private void endBuffer(ZipEntry ze) {
if (ze == null) {
return;
}
if (store != null) {
store.close(); // 終了処理は別スレッドで実行中
String digest = store.getDigest();
logPersister.addDigest(addDigests, digest);
store = null;
} else if (charsetDecoder != null) {
charBuffer.flip();
charBuffer.array();
String accessLogJson =
new String(charBuffer.array(), charBuffer.position(), charBuffer.limit());
charsetDecoder = null;
charBuffer = null;
AccessLog accessLog = AccessLog.fromJson(accessLogJson);
if (accessLog == null) {
return;
}
logPersister.addDigest(refDigests, accessLog.getRequestHeaderDigest());
logPersister.addDigest(refDigests, accessLog.getRequestBodyDigest());
logPersister.addDigest(refDigests, accessLog.getResponseHeaderDigest());
logPersister.addDigest(refDigests, accessLog.getResponseBodyDigest());
accessLog.setId(null);
accessLog.setPersist(true);
PersistenceManager pm = JdoUtil.getPersistenceManager();
logPersister.executeInsert(pm, accessLog);
if (pm.currentTransaction().isActive()) {
pm.currentTransaction().rollback();
}
}
}
@Override
public final boolean incrementToken() throws IOException {
if (isMailto) {
termAtt.setEmpty();
// return the scheme + the mail part
isMailto = false;
posIncrAtt.setPositionIncrement(0);
termAtt.copyBuffer(termBuffer.array(), 0, termBuffer.position());
return true;
}
if (input.incrementToken()) {
final String type = typeAtt.type();
if (type.equals(TupleTokenizer.getTokenTypes()[TupleTokenizer.URI])
&& this.isMailtoScheme()) {
this.updateBuffer();
termBuffer.put(termAtt.buffer(), 0, termAtt.length());
// return only the mail part
posIncrAtt.setPositionIncrement(1);
termAtt.copyBuffer(termBuffer.array(), 7, termBuffer.position() - 7);
}
return true;
}
return false;
}
private CoderResult decodeArrayLoop(ByteBuffer src, CharBuffer dst) {
byte[] sa = src.array();
int sp = src.arrayOffset() + src.position();
int sl = src.arrayOffset() + src.limit();
assert (sp <= sl);
sp = (sp <= sl ? sp : sl);
char[] da = dst.array();
int dp = dst.arrayOffset() + dst.position();
int dl = dst.arrayOffset() + dst.limit();
assert (dp <= dl);
dp = (dp <= dl ? dp : dl);
try {
while (sp < sl) {
byte b = sa[sp];
if (b >= 0) {
if (dp >= dl) return CoderResult.OVERFLOW;
da[dp++] = (char) b;
sp++;
continue;
}
return CoderResult.malformedForLength(1);
}
return CoderResult.UNDERFLOW;
} finally {
src.position(sp - src.arrayOffset());
dst.position(dp - dst.arrayOffset());
}
}
private static String decode(Charset charset, byte[] b) {
if (b == null) {
return null;
}
final CharBuffer cb = charset.decode(ByteBuffer.wrap(b));
return new String(cb.array(), 0, cb.length());
}
private CoderResult encodeArrayLoop(CharBuffer src, ByteBuffer dst) {
char[] sa = src.array();
int sp = src.arrayOffset() + src.position();
int sl = src.arrayOffset() + src.limit();
assert (sp <= sl);
sp = (sp <= sl ? sp : sl);
byte[] da = dst.array();
int dp = dst.arrayOffset() + dst.position();
int dl = dst.arrayOffset() + dst.limit();
assert (dp <= dl);
dp = (dp <= dl ? dp : dl);
try {
while (sp < sl) {
char c = sa[sp];
if (c < 0x80) {
