/// <summary>
/// Reimplements function from zlib (uncompress) that is not present in ZLIB.NET.
/// </summary>
/// <param name="dest">Destination array of bytes. May be trimmed if necessary.</param>
/// <param name="source">Source array of bytes.</param>
/// <returns>Zlib status code.</returns>
static int ZlibUncompress(ref byte[] dest, byte[] source)
{
ZStream stream = new ZStream();
int err;
stream.next_in = source;
stream.avail_in = source.Length;
stream.next_out = dest;
stream.avail_out = dest.Length;
err = stream.inflateInit();
if (err != zlibConst.Z_OK)
{
return(err);
}
err = stream.inflate(zlibConst.Z_FINISH);
if (err != zlibConst.Z_STREAM_END)
{
stream.inflateEnd();
return(err == zlibConst.Z_OK ? zlibConst.Z_BUF_ERROR : err);
}
if (stream.total_out != dest.Length)
{
byte[] output = new byte[stream.total_out];
Buffer.BlockCopy(stream.next_out, 0, output, 0, (int)stream.total_out);
dest = output;
}
return(stream.inflateEnd());
}
static void uncompress(ref byte[] dest, byte[] src)
{
ZStream stream = new ZStream();
stream.next_in = src;
stream.avail_in = src.Length;
stream.next_out = dest;
stream.avail_out = dest.Length;
stream.inflateInit();
int err = stream.inflate(zlibConst.Z_FINISH);
if (err != zlibConst.Z_STREAM_END)
{
stream.inflateEnd();
throw new ApplicationException();
}
Array.Resize <byte>(ref dest, (int)stream.total_out);
err = stream.inflateEnd();
if (err != zlibConst.Z_OK)
{
throw new ApplicationException();
}
}
/// <summary>
/// Uncompress a source byte array to a destination (old version)
/// </summary>
public static int UncompressOld(byte[] dest, ref ulong destLen, byte[] source, ref ulong sourceLen)
{
var stream = new ZStream
{
next_in = source,
avail_in = (int)sourceLen,
next_out = dest,
avail_out = (int)destLen,
};
destLen = 0;
sourceLen = 0;
// make second parameter negative to disable checksum verification
int err = stream.inflateInit(-Constants.MAX_WBITS);
if (err != zlibConst.Z_OK)
{
return(err);
}
while (stream.avail_in > 1)
{
err = stream.inflate(Constants.Z_BLOCK);
if (err != zlibConst.Z_OK)
{
stream.inflateEnd();
return(err);
}
}
destLen = (ulong)stream.total_out;
sourceLen = (ulong)stream.total_in;
return(stream.inflateEnd());
}
private void ZIPCleanup()
{
base.TIFFPredictorCleanup();
if ((m_state & ZSTATE_INIT_ENCODE) != 0)
{
m_stream.deflateEnd();
m_state = 0;
}
else if ((m_state & ZSTATE_INIT_DECODE) != 0)
{
m_stream.inflateEnd();
m_state = 0;
}
}
public static byte[] Uncompress(byte[] buff, int offset = 0)
{
//using (MemoryStream md = new MemoryStream())
//{
// Stream d = new ZOutputStream(md);
// d.Write(buff, offset, buff.Length - offset);
// d.Close();
// return md.ToArray();
//}
ZStream zs = new ZStream();
zs.next_in = buff;
zs.avail_in = buff.Length;
zs.next_out = _buffer;
zs.avail_out = _buffer.Length;
if (zlibConst.Z_OK != zs.inflateInit())
{
return(null);
}
if (zlibConst.Z_STREAM_END != zs.inflate(zlibConst.Z_FINISH))
{
return(null);
}
zs.inflateEnd();
byte[] result = new byte[zs.total_out];
System.Array.Copy(_buffer, result, zs.total_out);
return(result);
}
public void Decompress()
{
byte[] numArray = new byte[this.data.Count];
this.data.CopyTo(0, numArray, 0, this.data.Count);
byte[] numArray1 = new byte[800];
ZStream zStream = new ZStream()
{
avail_in = 0
};
zStream.inflateInit();
zStream.next_in = numArray;
zStream.next_in_index = 2;
zStream.avail_in = (int)numArray.Length - 4;
zStream.next_out = numArray1;
zStream.avail_out = 800;
if (zStream.inflate(4) != -3)
{
long totalOut = zStream.total_out;
zStream.inflateEnd();
zStream = null;
this.data.Clear();
this.data.Add(numArray[0]);
this.data.Add(numArray[1]);
for (int i = 0; (long)i < totalOut; i++)
{
this.data.Add(numArray1[i]);
}
this.data.Add(numArray[(int)numArray.Length - 3]);
this.data.Add(numArray[(int)numArray.Length - 2]);
this.data.Add(numArray[(int)numArray.Length - 1]);
}
}
public static byte[] Uncompress(byte[] compressed, int start, int size, int maxUncompressedSize)
{
ZStream stream = new ZStream();
stream.next_in = compressed;
stream.next_in_index = start;
stream.avail_in = compressed.Length;
byte[] uncompressed = new byte[maxUncompressedSize];
stream.next_out = uncompressed;
stream.next_out_index = 0;
stream.avail_out = maxUncompressedSize;
int err = stream.inflateInit();
if (err != zlibConst.Z_OK)
{
return(null);
}
err = stream.inflate(zlibConst.Z_FINISH);
if (err != zlibConst.Z_STREAM_END)
{
stream.inflateEnd();
return(null);
}
int realSize = (int)stream.total_out;
err = stream.inflateEnd();
if (err != zlibConst.Z_OK)
{
return(null);
}
if (realSize < maxUncompressedSize)
{
byte[] temp = new byte[realSize];
Array.Copy(uncompressed, temp, realSize);
return(temp);
}
else
{
return(uncompressed);
}
}
/// <summary>
/// Extract all files contained in the package in the folder pointed by the destination path.
