5Padding");
cipher.init(Cipher.ENCRYPT_MODE, secret);
AlgorithmParameters params = cipher.getParameters();
byte[] iv = params.getParameterSpec(IvParameterSpec.class).getIV();
Log.d("Encryption" + "iv data :", iv.toString());
/*Open two Cipher ouput streams to the same encrypted file*/
FileOutputStream os = new FileOutputStream(sdCard.getAbsolutePath() + "/Notes/sample.encrypted");
CipherOutputStream cos = new CipherOutputStream(os,cipher);
FileOutputStream os1 = new FileOutputStream(sdCard.getAbsolutePath() + "/Notes/sample.encrypted");
CipherOutputStream cos1 = new CipherOutputStream(os1,cipher);
int offset = 0;
Log.d("Encryption", "Writing cipher text to output file");
//Write 16 bytes header data with smallCase array
cos.write(smallCase, offset, 16);
// write 40 bytes actual data
cos.write(numBytes, offset, 40);
FileOutputStream ivStream = new FileOutputStream(sdCard.getAbsolutePath() + "/Notes/iv.dat");
if (ivStream != null) {
Log.d("Encryption", "Writing iv data to output file");
ivStream.write(iv);
}
cos.close();
// Overwrite header data with capitalCase array data
cos1.write(capitalCase, offset, 16);
cos1.close();
ivStream.close();
}catch (Exception e) {
e.printStackTrace();
}
}
protected void Decrypt()
{
byte[] dBytes = new byte[200];
try {
Log.d("Decryption", "Reading iv data ");
File f1 = new File(sdCard.getAbsolutePath()+"/Notes/iv.dat");
byte[] newivtext = new byte[(int)f1.length()];
FileInputStream readivStream = new FileInputStream(sdCard.getAbsolutePath()+"/Notes/iv.dat");
if(readivStream != null) {
readivStream.read(newivtext);
}
// Generate the secret key from same password and salt used in encryption
SecretKeyFactory dfactory = SecretKeyFactory.getInstance("PBKDF2withHmacSHA1And8BIT");
KeySpec dspec = new PBEKeySpec("junglebook".toCharArray(), "Salt".getBytes(), 65536, 256);
SecretKey dtmp = dfactory.generateSecret(dspec);
SecretKey dsecret = new SecretKeySpec(dtmp.getEncoded(), "AES");
// Initialize dcipher
Cipher dcipher = Cipher.getInstance("AES/CBC/PKCS5Padding");
dcipher.init(Cipher.DECRYPT_MODE, dsecret, new IvParameterSpec(newivtext));
FileInputStream inputStream = new FileInputStream(sdCard.getAbsolutePath()+"/Notes/sample.encrypted");
CipherInputStream cis = new CipherInputStream(inputStream,dcipher);
FileOutputStream os = new FileOutputStream(sdCard.getAbsolutePath() + "/Notes/sample.decrypted");
int b = cis.read(dBytes);
while(b != -1) {
Log.d("Decryption","Bytes decrypted" + b);
os.write(dBytes, 0, b);
b = cis.read(dBytes);
}
cis.close();
os.close();
} catch (Exception e) {
e.printStackTrace();
}
}

I suggest you update several things:
you are opening multiple outputstreams to the SAME file, which is very strange, the runtime should not allow you to do that. So - write only with a single output if you want any predictable results.
You may read about the mode of operations see the CRT mode uses no padding and allows you to update only a portion of the ciphertext (assuming you use no authenticated encryption). So AES/CTR/NoPadding could solve your problem. (and there should be no extra bytes if you do it correctly)
you can update a portion of the file using the RandomAccessFile and overwrite portion of the ciphertext what is needed.