if (dp >= dl) return CoderResult.OVERFLOW;
da[dp] = (byte) c;
sp++;
dp++;
continue;
}
if (sgp.parse(c, sa, sp, sl) < 0) return sgp.error();
return sgp.unmappableResult();
}
return CoderResult.UNDERFLOW;
} finally {
src.position(sp - src.arrayOffset());
dst.position(dp - dst.arrayOffset());
}
}
@Override
public boolean incrementToken() throws IOException {
if (!terms.isEmpty()) {
char[] buffer = terms.poll();
termAttribute.setEmpty();
termAttribute.copyBuffer(buffer, 0, buffer.length);
posIncAttr.setPositionIncrement(1);
return true;
}
if (!input.incrementToken()) {
return false;
} else {
final char term[] = termAttribute.buffer();
final int length = termAttribute.length();
int k = 0;
for (; k < length; k++) {
if (term[k] == tokenDelimiter) {
break;
}
}
LinkedList<CharBuffer> buffers = permuteTerms(term, 0, length);
Iterator iter = buffers.iterator();
while (iter.hasNext()) {
CharBuffer cb = (CharBuffer) iter.next();
terms.add(cb.array());
}
// we return true and leave the original token unchanged
return true;
}
}
private CoderResult decodeArrayLoop(ByteBuffer src, CharBuffer dst) {
byte[] sa = src.array();
int sp = src.arrayOffset() + src.position();
int sl = src.arrayOffset() + src.limit();
char[] da = dst.array();
int dp = dst.arrayOffset() + dst.position();
int dl = dst.arrayOffset() + dst.limit();
CoderResult cr = CoderResult.UNDERFLOW;
if ((dl - dp) < (sl - sp)) {
sl = sp + (dl - dp);
cr = CoderResult.OVERFLOW;
}
while (sp < sl) {
char c = decode(sa[sp]);
if (c == UNMAPPABLE_DECODING) {
return withResult(CoderResult.unmappableForLength(1), src, sp, dst, dp);
}
da[dp++] = c;
sp++;
}
return withResult(cr, src, sp, dst, dp);
}
private CoderResult encodeArrayLoop(CharBuffer src, ByteBuffer dst) {
char[] sa = src.array();
int sp = src.arrayOffset() + src.position();
int sl = src.arrayOffset() + src.limit();
byte[] da = dst.array();
int dp = dst.arrayOffset() + dst.position();
int dl = dst.arrayOffset() + dst.limit();
int len = Math.min(dl - dp, sl - sp);
while (len-- > 0) {
char c = sa[sp];
int b = encode(c);
if (b == UNMAPPABLE_ENCODING) {
if (Character.isSurrogate(c)) {
if (sgp == null) sgp = new Surrogate.Parser();
if (sgp.parse(c, sa, sp, sl) < 0) {
return withResult(sgp.error(), src, sp, dst, dp);
}
return withResult(sgp.unmappableResult(), src, sp, dst, dp);
}
return withResult(CoderResult.unmappableForLength(1), src, sp, dst, dp);
}
da[dp++] = (byte) b;
sp++;
}
return withResult(sp < sl ? CoderResult.OVERFLOW : CoderResult.UNDERFLOW, src, sp, dst, dp);
}
public static byte[] toBytes(char[] chars) {
CharBuffer charBuffer = CharBuffer.wrap(chars);
ByteBuffer byteBuffer = Charset.forName("UTF-8").encode(charBuffer);
byte[] bytes =
Arrays.copyOfRange(byteBuffer.array(), byteBuffer.position(), byteBuffer.limit());
Arrays.fill(charBuffer.array(), '\u0000'); // clear sensitive data
Arrays.fill(byteBuffer.array(), (byte) 0); // clear sensitive data
return bytes;
}
/**
* Wraps the result of {@linkplain #getCharContent} in a Reader. Subclasses can change this
* behavior as long as the contract of {@link FileObject} is obeyed.