/// </summary>
public void ExtractAll(String Destination)
{
Destination = Destination.Replace('/', '\\');
if (!Destination.EndsWith("\\"))
{
Destination += "\\";
}
using (FileStream Input = new FileStream(TpdFile.GetFilename(), FileMode.Open, FileAccess.Read, FileShare.Read))
{
Byte[] Buffer = new Byte[Kernel.MAX_BUFFER_SIZE];
Byte[] Tmp = new Byte[Kernel.MAX_BUFFER_SIZE];
foreach (Entry Entry in Entries.Values)
{
String DestPath = Destination + Entry.Path.Replace("/", "\\");
if (!Directory.Exists(Path.GetDirectoryName(DestPath)))
{
Directory.CreateDirectory(Path.GetDirectoryName(DestPath));
}
Input.Seek(Entry.Offset, SeekOrigin.Begin);
using (FileStream Output = new FileStream(DestPath, FileMode.Create, FileAccess.ReadWrite, FileShare.Read))
{
ZStream Stream = new ZStream();
Stream.inflateInit();
Int32 Result = 0;
Int32 Length = 0;
do
{
Stream.avail_in = Input.Read(Buffer, 0, Kernel.MAX_BUFFER_SIZE);
Stream.next_in = Buffer;
Stream.next_in_index = 0;
if (Stream.avail_in == 0)
{
break;
}
do
{
Stream.avail_out = Kernel.MAX_BUFFER_SIZE;
Stream.next_out = Tmp;
Stream.next_out_index = 0;
Result = Stream.inflate(zlibConst.Z_NO_FLUSH);
Length = Kernel.MAX_BUFFER_SIZE - Stream.avail_out;
Output.Write(Tmp, 0, Length);
}while (Stream.avail_out == 0);
}while (Result != zlibConst.Z_STREAM_END);
Stream.inflateEnd();
}
}
}
}
private static (byte[] bytes, int res) DecompressZ(byte[] inbuf, int index = 0)
{
var z = new ZStream();
var ms = new MemoryStream();
var outbuf = new byte[1024];
if (z.inflateInit() != zlibConst.Z_OK)
{
throw new InvalidOperationException("zlib.inflateInit Error");
}
z.next_in = inbuf;
z.avail_in = inbuf.Length;
z.next_in_index = index;
z.next_out = outbuf;
z.avail_out = outbuf.Length;
z.next_out_index = 0;
while (true)
{
int status = z.inflate(zlibConst.Z_NO_FLUSH); /* 展開 */
if (status == zlibConst.Z_STREAM_END)
{
break;
}
if (status != zlibConst.Z_OK)
{
throw new InvalidOperationException("zlib.inflate Error");
}
if (z.avail_out == 0)
{
ms.Write(outbuf, 0, outbuf.Length);
z.next_out = outbuf;
z.avail_out = outbuf.Length;
z.next_out_index = 0;
}
}
if ((outbuf.Length - z.avail_out) != 0)
{
ms.Write(outbuf, 0, outbuf.Length - z.avail_out);
}
if (z.inflateEnd() != zlibConst.Z_OK)
{
throw new InvalidOperationException("zlib.inflateEnd Error");
}
int count = z.next_in_index - index;
z.free();
return(ms.ToArray(), count);
}
public static PhpString gzdecode(byte[] data, int length = 0)
{
if (length < 0)
{
PhpException.Throw(PhpError.Warning, "length ({0}) must be greater or equal zero", length.ToString());
return(default(PhpString));
}
if (data.Length == 0)
{
return(default(PhpString));
}
if (data.Length < 10 || data[0] != GZIP_HEADER[0] || data[1] != GZIP_HEADER[1])
{
PhpException.Throw(PhpError.Warning, "incorrect gzip header");
return(default(PhpString));
}
var zs = new ZStream();
zs.next_in = data;
zs.next_in_index = GZIP_HEADER_LENGTH;
zs.avail_in = data.Length - GZIP_HEADER_LENGTH;
zs.total_out = 0;
// negative number omits the zlib header (undocumented feature of zlib)
int status = zs.inflateInit(-MAX_WBITS);
if (status == zlibConst.Z_OK)
{
status = zlib_inflate_rounds(zs, length, out byte[] output);
if (status == zlibConst.Z_STREAM_END)
{
zs.inflateEnd();
return(new PhpString(output));
}
}
PhpException.Throw(PhpError.Warning, zError(status) ?? zs.msg);
zs.inflateEnd();
return(default(PhpString));
}
public virtual void end()
{
if (compress)
{
z.deflateEnd();
}
else
{
z.inflateEnd();
}
z.free();
z = null;
}
/// <summary>
/// Closes any open connections between the Tibia client and game server, and stops listening for any
/// new incoming HTTP or TCP connection requests.