Java: write and read password based encrypted private key

I am trying to read a password based encrypted private key from a file, but I'm getting the following exception:
java.io.IOException: DerInputStream.getLength(): lengthTag=109, too big.
at sun.security.util.DerInputStream.getLength(DerInputStream.java:561)
at sun.security.util.DerValue.init(DerValue.java:365)
at sun.security.util.DerValue.<init>(DerValue.java:294)
at javax.crypto.EncryptedPrivateKeyInfo.<init>(EncryptedPrivateKeyInfo.java:84) ...
This is how I encrypt and write to file the private key:
public static void savePrivateKeyToDisk(PrivateKey privateKey, String passord){
try {
// unencrypted PKCS#8 private key
byte[] encodedPrivateKey = privateKey.getEncoded();
String MYPBEALG = "PBEWithSHA1AndDESede";
int count = 20;
SecureRandom random = new SecureRandom();
byte[] salt = new byte[8];
random.nextBytes(salt);
// Create PBE parameter set
PBEParameterSpec pbeParamSpec = new PBEParameterSpec(salt, count);
PBEKeySpec pbeKeySpec = new PBEKeySpec(password.toCharArray());
SecretKeyFactory keyFac = SecretKeyFactory.getInstance(MYPBEALG);
SecretKey pbeKey = keyFac.generateSecret(pbeKeySpec);
Cipher pbeCipher = Cipher.getInstance(MYPBEALG);
// Initialize PBE Cipher with key and parameters
pbeCipher.init(Cipher.ENCRYPT_MODE, pbeKey, pbeParamSpec);
// Encrypt the encoded Private Key with the PBE key
byte[] cipherText = pbeCipher.doFinal(encodedPrivateKey);
// Now construct PKCS #8 EncryptedPrivateKeyInfo object
AlgorithmParameters algparms = AlgorithmParameters.getInstance(MYPBEALG);
algparms.init(pbeParamSpec);
EncryptedPrivateKeyInfo encinfo = new EncryptedPrivateKeyInfo(algparms, cipherText);
// DER encoded PKCS#8 encrypted key
byte[] encryptedPkcs8 = encinfo.getEncoded();
File encryptedPrivate = new File(PRIVATE_KEY_FILE);
if (encryptedPrivate.getParentFile() != null) {
encryptedPrivate.getParentFile().mkdirs();
}
encryptedPrivate.createNewFile();
ObjectOutputStream publicKeyOS = new ObjectOutputStream(
new FileOutputStream(encryptedPrivate));
publicKeyOS.writeObject(encryptedPkcs8);
publicKeyOS.close();
}
catch (Exception e){
e.printStackTrace();
}
}
... and this is how I'm trying to read the encrypted private key:
public static PrivateKey getPrivateKey(String passwd){
try {
byte[] encodedPrivateKey = getFileBytes(PRIVATE_KEY_FILE);
// exception thrown from here
EncryptedPrivateKeyInfo encryptPKInfo = new EncryptedPrivateKeyInfo(encodedPrivateKey);
Cipher cipher = Cipher.getInstance(encryptPKInfo.getAlgName());
PBEKeySpec pbeKeySpec = new PBEKeySpec(passwd.toCharArray());
SecretKeyFactory secFac = SecretKeyFactory.getInstance(encryptPKInfo.getAlgName());
Key pbeKey = secFac.generateSecret(pbeKeySpec);
AlgorithmParameters algParams = encryptPKInfo.getAlgParameters();
cipher.init(Cipher.DECRYPT_MODE, pbeKey, algParams);
KeySpec pkcs8KeySpec = encryptPKInfo.getKeySpec(cipher);
KeyFactory kf = KeyFactory.getInstance(ALGORITHM);
return kf.generatePrivate(pkcs8KeySpec);
}
catch (Exception e){
e.printStackTrace();
return null;
}
}
... the getFileBytes method:
private static byte[] getFileBytes(String infile){
File f = new File(infile) ;
int sizecontent = ((int) f.length());
byte[] data = new byte[sizecontent];
try
{
FileInputStream freader = new FileInputStream(f);
freader.read(data, 0, sizecontent) ;
freader.close();
return data;
}
catch(IOException ioe)
{
System.out.println(ioe.toString());
return null;
}
}
It seems like the encrypted private key is not in the right format, but I save it in DER PKCS#8 format.
So, the question: What is the mistake in this code?