*
* @param ignoreEncodingErrors {@inheritDoc}
* @return a Reader wrapping the result of getCharContent
* @throws IllegalStateException {@inheritDoc}
* @throws UnsupportedOperationException {@inheritDoc}
* @throws IOException {@inheritDoc}
*/
public Reader openReader(boolean ignoreEncodingErrors) throws IOException {
CharSequence charContent = getCharContent(ignoreEncodingErrors);
if (charContent == null) throw new UnsupportedOperationException();
if (charContent instanceof CharBuffer) {
CharBuffer buffer = (CharBuffer) charContent;
if (buffer.hasArray()) return new CharArrayReader(buffer.array());
}
return new StringReader(charContent.toString());
}
// 将字节转为字符(解码)
public static char[] getChars(byte[] bytes) {
Charset cs = Charset.forName("UTF-8");
ByteBuffer bb = ByteBuffer.allocate(bytes.length);
bb.put(bytes);
bb.flip();
CharBuffer cb = cs.decode(bb);
return cb.array();
}
private BigDecimal toBigDecimal() {
if (lineBuffer.hasArray()) {
char[] array = lineBuffer.array();
int offset = lineBuffer.arrayOffset() + lineBuffer.position();
int length = lineBuffer.remaining();
return new BigDecimal(array, offset, length);
} else {
return new BigDecimal(lineBuffer.toString());
}
}
public void run() {
byteBuffer = ByteBuffer.allocate(BUFFER_SIZE);
charBuffer = CharBuffer.allocate(BUFFER_SIZE);
/* for East Asian character widths */
byte[] wideAttribute = new byte[BUFFER_SIZE];
byteArray = byteBuffer.array();
charArray = charBuffer.array();
CoderResult result;
int bytesRead = 0;
byteBuffer.limit(0);
int bytesToRead;
int offset;
int charWidth;
EastAsianWidth measurer = EastAsianWidth.getInstance();
try {
while (true) {
charWidth = bridge.charWidth;
bytesToRead = byteBuffer.capacity() - byteBuffer.limit();
offset = byteBuffer.arrayOffset() + byteBuffer.limit();
bytesRead = transport.read(byteArray, offset, bytesToRead);
if (bytesRead > 0) {
byteBuffer.limit(byteBuffer.limit() + bytesRead);
synchronized (this) {
result = decoder.decode(byteBuffer, charBuffer, false);
}
if (result.isUnderflow() && byteBuffer.limit() == byteBuffer.capacity()) {
byteBuffer.compact();
byteBuffer.limit(byteBuffer.position());
byteBuffer.position(0);
}
offset = charBuffer.position();
measurer.measure(charArray, 0, offset, wideAttribute, bridge.defaultPaint, charWidth);
buffer.putString(charArray, wideAttribute, 0, charBuffer.position());
bridge.propagateConsoleText(charArray, charBuffer.position());
charBuffer.clear();
bridge.redraw();
}
}
} catch (IOException e) {
Log.e(TAG, "Problem while handling incoming data in relay thread", e);
}
}
public static String newStringFromSplit(
CharsetDecoder decoder,
CharsetDecoder utf8Decoder,
String encoding,
byte[] fieldBytes,
int length) {
ByteBuffer fieldBuf = ByteBuffer.wrap(fieldBytes, 0, length);
CharBuffer fieldCharBuf = CharBuffer.allocate(length);
utf8Decoder.reset();
CoderResult res = utf8Decoder.decode(fieldBuf, fieldCharBuf, true);
if (res.isError() && decoder != null) {
decoder.reset();
res = decoder.decode(fieldBuf, fieldCharBuf, true);
if (!res.isError()) {
decoder.flush(fieldCharBuf);
return new String(fieldCharBuf.array());
}
} else {
utf8Decoder.flush(fieldCharBuf);
return new String(fieldCharBuf.array());
}
return "";
}
private CoderResult encodeArrayLoop(CharBuffer src, ByteBuffer dst) {
char[] sa = src.array();
int sp = src.arrayOffset() + src.position();
int sl = src.arrayOffset() + src.limit();
byte[] da = dst.array();
int dp = dst.arrayOffset() + dst.position();
int dl = dst.arrayOffset() + dst.limit();
int dlASCII = dp + Math.min(sl - sp, dl - dp);
// ASCII only loop
while (dp < dlASCII && sa[sp] < '\u0080') da[dp++] = (byte) sa[sp++];