/// </summary>
internal void Stop()
{
if (!_isStarted)
{
return;
}
try
{
_zStream.deflateEnd();
_zStream.inflateEnd();
_httpListener.Close();
if (_tcpListener != null)
{
_tcpListener.Stop();
}
if (_clientSocket != null)
{
_clientSocket.Close();
}
if (_serverSocket != null)
{
_serverSocket.Close();
}
}
catch (Exception ex)
{
_client.Logger.Error(ex.ToString());
}
_isStarted = false;
_xteaKey = null;
ConnectionState = ConnectionState.Disconnected;
}
/// <summary>
/// Reimplements function from zlib (uncompress) that is not present in ZLIB.NET.
/// </summary>
/// <param name="dest">Destination array of bytes. May be trimmed if necessary.</param>
/// <param name="source">Source array of bytes.</param>
/// <param name="msg">Eventual message from zstream.</param>
/// <returns>Zlib status code.</returns>
static int ZlibUncompress(ref byte[] dest, byte[] source, out string msg)
{
var zs = new ZStream();
int err;
zs.next_in = source;
zs.avail_in = source.Length;
zs.next_out = dest;
zs.avail_out = dest.Length;
err = zs.inflateInit();
if (err != zlibConst.Z_OK)
{
msg = zs.msg;
return(err);
}
err = zs.inflate(zlibConst.Z_FINISH);
if (err != zlibConst.Z_STREAM_END)
{
zs.inflateEnd();
msg = zs.msg;
return(err == zlibConst.Z_OK ? zlibConst.Z_BUF_ERROR : err);
}
if (zs.total_out != dest.Length)
{
byte[] output = new byte[zs.total_out];
Buffer.BlockCopy(zs.next_out, 0, output, 0, (int)zs.total_out);
dest = output;
}
msg = zs.msg;
return(zs.inflateEnd());
}
/// <summary>
///
/// </summary>
/// <param name="Block"></param>
/// <returns></returns>
public byte[] ReadBlockDecompressed(uint Block)
{
if (Block >= NumberOfBlocks)
{
return(new byte[0]);
}
var In = ReadBlockCompressed(Block);
// If block is not compressed, get the contents.
if (!Blocks[Block].IsCompressed)
{
return(In);
}
var Out = new byte[this.Header.BlockSize];
In = In.Concat(new byte[] { 0x00 });
var ZStream = new ZStream();
if (ZStream.inflateInit(-15) != zlibConst.Z_OK)
{
throw (new InvalidProgramException("Can't initialize inflater"));
}
try
{
ZStream.next_in = In;
ZStream.next_in_index = 0;
ZStream.avail_in = In.Length;
ZStream.next_out = Out;
ZStream.next_out_index = 0;
ZStream.avail_out = Out.Length;
int Status = ZStream.inflate(zlibConst.Z_FULL_FLUSH);
if (Status != zlibConst.Z_STREAM_END)
{
throw (new InvalidDataException("" + ZStream.msg));
}
}
finally
{
ZStream.inflateEnd();
}
return(Out);
}
internal void Decompress(int type)
{
if (this is NetworkClient)
{
throw new Exception("Trying to decompress data on Client connection!");
}
zStream_Length = 0;
zStream.avail_in = inMaxIndex - inIndex;
zStream.next_in = inData;
zStream.next_in_index = inIndex;
zStream.next_out = zStream_Out;
zStream.next_out_index = 0;
zStream.avail_out = zStream_Out.Length;
switch (zStream.inflate(type))
{
case zlibConst.Z_OK:
inIndex = zStream.next_in_index;
zStream_Length = (int)zStream.total_out;
zStream.total_out = 0;
break;
case zlibConst.Z_STREAM_END:
inIndex = zStream.next_in_index;
zStream_Length = (int)zStream.total_out;
zStream.inflateEnd();
zStream.free();
zStream = null;
break;
default:
//case zlibConst.Z_STREAM_ERROR:
throw new Exception("Error while decompressing: " + (zStream.msg ?? "unknown error") + "!");
}
}
public static PhpString gzinflate(byte[] data, long length = 0)
{
uint factor = 1, maxfactor = 16;
long ilength;
var zs = new ZStream();
zs.avail_in = data.Length;
zs.next_in = data;
zs.total_out = 0;
// -15 omits the header (undocumented feature of zlib)
int status = zs.inflateInit(-15);
if (status != zlibConst.Z_OK)
{
PhpException.Throw(PhpError.Warning, zError(status));
return(default(PhpString));
}
do
{
ilength = length != 0 ? length : data.Length * (1 << (int)(factor++));
try
{
byte[] newOutput = new byte[ilength];
if (zs.next_out != null)
{
Buffer.BlockCopy(zs.next_out, 0, newOutput, 0, zs.next_out.Length);
}
zs.next_out = newOutput;
}
catch (OutOfMemoryException)
{
zs.inflateEnd();
return(default(PhpString));
}
zs.next_out_index = (int)zs.total_out;
zs.avail_out = unchecked ((int)(ilength - zs.total_out));
status = zs.inflate(zlibConst.Z_NO_FLUSH);
}while ((status == zlibConst.Z_BUF_ERROR || (status == zlibConst.Z_OK && (zs.avail_in != 0 || zs.avail_out == 0))) && length == 0 && factor < maxfactor);
zs.inflateEnd();
if ((length != 0 && status == zlibConst.Z_OK) || factor >= maxfactor)
{
status = zlibConst.Z_MEM_ERROR;
}
if (status == zlibConst.Z_STREAM_END || status == zlibConst.Z_OK)
{
byte[] result = new byte[zs.total_out];
Buffer.BlockCopy(zs.next_out, 0, result, 0, (int)zs.total_out);
return(new PhpString(result));
}
else
{
PhpException.Throw(PhpError.Warning, zError(status) ?? zs.msg);
return(default(PhpString));
}
}
public static void main(String[] arg)
{
int err;
int comprLen = 40000;
int uncomprLen = comprLen;
byte[] uncompr = new byte[uncomprLen];