I guess the problem is that you write an Object, but then you read byte[] (not an Object)
I would suggest that you either read the whole object and then get the required bytes or even better write byte[] directly (don't use ObjectOutputStream) and then load these bytes, eg:
FileOutputStream fos = new FileOutputStream(PRIVATE_KEY_FILE);
fos.write(myByteArray);
fos.close();
and then to retrieve it:
byte[] bytes = Files.readAllBytes(Paths.get(PRIVATE_KEY_FILE));

Encrypted Data with DES - JAVA

Given the following example:
String f="A000000000000000";
FileInputStream fis = new FileInputStream("C:\\Users\\original.txt");
byte[] bytes = DatatypeConverter.parseHexBinary(f);
SecretKey key = new SecretKeySpec(bytes, 0, bytes.length, "DES");
String strDataToEncrypt = new String();
String strCipherText = new String();
String strDecryptedText = new String();
try{
Cipher desCipher = Cipher.getInstance("DES/CBC/PKCS5Padding");
desCipher.init(Cipher.ENCRYPT_MODE,key);
//read from file and transform to String
try{
builder = new StringBuilder();
int ch;
while((ch = fis.read()) != -1){
builder.append((char)ch);
}
}catch (IOException e){
}
byte[] byteDataToEncrypt = builder.toString().getBytes();
byte[] byteCipherText = desCipher.doFinal(byteDataToEncrypt);
strCipherText = new BASE64Encoder().encode(byteCipherText);
System.out.println(strCipherText);
the encrypted data is different everytime I compile with the same key value i , i tried different codes and the encrypted data was always the same , what's wrong here ?

The documentation for javax.crypto.Cipher.init says, in part:
If this cipher requires any algorithm parameters that cannot be
derived from the given key, the underlying cipher implementation is
supposed to generate the required parameters itself (using
provider-specific default or random values)
DES CBC (Cipher Block Chaining) mode requires an Initialization Vector (IV). If you do not provide one (and you should not, because it opens you up to dictionary attacks), a random one will be generated.
But if you want the encrypted data to be the same every time, you need to specify the IV using an IvParameterSpec:
byte[] iv = DatatypeConverter.parseHexBinary("0000000000000000");
IvParameterSpec ips = new IvParameterSpec(iv);
desCipher.init(Cipher.ENCRYPT_MODE, key, ips);
If you do let it generate a random IV, you can retrieve the generated IV with desCipher.getIV().