while (sp < sl) {
char c = sa[sp];
if (c < 0x80) {
// Have at most seven bits
if (dp >= dl) return overflow(src, sp, dst, dp);
da[dp++] = (byte) c;
} else if (c < 0x800) {
// 2 bytes, 11 bits
if (dl - dp < 2) return overflow(src, sp, dst, dp);
da[dp++] = (byte) (0xc0 | (c >> 6));
da[dp++] = (byte) (0x80 | (c & 0x3f));
} else if (isSurrogate(c)) {
// Have a surrogate pair
if (sgp == null) sgp = new Parser();
int uc = sgp.parse(c, sa, sp, sl);
if (uc < 0) {
updatePositions(src, sp, dst, dp);
return sgp.error();
}
if (dl - dp < 4) return overflow(src, sp, dst, dp);
da[dp++] = (byte) (0xf0 | ((uc >> 18)));
da[dp++] = (byte) (0x80 | ((uc >> 12) & 0x3f));
da[dp++] = (byte) (0x80 | ((uc >> 6) & 0x3f));
da[dp++] = (byte) (0x80 | (uc & 0x3f));
sp++; // 2 chars
} else {
// 3 bytes, 16 bits
if (dl - dp < 3) return overflow(src, sp, dst, dp);
da[dp++] = (byte) (0xe0 | ((c >> 12)));
da[dp++] = (byte) (0x80 | ((c >> 6) & 0x3f));
da[dp++] = (byte) (0x80 | (c & 0x3f));
}
sp++;
}
updatePositions(src, sp, dst, dp);
return CoderResult.UNDERFLOW;
}
private void fillBuffer() throws IOException {
if (!endOfInput && (lastCoderResult == null || lastCoderResult.isUnderflow())) {
encoderIn.compact();
int i = encoderIn.position();
int j = reader.read(encoderIn.array(), i, encoderIn.remaining());
if (j == -1) {
endOfInput = true;
} else {
encoderIn.position(i + j);
}
encoderIn.flip();
}
encoderOut.compact();
lastCoderResult = encoder.encode(encoderIn, encoderOut, endOfInput);
encoderOut.flip();
}
static Reader adjustReader2(Reader reader) {
try {
StringBuilder result = new StringBuilder(40);
int pretype = 0;
CharBuffer cb = CharBuffer.allocate(40);
while (reader.read(cb) != -1) {
for (char c : cb.array()) {
int currtype = Character.getType(c);
if (isSplit(pretype, currtype)) result.append(' ');
result.append(c);
pretype = currtype;
}
cb.flip();
}
return new StringReader(result.toString());
} catch (IOException ex) {
ex.printStackTrace();
return new StringReader("");
}
}
public String readAsString(Charset charset) throws CharacterCodingException {
int unreadSize = totalBytesUnread();
if (unreadSize > 0) {
CharsetDecoder decoder =
charset
.newDecoder()
.onMalformedInput(CodingErrorAction.REPLACE)
.onUnmappableCharacter(CodingErrorAction.REPLACE);
CharBuffer charbuffer = CharBuffer.allocate(unreadSize);
ByteBuffer buf = null;
while (prepareRead() != -1) {
buf = currentReadChunk.readToNioBuffer();
boolean endOfInput = (prepareRead() == -1);
CoderResult result = decoder.decode(buf, charbuffer, endOfInput);
if (endOfInput) {
if (!result.isUnderflow()) {
result.throwException();
}
}
}
CoderResult result = decoder.flush(charbuffer);
if (buf.hasRemaining()) {
throw new IllegalStateException("There's a bug here, buffer wasn't read fully.");
}
if (!result.isUnderflow()) result.throwException();
charbuffer.flip();
String str;
if (charbuffer.hasArray()) {
int len = charbuffer.remaining();
char[] ch = charbuffer.array();
if (len != ch.length) {
ch = ArrayUtils.subarray(ch, 0, len);
}
str = StringCharArrayAccessor.createString(ch);
} else {
str = charbuffer.toString();
}
return str;
}
return null;
}
/**
* Write the UTF-8 representation of a single Unicode code point to the terminal output. The
* written data will be consumed by the emulation client as input.
*
* <p>This implementation encodes the code point and then calls {@link #write(byte[], int, int)}
* to do the actual writing. It should therefore usually be unnecessary to override this method;
* override {@link #write(byte[], int, int)} instead.
*
* @param codePoint The Unicode code point to write to the terminal.