byte[] compr = new byte[comprLen];
long dictId;
ZStream c_stream = new ZStream();
err = c_stream.deflateInit(JZlib.Z_BEST_COMPRESSION);
CHECK_ERR(c_stream, err, "deflateInit");
err = c_stream.deflateSetDictionary(dictionary, dictionary.Length);
CHECK_ERR(c_stream, err, "deflateSetDictionary");
dictId = c_stream.adler;
c_stream.next_out = compr;
c_stream.next_out_index = 0;
c_stream.avail_out = comprLen;
c_stream.next_in = hello;
c_stream.next_in_index = 0;
c_stream.avail_in = hello.Length;
err = c_stream.deflate(JZlib.Z_FINISH);
if (err != JZlib.Z_STREAM_END)
{
java.lang.SystemJ.outJ.println("deflate should report Z_STREAM_END");
java.lang.SystemJ.exit(1);
}
err = c_stream.deflateEnd();
CHECK_ERR(c_stream, err, "deflateEnd");
ZStream d_stream = new ZStream();
d_stream.next_in = compr;
d_stream.next_in_index = 0;
d_stream.avail_in = comprLen;
err = d_stream.inflateInit();
CHECK_ERR(d_stream, err, "inflateInit");
d_stream.next_out = uncompr;
d_stream.next_out_index = 0;
d_stream.avail_out = uncomprLen;
while (true)
{
err = d_stream.inflate(JZlib.Z_NO_FLUSH);
if (err == JZlib.Z_STREAM_END)
{
break;
}
if (err == JZlib.Z_NEED_DICT)
{
if ((int)d_stream.adler != (int)dictId)
{
java.lang.SystemJ.outJ.println("unexpected dictionary");
java.lang.SystemJ.exit(1);
}
err = d_stream.inflateSetDictionary(dictionary, dictionary.Length);
}
CHECK_ERR(d_stream, err, "inflate with dict");
}
err = d_stream.inflateEnd();
CHECK_ERR(d_stream, err, "inflateEnd");
int j = 0;
for (; j < uncompr.Length; j++)
{
if (uncompr[j] == 0)
{
break;
}
}
java.lang.SystemJ.outJ.println("after inflateSync(): hel" + new java.lang.StringJ(uncompr, 0, j));
}
/// <summary>
/// Get the data of the entry linked by the specified path.
/// All the data will be allocated in memory. It may fail.
///
/// Return false if the entry does not exist.
/// </summary>
public Boolean GetEntryData(String Path, out Byte[] Data)
{
Data = null;
if (Path.StartsWith("/") || Path.StartsWith("\\"))
{
return(false);
}
Entry Entry;
lock (Entries)
{
if (!Entries.TryGetValue(Path.ToLowerInvariant().Replace('\\', '/'), out Entry))
{
return(false);
}
}
Data = new Byte[(Int32)Entry.UncompressedSize];
using (var Input = new FileStream(TpdFile.GetFilename(), FileMode.Open, FileAccess.Read, FileShare.Read))
{
var Buffer = new Byte[Kernel.MAX_BUFFER_SIZE];
var Tmp = new Byte[Kernel.MAX_BUFFER_SIZE];
var Pos = 0;
Input.Seek(Entry.Offset, SeekOrigin.Begin);
{
var Stream = new ZStream();
Stream.inflateInit();
var Result = 0;
var Length = 0;
do
{
Stream.avail_in = Input.Read(Buffer, 0, Kernel.MAX_BUFFER_SIZE);
Stream.next_in = Buffer;
Stream.next_in_index = 0;
if (Stream.avail_in == 0)
{
break;
}
do
{
Stream.avail_out = Kernel.MAX_BUFFER_SIZE;
Stream.next_out = Tmp;
Stream.next_out_index = 0;
Result = Stream.inflate(zlibConst.Z_NO_FLUSH);
Length = Kernel.MAX_BUFFER_SIZE - Stream.avail_out;
Array.Copy(Buffer, 0, Data, Pos, Length);
Pos += Length;
}while (Stream.avail_out == 0);
}while (Result != zlibConst.Z_STREAM_END);
Stream.inflateEnd();
}
}
return(true);
}
protected override int EndZlibOperation(ZStream zs)
{
return(zs.inflateEnd());
}
internal static byte[] Decompress(byte[] input, int wbits = MAX_WBITS, int bufsize = DEFAULTALLOC)
{
byte[] outputBuffer = new byte[bufsize];
byte[] output = new byte[bufsize];
int outputOffset = 0;
ZStream zst = new ZStream();
zst.next_in = input;
zst.avail_in = input.Length;
zst.next_out = outputBuffer;
zst.avail_out = outputBuffer.Length;
int err = zst.inflateInit(wbits);
if (err != Z_OK)
{
zst.inflateEnd();
throw zlib_error(zst, err, "while preparing to decompress data");
}
do
{
err = zst.inflate(FlushStrategy.Z_FINISH);
if (err != Z_STREAM_END)
{
if (err == Z_BUF_ERROR && zst.avail_out > 0)
{
zst.inflateEnd();
throw zlib_error(zst, err, "while decompressing data");
}
else if (err == Z_OK || (err == Z_BUF_ERROR && zst.avail_out == 0))
{
// copy to the output and reset the buffer
if (outputOffset + outputBuffer.Length > output.Length)
{
Array.Resize(ref output, output.Length * 2);
}
Array.Copy(outputBuffer, 0, output, outputOffset, outputBuffer.Length);
outputOffset += outputBuffer.Length;
zst.next_out = outputBuffer;
zst.avail_out = outputBuffer.Length;
zst.next_out_index = 0;
}
else
{
zst.inflateEnd();
throw zlib_error(zst, err, "while decompressing data");
}
}
} while(err != Z_STREAM_END);
err = zst.inflateEnd();
if (err != Z_OK)
{
throw zlib_error(zst, err, "while finishing data decompression");
}
if (outputOffset + outputBuffer.Length - zst.avail_out > output.Length)
{
Array.Resize(ref output, output.Length * 2);
}
Array.Copy(outputBuffer, 0, output, outputOffset, outputBuffer.Length - zst.avail_out);
outputOffset += outputBuffer.Length - zst.avail_out;
return(output.Take(outputOffset).ToArray());
}
/// <summary>
/// Get the data of the entry linked by the specified path.