Using password-based encryption on a file in Java

I'm trying to encrypt the contents of one file into another file using a passphrase in Java. The file is getting read to a byte array, encrypted to another byte array, and then written to the new file. Unfortunately, when I try to reverse the encryption, the output file gets decrypted as garbage.
I strongly suspect that the issue has to do with generating an identical key every time the same passphrase is used. I wrote a testing method that dumps the key into a file whenever one gets generated. The key is recorded both directly and in encoded form. The former is identical every time, but the latter is always different for some reason.
In all honesty, I don't know a great deal about encryption methods, especially in Java. I only need the data to be moderately secure, and the encryption doesn't have to withstand an attack from anyone with significant time and skills. Thanks in advance to anyone who has advice on this.
Edit: Esailija was kind enough to point out that I was always setting the cipher with ENCRYPT_MODE. I corrected the problem using a boolean argument, but now I'm getting the following exception:
javax.crypto.IllegalBlockSizeException: Input length must be multiple of 8 when decrypting with padded cipher
That sounds to me like the passphrase isn't being used properly. I was under the impression that "PBEWithMD5AndDES" would hash it into a 16 byte code, which most certainly is a multiple of 8. I'm wondering why the key generates and gets used just fine for encryption mode, but then it complains when trying to decrypt under the exact same conditions.
import java.various.stuff;
/**Utility class to encrypt and decrypt files**/
public class FileEncryptor {
//Arbitrarily selected 8-byte salt sequence:
private static final byte[] salt = {
(byte) 0x43, (byte) 0x76, (byte) 0x95, (byte) 0xc7,
(byte) 0x5b, (byte) 0xd7, (byte) 0x45, (byte) 0x17
};
private static Cipher makeCipher(String pass, Boolean decryptMode) throws GeneralSecurityException{
//Use a KeyFactory to derive the corresponding key from the passphrase:
PBEKeySpec keySpec = new PBEKeySpec(pass.toCharArray());
SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
SecretKey key = keyFactory.generateSecret(keySpec);
//Create parameters from the salt and an arbitrary number of iterations:
PBEParameterSpec pbeParamSpec = new PBEParameterSpec(salt, 42);
/*Dump the key to a file for testing: */
FileEncryptor.keyToFile(key);
//Set up the cipher:
Cipher cipher = Cipher.getInstance("PBEWithMD5AndDES");
//Set the cipher mode to decryption or encryption:
if(decryptMode){
cipher.init(Cipher.ENCRYPT_MODE, key, pbeParamSpec);
} else {
cipher.init(Cipher.DECRYPT_MODE, key, pbeParamSpec);
}
return cipher;
}
/**Encrypts one file to a second file using a key derived from a passphrase:**/
public static void encryptFile(String fileName, String pass)
throws IOException, GeneralSecurityException{
byte[] decData;
byte[] encData;
File inFile = new File(fileName);
//Generate the cipher using pass:
Cipher cipher = FileEncryptor.makeCipher(pass, false);
//Read in the file:
FileInputStream inStream = new FileInputStream(inFile);
decData = new byte[(int)inFile.length()];
inStream.read(decData);
inStream.close();
//Encrypt the file data:
encData = cipher.doFinal(decData);
//Write the encrypted data to a new file:
FileOutputStream outStream = new FileOutputStream(new File(fileName + ".encrypted"));
outStream.write(encData);
outStream.close();
}
/**Decrypts one file to a second file using a key derived from a passphrase:**/
public static void decryptFile(String fileName, String pass)
throws GeneralSecurityException, IOException{
byte[] encData;
byte[] decData;
File inFile = new File(fileName);
//Generate the cipher using pass:
Cipher cipher = FileEncryptor.makeCipher(pass, true);
//Read in the file:
FileInputStream inStream = new FileInputStream(inFile);
encData = new byte[(int)inFile.length()];
inStream.read(encData);
inStream.close();
//Decrypt the file data:
decData = cipher.doFinal(encData);
//Write the decrypted data to a new file:
FileOutputStream target = new FileOutputStream(new File(fileName + ".decrypted.txt"));
target.write(decData);
target.close();
}
/**Record the key to a text file for testing:**/
private static void keyToFile(SecretKey key){
try {
File keyFile = new File("C:\\keyfile.txt");
FileWriter keyStream = new FileWriter(keyFile);
String encodedKey = "\n" + "Encoded version of key: " + key.getEncoded().toString();
keyStream.write(key.toString());
keyStream.write(encodedKey);
keyStream.close();
} catch (IOException e) {
System.err.println("Failure writing key to file");
e.printStackTrace();
}
}
}