*/
public void write(int codePoint) {
ByteBuffer byteBuf = mWriteByteBuffer;
if (codePoint < 128) {
// Fast path for ASCII characters
byte[] buf = byteBuf.array();
buf[0] = (byte) codePoint;
write(buf, 0, 1);
return;
}
CharBuffer charBuf = mWriteCharBuffer;
CharsetEncoder encoder = mUTF8Encoder;
charBuf.clear();
byteBuf.clear();
Character.toChars(codePoint, charBuf.array(), 0);
encoder.reset();
encoder.encode(charBuf, byteBuf, true);
encoder.flush(byteBuf);
write(byteBuf.array(), 0, byteBuf.position() - 1);
}
/**
* Writes any remaining output to the output buffer and resets the converter to its initial state.
*
* @param output char array to receive flushed output.
* @param outStart start writing to output array at this offset.
* @param outEnd stop writing to output array at this offset (exclusive).
* @exception MalformedInputException if the output to be flushed contained a partial or invalid
* multibyte character sequence. flush will write what it can to the output buffer and reset
* the converter before throwing this exception. An additional call to flush is not required.
* @exception ConversionBufferFullException if output array is filled before all the output can be
* flushed. flush will write what it can to the output buffer and remember its state. An
* additional call to flush with a new output buffer will conclude the operation.
*/
public int flush(char[] output, int outStart, int outEnd)
throws MalformedInputException, ConversionBufferFullException {
byteOff = charOff = 0;
if (outStart >= outEnd || outStart >= output.length) throw new ConversionBufferFullException();
if (dst != null && dst.array() == output) dst.position(outStart).limit(outEnd);
else dst = CharBuffer.wrap(output, outStart, outEnd - outStart);
CoderResult cr = null;
try {
if (src != null) cr = decoder.decode((ByteBuffer) src.clear(), dst, true);
assert !cr.isUnmappable();
if (cr.isMalformed()) {
badInputLength = cr.length();
reset();
throw new MalformedInputException();
}
} catch (IllegalStateException ise) {
if (src != null) cr = decoder.reset().decode(src, dst, true);
}
try {
cr = decoder.flush(dst);
} catch (Exception e) {
assert false;
} finally {
byteOff = 0;
charOff = dst.position();
src = null;
}
if (cr.isOverflow()) throw new ConversionBufferFullException();
// Return the length written to the output buffer
if (cr.isUnderflow()) {
int written = charOff - outStart;
reset();
return written;
}
assert false;
return -1; // should be never reached
}
private void consumeDecoded() {
decodeBuffer.flip();
if (decodeBuffer.hasRemaining()) {
char[] array = decodeBuffer.array();
for (int i = decodeBuffer.position(), n = decodeBuffer.limit(); i < n; i++) {
char c = array[i];
if (c == '\t') {
lineBuffer.append(ESCAPE_CHAR);
lineBuffer.append(ESCAPE_HT);
} else if (c == '\n') {
lineBuffer.append(ESCAPE_CHAR);
lineBuffer.append(ESCAPE_LF);
} else if (c == '\\') {
lineBuffer.append(ESCAPE_CHAR);
lineBuffer.append(ESCAPE_CHAR);
} else {
lineBuffer.append(c);
}
}
}
decodeBuffer.clear();
}
/**
* Converts an array of bytes containing characters in an external encoding into an array of
* Unicode characters. This method allows a buffer by buffer conversion of a data stream. The
* state of the conversion is saved between calls to convert. Among other things, this means
* multibyte input sequences can be split between calls. If a call to convert results in an
* exception, the conversion may be continued by calling convert again with suitably modified
* parameters. All conversions should be finished with a call to the flush method.
*
* @return the number of bytes written to output.
* @param input byte array containing text to be converted.
* @param inStart begin conversion at this offset in input array.
* @param inEnd stop conversion at this offset in input array (exclusive).
* @param output character array to receive conversion result.
* @param outStart start writing to output array at this offset.
* @param outEnd stop writing to output array at this offset (exclusive).
* @exception MalformedInputException if the input buffer contains any sequence of bytes that is
* illegal for the input character set.