/// All the data will be allocated in memory. It may fail.
///
/// Return false if the entry does not exist.
/// </summary>
public Boolean GetEntryData(String Path, Byte **pData, Int32 *pLength)
{
*pData = null;
if (Path.StartsWith("/") || Path.StartsWith("\\"))
{
return(false);
}
Entry Entry;
lock (Entries)
{
if (!Entries.TryGetValue(Path.ToLowerInvariant().Replace('\\', '/'), out Entry))
{
return(false);
}
}
*pData = (Byte *)Kernel.malloc((Int32)Entry.UncompressedSize);
*pLength = (Int32)Entry.UncompressedSize;
using (FileStream Input = new FileStream(TpdFile.GetFilename(), FileMode.Open, FileAccess.Read, FileShare.Read))
{
Byte[] Buffer = new Byte[Kernel.MAX_BUFFER_SIZE];
Byte[] Tmp = new Byte[Kernel.MAX_BUFFER_SIZE];
Int32 Pos = 0;
Input.Seek(Entry.Offset, SeekOrigin.Begin);
{
ZStream Stream = new ZStream();
Stream.inflateInit();
Int32 Result = 0;
Int32 Length = 0;
do
{
Stream.avail_in = Input.Read(Buffer, 0, Kernel.MAX_BUFFER_SIZE);
Stream.next_in = Buffer;
Stream.next_in_index = 0;
if (Stream.avail_in == 0)
{
break;
}
do
{
Stream.avail_out = Kernel.MAX_BUFFER_SIZE;
Stream.next_out = Tmp;
Stream.next_out_index = 0;
Result = Stream.inflate(zlibConst.Z_NO_FLUSH);
Length = Kernel.MAX_BUFFER_SIZE - Stream.avail_out;
Kernel.memcpy((*pData) + Pos, Tmp, Length);
Pos += Length;
}while (Stream.avail_out == 0);
}while (Result != zlibConst.Z_STREAM_END);
Stream.inflateEnd();
}
}
return(true);
}
/// <summary>
/// Returns the spectrum-data (m/z and intensity) of the given scan number. The boundries
/// for the scan number can be retrieved with <see cref="GetFirstSpectrumNumber"/> and
/// <see cref="GetLastSpectrumNumber"/>. This method will throw an exception when the given
/// scan number is outside these boundries. The spectrum data is returned as a 2-dimensional
/// list of size (2, nrspectra) in emulation of the thermo RAW access DLL.