You are using the Cipher.ENCRYPT_MODE for both, decrypting and encrypting. You should use Cipher.DECRYPT_MODE for decrypting the file.
That has been fixed, but your boolean is wrong. It should be true for encrypt and false for decrypt. I would strongly recommend against using false/true as function arguments and always use enum like Cipher.ENCRYPT... moving on
Then you are encrypting to .encrypted file, but trying to decrypt the original plain text file.
Then you are not applying padding to encryption. I am surprised this actually has to be done manually,
but padding is explained here. The padding scheme PKCS5 appeared to be implicitly used here.
This is full working code, writing encrypted file to test.txt.encrypted, and decrypted file to test.txt.decrypted.txt.
Adding padding in encryption and removing it in decryption is explained in the comments.
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.security.GeneralSecurityException;
import java.util.Arrays;
import javax.crypto.Cipher;
import javax.crypto.SecretKey;
import javax.crypto.SecretKeyFactory;
import javax.crypto.spec.PBEKeySpec;
import javax.crypto.spec.PBEParameterSpec;
public class FileEncryptor {
public static void main( String[] args ) {
try {
encryptFile( "C:\\test.txt", "password" );
decryptFile( "C:\\test.txt", "password" );
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (GeneralSecurityException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
//Arbitrarily selected 8-byte salt sequence:
private static final byte[] salt = {
(byte) 0x43, (byte) 0x76, (byte) 0x95, (byte) 0xc7,
(byte) 0x5b, (byte) 0xd7, (byte) 0x45, (byte) 0x17
};
private static Cipher makeCipher(String pass, Boolean decryptMode) throws GeneralSecurityException{
//Use a KeyFactory to derive the corresponding key from the passphrase:
PBEKeySpec keySpec = new PBEKeySpec(pass.toCharArray());
SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
SecretKey key = keyFactory.generateSecret(keySpec);
//Create parameters from the salt and an arbitrary number of iterations:
PBEParameterSpec pbeParamSpec = new PBEParameterSpec(salt, 42);
/*Dump the key to a file for testing: */
FileEncryptor.keyToFile(key);
//Set up the cipher:
Cipher cipher = Cipher.getInstance("PBEWithMD5AndDES");
//Set the cipher mode to decryption or encryption:
if(decryptMode){
cipher.init(Cipher.ENCRYPT_MODE, key, pbeParamSpec);
} else {
cipher.init(Cipher.DECRYPT_MODE, key, pbeParamSpec);
}
return cipher;
}
/**Encrypts one file to a second file using a key derived from a passphrase:**/
public static void encryptFile(String fileName, String pass)
throws IOException, GeneralSecurityException{
byte[] decData;
byte[] encData;
File inFile = new File(fileName);
//Generate the cipher using pass:
Cipher cipher = FileEncryptor.makeCipher(pass, true);
//Read in the file:
FileInputStream inStream = new FileInputStream(inFile);
int blockSize = 8;
//Figure out how many bytes are padded
int paddedCount = blockSize - ((int)inFile.length() % blockSize );
//Figure out full size including padding
int padded = (int)inFile.length() + paddedCount;
decData = new byte[padded];
inStream.read(decData);
inStream.close();
//Write out padding bytes as per PKCS5 algorithm
for( int i = (int)inFile.length(); i < padded; ++i ) {
decData[i] = (byte)paddedCount;
}
//Encrypt the file data:
encData = cipher.doFinal(decData);
//Write the encrypted data to a new file:
FileOutputStream outStream = new FileOutputStream(new File(fileName + ".encrypted"));
outStream.write(encData);
outStream.close();
}
/**Decrypts one file to a second file using a key derived from a passphrase:**/
public static void decryptFile(String fileName, String pass)
throws GeneralSecurityException, IOException{
byte[] encData;
byte[] decData;
File inFile = new File(fileName+ ".encrypted");
//Generate the cipher using pass:
Cipher cipher = FileEncryptor.makeCipher(pass, false);
//Read in the file:
FileInputStream inStream = new FileInputStream(inFile );
encData = new byte[(int)inFile.length()];
inStream.read(encData);
inStream.close();
//Decrypt the file data:
decData = cipher.doFinal(encData);
//Figure out how much padding to remove
int padCount = (int)decData[decData.length - 1];
//Naive check, will fail if plaintext file actually contained
//this at the end
//For robust check, check that padCount bytes at the end have same value
if( padCount >= 1 && padCount <= 8 ) {
decData = Arrays.copyOfRange( decData , 0, decData.length - padCount);
}
//Write the decrypted data to a new file:
FileOutputStream target = new FileOutputStream(new File(fileName + ".decrypted.txt"));
target.write(decData);
target.close();
}
/**Record the key to a text file for testing:**/
private static void keyToFile(SecretKey key){
try {
File keyFile = new File("C:\\keyfile.txt");
FileWriter keyStream = new FileWriter(keyFile);
String encodedKey = "\n" + "Encoded version of key: " + key.getEncoded().toString();
keyStream.write(key.toString());
keyStream.write(encodedKey);
keyStream.close();
} catch (IOException e) {
System.err.println("Failure writing key to file");
e.printStackTrace();
}
}
}