* @exception UnknownCharacterException for any character that that cannot be converted to
* Unicode. Thrown only when converter is not in substitution mode.
* @exception ConversionBufferFullException if output array is filled prior to converting all the
* input.
*/
public int convert(byte[] input, int inStart, int inEnd, char[] output, int outStart, int outEnd)
throws UnknownCharacterException, MalformedInputException, ConversionBufferFullException {
byteOff = inStart;
charOff = outStart;
// throw exceptions compatible to legacy ByteToCharXxx converters
if (inStart >= inEnd) return 0;
if (inStart >= input.length) throw new ArrayIndexOutOfBoundsException(inStart);
if (outStart >= outEnd || outStart >= output.length) throw new ConversionBufferFullException();
if (src != null && src.array() == input) src.position(inStart).limit(inEnd);
else src = ByteBuffer.wrap(input, inStart, inEnd - inStart);
if (dst != null && dst.array() == output) dst.position(outStart).limit(outEnd);
else dst = CharBuffer.wrap(output, outStart, outEnd - outStart);
CoderResult cr;
try {
cr = decoder.decode(src, dst, false);
} catch (IllegalStateException ise) {
cr = decoder.reset().decode(src, dst, false);
} finally {
byteOff = src.position();
charOff = dst.position();
}
if (cr.isUnmappable()) {
badInputLength = cr.length();
throw new UnknownCharacterException();
}
if (cr.isMalformed()) {
badInputLength = cr.length();
throw new MalformedInputException();
}
if (cr.isOverflow()) throw new ConversionBufferFullException();
// Return the length written to the output buffer
if (cr.isUnderflow()) return charOff - outStart;
return -1; // should be never reached
}
/**
* Creates a new big-endian buffer whose content is a subregion of the specified {@code string}
* encoded in the specified {@code charset}. The new buffer's {@code readerIndex} and {@code
* writerIndex} are {@code 0} and the length of the encoded string respectively.
*/
public static ByteBuf copiedBuffer(CharSequence string, int offset, int length, Charset charset) {
if (string == null) {
throw new NullPointerException("string");
}
if (length == 0) {
return EMPTY_BUFFER;
}
if (string instanceof CharBuffer) {
CharBuffer buf = (CharBuffer) string;
if (buf.hasArray()) {
return copiedBuffer(
buf.array(), buf.arrayOffset() + buf.position() + offset, length, charset);
}
buf = buf.slice();
buf.limit(length);
buf.position(offset);
return copiedBuffer(buf, charset);
}
return copiedBuffer(CharBuffer.wrap(string, offset, offset + length), charset);
}
public String ascii_to_latin1(String str) {
if (str != null) {
try {
InputStream is = new ByteArrayInputStream(str.getBytes());
String text = "";
// setup readers with Latin-1 (ISO 8859-1) encoding
BufferedReader i = new BufferedReader(new InputStreamReader(is, "8859_1"));
int numBytes;
CharBuffer buf = CharBuffer.allocate(512);
while ((numBytes = i.read(buf)) != -1) {
text += String.copyValueOf(buf.array(), 0, numBytes);
buf.clear();
}
return text;
} catch (Exception e) {
e.printStackTrace();
}
}
return "";
}
/**
* Convert the byte array to char array with respect to given charset.