/// </summary>
/// <param name="scannumber">The scan number.</param>
/// <returns>The scan-data.</returns>
public double[,] GetMassListFromScanNum(int scannumber)
{
if (scannumber < minScanNumber || scannumber > maxScanNumber)
{
throw new Exception("Undefined scan number: " + scannumber + " outside (" + minScanNumber + "," + maxScanNumber +
")");
}
int compressedLength = 0;
string compressionType = null;
int precision = -1;
string byteOrder = null;
string contentType = null;
string data = null;
string peakData = GetScanPeakData(scannumber);
XmlTextReader xmlReader = new XmlTextReader(new StringReader(peakData));
while (xmlReader.Read())
{
xmlReader.MoveToElement();
if (!xmlReader.IsStartElement("peaks"))
{
continue;
}
precision = Parser.Int(xmlReader.GetAttribute("precision"));
byteOrder = xmlReader.GetAttribute("byteOrder");
contentType = xmlReader.GetAttribute("contentType");
if (string.IsNullOrEmpty(contentType))
{
contentType = xmlReader.GetAttribute("pairOrder");
}
compressionType = xmlReader.GetAttribute("compressionType");
string sCompressedLen = xmlReader.GetAttribute("compressedLen");
compressedLength = string.IsNullOrEmpty(sCompressedLen) ? -1 : Parser.Int(sCompressedLen);
data = xmlReader.ReadElementContentAsString();
}
if (byteOrder == null || contentType == null || data == null)
{
throw new Exception("Malformed mz-xml File.");
}
if (!contentType.Equals("m/z-int") && !contentType.Equals("mz-int"))
{
throw new Exception("Non-supported content type: ' " + contentType + "'.");
}
// convert from base64 encoding
byte[] bytes = Convert.FromBase64String(data);
// decompress
if (compressionType != null && compressionType.Equals("zlib"))
{
if (compressedLength != bytes.Length)
{
throw new Exception("Attribute 'compressedLen' has a different value from the reconstructed data array.");
}
ZStream z = new ZStream();
const int bufferLen = 1024;
z.next_in = bytes;
z.next_in_index = 0;
z.avail_in = bytes.Length;
z.inflateInit();
int totalLength = 0;
List <byte[]> pieces = new List <byte[]>();
while (true)
{
z.next_out = new byte[bufferLen];
z.next_out_index = 0;
z.avail_out = bufferLen;
pieces.Add(z.next_out);
int err = z.inflate(zlibConst.Z_NO_FLUSH);
totalLength += bufferLen - z.avail_out;
if (err == zlibConst.Z_STREAM_END)
{
break;
}
if (err != zlibConst.Z_OK)
{
throw new ZStreamException(z.msg);
}
}
z.inflateEnd();
bytes = new byte[totalLength];
int pos = 0;
foreach (byte[] piece in pieces)
{
Buffer.BlockCopy(piece, 0, bytes, pos, totalLength - pos > 1024 ? bufferLen : totalLength - pos);
pos += piece.Length;
}
}
// convert from byte encoding
double[] massintensities = ByteArray.ToDoubleArray(bytes,
byteOrder.Equals("network") ? ByteArray.endianBig : ByteArray.endianLittle, precision);
double[,] masslist = new double[2, massintensities.Length / 2];
for (int i = 0; i < massintensities.Length; i += 2)
{
masslist[0, i / 2] = massintensities[i];
masslist[1, i / 2] = massintensities[i + 1];
}
return(masslist);
}
public static string decompress([BytesConversion] IList <byte> data,
[DefaultParameterValue(MAX_WBITS)] int wbits,
[DefaultParameterValue(DEFAULTALLOC)] int bufsize)
{
byte[] input = data.ToArray();
byte[] outputBuffer = new byte[bufsize];
byte[] output = new byte[bufsize];
int outputOffset = 0;
ZStream zst = new ZStream();
zst.next_in = input;
zst.avail_in = input.Length;
zst.next_out = outputBuffer;
zst.avail_out = outputBuffer.Length;
int err = zst.inflateInit(wbits);
if (err != Z_OK)
{
zst.inflateEnd();
throw zlib_error(zst, err, "while preparing to decompress data");
}
do
{
err = zst.inflate(FlushStrategy.Z_FINISH);
if (err != Z_STREAM_END)
{
if (err == Z_BUF_ERROR && zst.avail_out > 0)
{
zst.inflateEnd();
throw zlib_error(zst, err, "while decompressing data");
}
else if (err == Z_OK || (err == Z_BUF_ERROR && zst.avail_out == 0))
{
// copy to the output and reset the buffer
if (outputOffset + outputBuffer.Length > output.Length)
{
Array.Resize(ref output, output.Length * 2);
}
Array.Copy(outputBuffer, 0, output, outputOffset, outputBuffer.Length);
outputOffset += outputBuffer.Length;
zst.next_out = outputBuffer;
zst.avail_out = outputBuffer.Length;
zst.next_out_index = 0;
}
else
{
zst.inflateEnd();
throw zlib_error(zst, err, "while decompressing data");
}
}
} while(err != Z_STREAM_END);
err = zst.inflateEnd();
if (err != Z_OK)
{
throw zlib_error(zst, err, "while finishing data decompression");
}
if (outputOffset + outputBuffer.Length - zst.avail_out > output.Length)
{
Array.Resize(ref output, output.Length * 2);
}