These are some improvements to the #Esailija 's answer given some new features in Java.
By using the CipherInputStream and CipherOutputStream classes, the length and complexity of the code is greatly reduced.
I also use char[] instead of String for the password.
You can use System.console().readPassword("input password: ") to get the password as a char[] so that it is never a String.
public static void encryptFile(String inFileName, String outFileName, char[] pass) throws IOException, GeneralSecurityException {
Cipher cipher = PasswordProtectFile.makeCipher(pass, true);
try (CipherOutputStream cipherOutputStream = new CipherOutputStream(new FileOutputStream(outFileName), cipher);
BufferedInputStream bis = new BufferedInputStream(new FileInputStream(inFileName))) {
int i;
while ((i = bis.read()) != -1) {
cipherOutputStream.write(i);
}
}
}
public static void decryptFile(String inFileName, String outFileName, char[] pass) throws GeneralSecurityException, IOException {
Cipher cipher = PasswordProtectFile.makeCipher(pass, false);
try (CipherInputStream cipherInputStream = new CipherInputStream(new FileInputStream(inFileName), cipher);
BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(outFileName))) {
int i;
while ((i = cipherInputStream.read()) != -1) {
bos.write(i);
}
}
}
private static Cipher makeCipher(char[] pass, Boolean decryptMode) throws GeneralSecurityException {
// Use a KeyFactory to derive the corresponding key from the passphrase:
PBEKeySpec keySpec = new PBEKeySpec(pass);
SecretKeyFactory keyFactory = SecretKeyFactory.getInstance("PBEWithMD5AndDES");
SecretKey key = keyFactory.generateSecret(keySpec);
// Create parameters from the salt and an arbitrary number of iterations:
PBEParameterSpec pbeParamSpec = new PBEParameterSpec(salt, 43);
// Set up the cipher:
Cipher cipher = Cipher.getInstance("PBEWithMD5AndDES");
// Set the cipher mode to decryption or encryption:
if (decryptMode) {
cipher.init(Cipher.ENCRYPT_MODE, key, pbeParamSpec);
} else {
cipher.init(Cipher.DECRYPT_MODE, key, pbeParamSpec);
}
return cipher;
}

How to Encrypt or Decrypt a File in Java?

I want to encrypt and decrypt a file in java, i had read this url http://www-users.york.ac.uk/~mal503/lore/pkencryption.htm and i got two files namely public Security certificate and private security certificate file and private.pem file, i copied these files and pasted in the current directory and worte java code as follows, when i run this no encryption or decryption is performed, pls see this and tell me where i went wrong
Encrypt Code
File ecryptfile=new File("encrypt data");
File publickeydata=new File("/publickey");
File encryptmyfile=new File("/sys_data.db");
File copycontent =new File("Copy Data");
secure.makeKey();
secure.saveKey(ecryptfile, publickeydata);
secure.encrypt(encryptmyfile, copycontent);
Decrypt code
File ecryptfile=new File("encrypt data");
File privateKeyFile=new File("/privatekey");
File encryptmyfile=new File("/sys_data.db");
File unencryptedFile =new File("unencryptedFile");
try {
secure.loadKey(encryptmyfile, privateKeyFile);
secure.decrypt(encryptmyfile, unencryptedFile);
} catch (GeneralSecurityException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}

You simply have muddled your files. This code works using the DER files generated from openssl as described in the article you linked:
FileEncryption secure = new FileEncryption();
// Encrypt code
{
File encryptFile = new File("encrypt.data");
File publicKeyData = new File("public.der");
File originalFile = new File("sys_data.db");
File secureFile = new File("secure.data");
// create AES key
secure.makeKey();
// save AES key using public key
secure.saveKey(encryptFile, publicKeyData);
// save original file securely
secure.encrypt(originalFile, secureFile);
}
// Decrypt code
{
File encryptFile = new File("encrypt.data");
File privateKeyFile = new File("private.der");
File secureFile = new File("secure.data");
File unencryptedFile = new File("unencryptedFile");
// load AES key
secure.loadKey(encryptFile, privateKeyFile);
// decrypt file
secure.decrypt(secureFile, unencryptedFile);
}

Here is the Simplest Piece of Code for encrypting a document with any Key(Here Random Key)
randomKey = randomKey.substring(0, 16);
keyBytes = randomKey.getBytes();
key = new SecretKeySpec(keyBytes, "AES");
paramSpec = new IvParameterSpec(iv);
ecipher = Cipher.getInstance("AES/CBC/PKCS5Padding");
ecipher.init(Cipher.ENCRYPT_MODE, key, paramSpec);
in = new FileInputStream(srcFile);
out = new FileOutputStream(encryptedFile);
out = new CipherOutputStream(out, ecipher);
int numRead = 0;
while ((numRead = in.read(buf)) >= 0) {
out.write(buf, 0, numRead);
}
in.close();
out.flush();
out.close();