*
* @param byteArray
* @param charset null or "" means default charset
* @exception CharacterCodingException
*/
public static char[] convertByteArrayToCharArray(byte[] byteArray, String charset)
throws CharacterCodingException {
if (byteArray == null) {
return null;
}
byte[] bArray = (byte[]) byteArray.clone();
ByteBuffer byteBuffer = ByteBuffer.wrap(bArray);
Charset charSet;
if (charset == null || "".equals(charset)) {
charSet = Charset.defaultCharset();
} else if (Charset.isSupported(charset)) {
charSet = Charset.forName(charset);
} else {
CharacterCodingException e = new CharacterCodingException();
e.initCause(new UnsupportedCharsetException(charset));
throw e;
}
CharsetDecoder decoder = charSet.newDecoder();
CharBuffer charBuffer = null;
try {
charBuffer = decoder.decode(byteBuffer);
} catch (CharacterCodingException cce) {
throw cce;
} catch (Throwable t) {
CharacterCodingException e = new CharacterCodingException();
e.initCause(t);
throw e;
}
char[] result = (char[]) charBuffer.array().clone();
clear(byteBuffer);
clear(charBuffer);
return result;
}
@Override
public void run() {
try {
InputStream in = client.getInputStream();
CharBuffer buffer = CharBuffer.allocate(5000);
char ch;
while (true) {
ch = (char) in.read();
if (((int) ch) == -1) {
break;
}
while (ch != EOL) {
buffer.put(ch);
ch = (char) in.read();
}
buffer.flip();
String s = new String(buffer.array(), 0, buffer.limit());
messageReceiver.sendMessage(s + "\n");
buffer.position(0);
buffer.limit(5000);
}
} catch (Exception e) {
e.printStackTrace();
if (LOGGER.isLoggable(Level.WARNING)) {
LOGGER.warning("Unable to process mesages from client" + client);
}
} finally {
if (client != null) {
try {
client.close();
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
/**
* Returns the password that is bound to the username and is stored for the specified <code>
* forUser</code> If the <code>forUser</code> is not specified the system user is used.
*
* @param forUser the user for whom the password is being retrieved
* @param username the matching username to go with the password
* @return the password as a character array or empty object if password could not be loaded
*/
public static Optional<char[]> getPassword(Optional<String> forUser, String username) {
if (username == null) {
return Optional.empty();
}
final String user = forUser.orElse(System.getProperty(SYSTEM_PROPERTY_USER_NAME));
try {
byte[] val =
SecurePreferences.getSecurePreferences()
.node(Activator.ID)
.node(user)
.node(username)
.getByteArray(PREF_PASSWORD, null);
if (val != null) {
CharBuffer buffer = StandardCharsets.UTF_8.newDecoder().decode(ByteBuffer.wrap(val));
return Optional.of(Arrays.copyOfRange(buffer.array(), buffer.position(), buffer.limit()));
}
} catch (StorageException | IOException e) {
SaveRestoreService.LOGGER.log(
Level.WARNING,
e,
() -> String.format("Could not read the password for '%s' from secured storage.", user));
}
return Optional.empty();
}
/* Read in DNA or Peptide FA record in mixed case. Allow any upper or lower case
* letter, or the dash character in.
*
* boolean faMixedSpeedReadNext(struct lineFile *lf, DNA **retDna, int *retSize, char **retName)
* */
public boolean faMixedSpeedReadNext(LineFile f, DnaSeq seq)
throws IOException, FaFormatException {
char c;
int bufIx = 0;
String name = null; // the name of teh fa sequence.
int lineSize, i;
String line;
// this could be necesary
// dnaUtilOpen();
/* Read first line, make sure it starts with '>', and read first word
* as name of sequence. */
if ((line = f.lineFileNext()) == null) { // f, &line, &lineSize
// *retDna = NULL;
// *retSize = 0;
return false;
}
if (line.charAt(0) == '>') {
name = line.substring(1).split(" ")[0]; // .substring(1).replaceAll(" ", "");
if (line.equals("")) {
System.err.println("Expecting sequence name after '>' " + f.getFile().getName());
throw new FaFormatException();
}
} else {
System.err.println("Expecting '>' line " + f.getFile().getName());
throw new FaFormatException();
}
/* Read until next '>' */
for (; ; ) {
if ((line = f.lineFileNext()) == null) // !lineFileNext(lf, &line, &lineSize)
break;
if (line.charAt(0) == '>') {
f.lineFileReuse(line);
break;
}
for (char m : line.toCharArray()) {
if (Character.isLetter(m) || m == '-') {
buff.put(m);
}
}
}
// if (bufIx >= faFastBufSize)
// expandFaFastBuf(bufIx, 0);
// faFastBuf[bufIx] = 0;
// *retDna = faFastBuf;
// *retSize = bufIx;
char[] dna = new char[buff.position()];
char[] c_buff = buff.array();
for (int k = 0; k < dna.length; k++) {
dna[k] = c_buff[k];
}
seq.setName(name);
seq.setDna(dna);
// if (bufIx == 0){
// System.err.println("Invalid fasta format: sequence size == 0 for element " + name);
// }
buff.clear();
return true;
}
private void flushOutput() throws IOException {
writer.write(out.array(), 0, out.position());
out.clear();
}
private CoderResult decodeArrayLoop(ByteBuffer src, CharBuffer dst) {
// This method is optimized for ASCII input.