Array.Copy(outputBuffer, 0, output, outputOffset, outputBuffer.Length - zst.avail_out);
outputOffset += outputBuffer.Length - zst.avail_out;
return(PythonAsciiEncoding.Instance.GetString(output, 0, outputOffset));
}
public static BufLen BCGZipDecompressNew(BufLen buf)
{
var reader = new BufRefLen(buf);
// Skip gzip header
var gzheader = reader.ReadBufLen(10);
var flag = gzheader.Peek8(3);
if ((flag & 0x04) != 0)
{
reader.Seek(reader.Read16()); // "Extra"
}
if ((flag & 0x08) != 0)
{
while (reader.Read8() != 0)
{
; // "Name"
}
}
if ((flag & 0x10) != 0)
{
while (reader.Read8() != 0)
{
; // "Comment"
}
}
if ((flag & 0x02) != 0)
{
reader.Read16(); // "CRC16"
}
var z = new ZStream();
z.inflateInit(true);
var dest = new byte[buf.Length * 2];
var destix = 0;
z.next_in_index = reader.BaseArrayOffset;
z.next_in = reader.BaseArray;
z.avail_in = reader.Length - 8;
bigger_dest:
z.next_out = dest;
z.next_out_index = destix;
z.avail_out = dest.Length - destix;
var err = z.inflate(JZlib.Z_FINISH);
if (err != JZlib.Z_BUF_ERROR && err != JZlib.Z_OK && err != JZlib.Z_STREAM_END)
{
throw new IOException("inflating: " + z.msg);
}
if (z.avail_out == 0)
{
var newdest = new byte[dest.Length * 2];
Array.Copy(dest, newdest, dest.Length);
destix = dest.Length;
dest = newdest;
goto bigger_dest;
}
var result = new BufLen(dest, 0, dest.Length - z.avail_out);
z.inflateEnd();
return(result);
}
public static void main(String[] arg)
{
int err;
int comprLen = 40000;
int uncomprLen = comprLen;
byte[] compr = new byte[comprLen];
byte[] uncompr = new byte[uncomprLen];
int len = hello.Length;
ZStream c_stream = new ZStream();
err = c_stream.deflateInit(JZlib.Z_DEFAULT_COMPRESSION);
CHECK_ERR(c_stream, err, "deflate");
c_stream.next_in = hello;
c_stream.next_in_index = 0;
c_stream.next_out = compr;
c_stream.next_out_index = 0;
c_stream.avail_in = 3;
c_stream.avail_out = comprLen;
err = c_stream.deflate(JZlib.Z_FULL_FLUSH);
CHECK_ERR(c_stream, err, "deflate");
compr[3]++; // force an error in first compressed block
c_stream.avail_in = len - 3;
err = c_stream.deflate(JZlib.Z_FINISH);
if (err != JZlib.Z_STREAM_END)
{
CHECK_ERR(c_stream, err, "deflate");
}
err = c_stream.deflateEnd();
CHECK_ERR(c_stream, err, "deflateEnd");
comprLen = (int)(c_stream.total_out);
ZStream d_stream = new ZStream();
d_stream.next_in = compr;
d_stream.next_in_index = 0;
d_stream.avail_in = 2;
err = d_stream.inflateInit();
CHECK_ERR(d_stream, err, "inflateInit");
d_stream.next_out = uncompr;
d_stream.next_out_index = 0;
d_stream.avail_out = uncomprLen;
err = d_stream.inflate(JZlib.Z_NO_FLUSH);
CHECK_ERR(d_stream, err, "inflate");
d_stream.avail_in = comprLen - 2;
err = d_stream.inflateSync();
CHECK_ERR(d_stream, err, "inflateSync");
err = d_stream.inflate(JZlib.Z_FINISH);
if (err != JZlib.Z_DATA_ERROR)
{
java.lang.SystemJ.outJ.println("inflate should report DATA_ERROR");
/* Because of incorrect adler32 */
java.lang.SystemJ.exit(1);
}
err = d_stream.inflateEnd();
CHECK_ERR(d_stream, err, "inflateEnd");
int j = 0;
for (; j < uncompr.Length; j++)
{
if (uncompr[j] == 0)
{
break;
}
}
java.lang.SystemJ.outJ.println("after inflateSync(): hel" + new java.lang.StringJ(uncompr, 0, j));
}
/// <summary>
/// Reads NBT data from the specified (compressed) stream.
/// </summary>
public static NBTNamedTag <INBTData> ReadChunk(Stream fs, Point <int> Pos)
{
// Read the chunk from the file.
byte[] buf = new byte[5];
long seekOffset = 0;
int sectorNumber = 0;
int offset = 0;
// Read the chunk offset.
Point <int> chunkOffsetInRegion;
chunkOffsetInRegion.X = Pos.X % 32;
if (chunkOffsetInRegion.X < 0)
{
chunkOffsetInRegion.X += 32;
}
chunkOffsetInRegion.Y = Pos.Y % 32;
if (chunkOffsetInRegion.Y < 0)
{
chunkOffsetInRegion.Y += 32;
}
seekOffset = 4 * (chunkOffsetInRegion.X + chunkOffsetInRegion.Y * 32);
fs.Position = seekOffset;
fs.Read(buf, 0, 4);
sectorNumber = (int)buf[3];
offset = (int)buf[0] << 16 | (int)buf[1] << 8 | (int)buf[2];
if (offset == 0)
{
throw new ArithmeticException();
}
// Get the chunk length and version.
int chunkLength = 0;
fs.Position = offset * 4096;
fs.Read(buf, 0, 5);
chunkLength = (int)buf[0] << 24 | (int)buf[1] << 14 | (int)buf[2] << 8 | (int)buf[3];
if (chunkLength > sectorNumber * 4096 || chunkLength > CHUNK_DEFLATE_MAX)
{
throw new ArithmeticException();
}
if (buf[4] != 2)
{
throw new ArithmeticException();
}
// Read compressed chunk data.
byte[] inChunk = new byte[CHUNK_DEFLATE_MAX];
byte[] outChunk = new byte[CHUNK_INFLATE_MAX];
fs.Read(inChunk, 0, chunkLength - 1);
fs.Close();
// Decompress it.