byte[] sa = src.array();
int sp = src.arrayOffset() + src.position();
int sl = src.arrayOffset() + src.limit();
char[] da = dst.array();
int dp = dst.arrayOffset() + dst.position();
int dl = dst.arrayOffset() + dst.limit();
int dlASCII = dp + Math.min(sl - sp, dl - dp);
// ASCII only loop
while (dp < dlASCII && sa[sp] >= 0) da[dp++] = (char) sa[sp++];
while (sp < sl) {
int b1 = sa[sp];
if (b1 >= 0) {
// 1 byte, 7 bits: 0xxxxxxx
if (dp >= dl) return xflow(src, sp, sl, dst, dp, 1);
da[dp++] = (char) b1;
sp++;
} else if ((b1 >> 5) == -2 && (b1 & 0x1e) != 0) {
// 2 bytes, 11 bits: 110xxxxx 10xxxxxx
if (sl - sp < 2 || dp >= dl) return xflow(src, sp, sl, dst, dp, 2);
int b2 = sa[sp + 1];
if (isNotContinuation(b2)) return malformedForLength(src, sp, dst, dp, 1);
da[dp++] = (char) (((b1 << 6) ^ b2) ^ (((byte) 0xC0 << 6) ^ ((byte) 0x80)));
sp += 2;
} else if ((b1 >> 4) == -2) {
// 3 bytes, 16 bits: 1110xxxx 10xxxxxx 10xxxxxx
int srcRemaining = sl - sp;
if (srcRemaining < 3 || dp >= dl) {
if (srcRemaining > 1 && isMalformed3_2(b1, sa[sp + 1]))
return malformedForLength(src, sp, dst, dp, 1);
return xflow(src, sp, sl, dst, dp, 3);
}
int b2 = sa[sp + 1];
int b3 = sa[sp + 2];
if (isMalformed3(b1, b2, b3)) return malformed(src, sp, dst, dp, 3);
char c =
(char)
((b1 << 12)
^ (b2 << 6)
^ (b3 ^ (((byte) 0xE0 << 12) ^ ((byte) 0x80 << 6) ^ ((byte) 0x80))));
if (isSurrogate(c)) return malformedForLength(src, sp, dst, dp, 3);
da[dp++] = c;
sp += 3;
} else if ((b1 >> 3) == -2) {
// 4 bytes, 21 bits: 11110xxx 10xxxxxx 10xxxxxx 10xxxxxx
int srcRemaining = sl - sp;
if (srcRemaining < 4 || dl - dp < 2) {
if (srcRemaining > 1 && isMalformed4_2(b1, sa[sp + 1]))
return malformedForLength(src, sp, dst, dp, 1);
if (srcRemaining > 2 && isMalformed4_3(sa[sp + 2]))
return malformedForLength(src, sp, dst, dp, 2);
return xflow(src, sp, sl, dst, dp, 4);
}
int b2 = sa[sp + 1];
int b3 = sa[sp + 2];
int b4 = sa[sp + 3];
int uc =
((b1 << 18)
^ (b2 << 12)
^ (b3 << 6)
^ (b4
^ (((byte) 0xF0 << 18)
^ ((byte) 0x80 << 12)
^ ((byte) 0x80 << 6)
^ ((byte) 0x80))));
if (isMalformed4(b2, b3, b4)
||
// shortest form check
!Character.isSupplementaryCodePoint(uc)) {
return malformed(src, sp, dst, dp, 4);
}
da[dp++] = highSurrogate(uc);
da[dp++] = lowSurrogate(uc);
sp += 4;
} else return malformed(src, sp, dst, dp, 1);
}
return xflow(src, sp, sl, dst, dp, 0);
}