ZStream z = new ZStream();
z.next_out = outChunk;
z.avail_out = CHUNK_INFLATE_MAX;
z.next_in = inChunk;
z.avail_in = chunkLength - 1;
z.inflateInit();
z.inflate(zlibConst.Z_NO_FLUSH);
z.inflateEnd();
System.IO.MemoryStream msUncompressed = new System.IO.MemoryStream(outChunk);
return(NBT.ReadUncompressed(msUncompressed));
}
public static void main(String[] arg)
{
int err;
int comprLen = 40000;
int uncomprLen = comprLen;
byte[] compr = new byte[comprLen];
byte[] uncompr = new byte[uncomprLen];
ZStream c_stream = new ZStream();
err = c_stream.deflateInit(JZlib.Z_BEST_SPEED);
CHECK_ERR(c_stream, err, "deflateInit");
c_stream.next_out = compr;
c_stream.next_out_index = 0;
c_stream.avail_out = comprLen;
// At this point, uncompr is still mostly zeroes, so it should compress
// very well:
c_stream.next_in = uncompr;
c_stream.avail_in = uncomprLen;
err = c_stream.deflate(JZlib.Z_NO_FLUSH);
CHECK_ERR(c_stream, err, "deflate");
if (c_stream.avail_in != 0)
{
java.lang.SystemJ.outJ.println("deflate not greedy");
java.lang.SystemJ.exit(1);
}
// Feed in already compressed data and switch to no compression:
c_stream.deflateParams(JZlib.Z_NO_COMPRESSION, JZlib.Z_DEFAULT_STRATEGY);
c_stream.next_in = compr;
c_stream.next_in_index = 0;
c_stream.avail_in = comprLen / 2;
err = c_stream.deflate(JZlib.Z_NO_FLUSH);
CHECK_ERR(c_stream, err, "deflate");
// Switch back to compressing mode:
c_stream.deflateParams(JZlib.Z_BEST_COMPRESSION, JZlib.Z_FILTERED);
c_stream.next_in = uncompr;
c_stream.next_in_index = 0;
c_stream.avail_in = uncomprLen;
err = c_stream.deflate(JZlib.Z_NO_FLUSH);
CHECK_ERR(c_stream, err, "deflate");
err = c_stream.deflate(JZlib.Z_FINISH);
if (err != JZlib.Z_STREAM_END)
{
java.lang.SystemJ.outJ.println("deflate should report Z_STREAM_END");
java.lang.SystemJ.exit(1);
}
err = c_stream.deflateEnd();
CHECK_ERR(c_stream, err, "deflateEnd");
ZStream d_stream = new ZStream();
d_stream.next_in = compr;
d_stream.next_in_index = 0;
d_stream.avail_in = comprLen;
err = d_stream.inflateInit();
CHECK_ERR(d_stream, err, "inflateInit");
while (true)
{
d_stream.next_out = uncompr;
d_stream.next_out_index = 0;
d_stream.avail_out = uncomprLen;
err = d_stream.inflate(JZlib.Z_NO_FLUSH);
if (err == JZlib.Z_STREAM_END)
{
break;
}
CHECK_ERR(d_stream, err, "inflate large");
}
err = d_stream.inflateEnd();
CHECK_ERR(d_stream, err, "inflateEnd");
if (d_stream.total_out != 2 * uncomprLen + comprLen / 2)
{
java.lang.SystemJ.outJ.println("bad large inflate: " + d_stream.total_out);
java.lang.SystemJ.exit(1);
}
else
{
java.lang.SystemJ.outJ.println("large_inflate(): OK");
}
}
public static void main(String[] arg)
{
int err;
int comprLen = 40000;
int uncomprLen = comprLen;
byte[] compr = new byte[comprLen];
byte[] uncompr = new byte[uncomprLen];
ZStream c_stream = new ZStream();
err = c_stream.deflateInit(JZlib.Z_DEFAULT_COMPRESSION);
CHECK_ERR(c_stream, err, "deflateInit");
c_stream.next_in = hello;
c_stream.next_in_index = 0;
c_stream.next_out = compr;
c_stream.next_out_index = 0;
while (c_stream.total_in != hello.Length &&
c_stream.total_out < comprLen)
{
c_stream.avail_in = c_stream.avail_out = 1; // force small buffers
err = c_stream.deflate(JZlib.Z_NO_FLUSH);
CHECK_ERR(c_stream, err, "deflate");
}
while (true)
{
c_stream.avail_out = 1;
err = c_stream.deflate(JZlib.Z_FINISH);
if (err == JZlib.Z_STREAM_END)
{
break;
}
CHECK_ERR(c_stream, err, "deflate");
}
err = c_stream.deflateEnd();
CHECK_ERR(c_stream, err, "deflateEnd");
ZStream d_stream = new ZStream();
d_stream.next_in = compr;
d_stream.next_in_index = 0;
d_stream.next_out = uncompr;
d_stream.next_out_index = 0;
err = d_stream.inflateInit();
CHECK_ERR(d_stream, err, "inflateInit");
while (d_stream.total_out < uncomprLen &&
d_stream.total_in < comprLen)
{
d_stream.avail_in = d_stream.avail_out = 1; /* force small buffers */
err = d_stream.inflate(JZlib.Z_NO_FLUSH);
if (err == JZlib.Z_STREAM_END)
{
break;
}
CHECK_ERR(d_stream, err, "inflate");
}
err = d_stream.inflateEnd();
CHECK_ERR(d_stream, err, "inflateEnd");
int i = 0;
for (; i < hello.Length; i++)
{
if (hello[i] == 0)
{
break;
}
}
int j = 0;
for (; j < uncompr.Length; j++)
{
if (uncompr[j] == 0)
{
break;
}
}
if (i == j)
{
for (i = 0; i < j; i++)
{
if (hello[i] != uncompr[i])
{
break;
}
}
if (i == j)
{
java.lang.SystemJ.outJ.println("inflate(): " + new java.lang.StringJ(uncompr, 0, j).ToString());
return;
}
}
else
{
java.lang.SystemJ.outJ.println("bad inflate");
}
}
