public override void Parse(ExtendedBinaryReader br)
{
base.Parse(br);
//Because the box size is not a reliable metric. So useful.
Payload = br.ReadToEnd();
}
public static SegmentRunEntry Parse(ExtendedBinaryReader br)
{
return new SegmentRunEntry
{
FirstSegment = br.ReadUInt32(),
FragmentsPerSegment = br.ReadUInt32()
};
}
public virtual void Parse(ExtendedBinaryReader br)
{
if (BoxHeader == null)
{
BoxHeader = new F4VBoxHeader();
BoxHeader.Parse(br);
}
}
public void Parse(ExtendedBinaryReader br)
{
TotalSize = br.ReadUInt32();
BoxType = br.ReadUInt32();
if (TotalSize == 1)
ExtendedSize = br.ReadUInt64();
else
ExtendedSize = null;
}
public static FragmentRunEntry Parse(ExtendedBinaryReader br)
{
var entry = new FragmentRunEntry();
entry.FirstFragment= br.ReadUInt32();
entry.FirstFragmentTimestamp = br.ReadUInt64();
entry.FragmentDuration = br.ReadUInt32();
if(entry.FragmentDuration == 0)
entry.DiscontinuityIndicator = br.ReadByte();
else
entry.DiscontinuityIndicator = null;
return entry;
}
public override void Parse(ExtendedBinaryReader br)
{
base.Parse(br);
if (BoxHeader.TotalSize == 0)
br.ReadToEnd();
else if (BoxHeader.TotalSize == 1)
{
br.ReadChunkedBytes(BoxHeader.ExtendedSize.Value - (ulong)BoxHeader.HeaderSize).Select(s => s);
}
else
{
foreach (var s in br.ReadChunkedBytes((ulong)BoxHeader.TotalSize - (ulong)BoxHeader.HeaderSize)) ;
}
}
protected virtual TF.Core.TranslationEntities.Subtitle ReadSubtitle(ExtendedBinaryReader input, long offset, bool returnToPos)
{
var pos = input.Position;
input.Seek(offset, SeekOrigin.Begin);
var text = input.ReadString();
var subtitle = new TF.Core.TranslationEntities.Subtitle
{
Offset = offset,
Text = text,
Translation = text,
Loaded = text,
};
if (returnToPos)
{
input.Seek(pos, SeekOrigin.Begin);
}
return(subtitle);
}
public void Serialization()
{
var expectedMetadata = new ReferenceMetadata("chr1", "1");
ReferenceMetadata observedMetadata;
using (var ms = new MemoryStream())
{
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
expectedMetadata.Write(writer);
}
ms.Position = 0;
using (var reader = new ExtendedBinaryReader(ms))
{
observedMetadata = ReferenceMetadata.Read(reader);
}
}
Assert.Equal(expectedMetadata.EnsemblName, observedMetadata.EnsemblName);
Assert.Equal(expectedMetadata.UcscName, observedMetadata.UcscName);
}
protected override IList <Subtitle> GetSubtitles()
{
var result = new List <Subtitle>();
using (var fs = new FileStream(Path, FileMode.Open))
using (var input = new ExtendedBinaryReader(fs, FileEncoding, Endianness.BigEndian))
{
input.Skip(4);
var tableEnd = input.ReadInt32();
input.Skip(4);
while (input.Position < tableEnd)
{
var subtitle = ReadSubtitle(input);
subtitle.PropertyChanged += SubtitlePropertyChanged;
result.Add(subtitle);
}
}
LoadChanges(result);
return(result);
}
public override void Rebuild(string outputFolder)
{
var outputPath = System.IO.Path.Combine(outputFolder, RelativePath);
Directory.CreateDirectory(System.IO.Path.GetDirectoryName(outputPath));
var subtitles = GetSubtitles();
using (var fsInput = new FileStream(Path, FileMode.Open))
using (var input = new ExtendedBinaryReader(fsInput, FileEncoding))
using (var fsOutput = new FileStream(outputPath, FileMode.Create))
using (var output = new ExtendedBinaryWriter(fsOutput, FileEncoding))
{
var tableEnd = input.PeekUInt16();
long outputOffset = tableEnd;
while (input.Position < tableEnd)
{
var inputSubtitle = ReadSubtitle(input);
outputOffset = WriteSubtitle(output, subtitles, inputSubtitle.Offset, outputOffset);
}
}
}
public NinjaNodeNameList ReadNinjaNodeNameList(ExtendedBinaryReader reader, long pos)
{
NinjaNodeNameList = new NinjaNodeNameList()
{
NodeName = new string(reader.ReadChars(4))
};
uint NodeLength = reader.ReadUInt32();
pos = reader.BaseStream.Position; //Save Position
uint NodeOffset = reader.ReadUInt32();
reader.JumpTo(NodeOffset, false);
uint Unknown1 = reader.ReadUInt32(); //Padding?
uint NodeTableCount = reader.ReadUInt32();
uint NodeTableOffset = reader.ReadUInt32();
reader.JumpTo(NodeTableOffset, false);
for (int i = 0; i < NodeTableCount; i++)
{
NinjaNodeName NodeName = new NinjaNodeName()
{
ID = reader.ReadUInt32()
};
uint NodeNameIndex = reader.ReadUInt32();
long currentPos = reader.BaseStream.Position; //Save Position
reader.JumpTo(NodeNameIndex, false);
NodeName.Name = reader.ReadNullTerminatedString();
reader.JumpTo(currentPos, true);
NinjaNodeNameList.NinjaNodeNames.Add(NodeName);
}
reader.JumpTo(pos, true);
reader.JumpAhead(NodeLength);
return(NinjaNodeNameList);
}
public static NsiReader Read(Stream stream)
{
(IDataSourceVersion version, GenomeAssembly assembly, string jsonKey, ReportFor reportFor, int schemaVersion) = ReadHeader(stream);
if (schemaVersion != SaCommon.SchemaVersion)
{
throw new UserErrorException($"Schema version mismatch!! Expected {SaCommon.SchemaVersion}, observed {schemaVersion} for {jsonKey}");
}
using (var blockStream = new BlockStream(new Zstandard(), stream, CompressionMode.Decompress))
using (var reader = new ExtendedBinaryReader(blockStream))
{
int count = reader.ReadOptInt32();
var suppIntervals = new Dictionary <ushort, List <Interval <string> > >();
for (var i = 0; i < count; i++)
{
var saInterval = SuppInterval.Read(reader);
if (suppIntervals.TryGetValue(saInterval.Chromosome.Index, out var intervals))
{
intervals.Add(new Interval <string>(saInterval.Start, saInterval.End, saInterval.GetJsonString()));
}
else
{
suppIntervals[saInterval.Chromosome.Index] = new List <Interval <string> > {
new Interval <string>(saInterval.Start, saInterval.End, saInterval.GetJsonString())
}
};
}
var intervalArrays = new Dictionary <ushort, IntervalArray <string> >(suppIntervals.Count);
foreach ((ushort chromIndex, List <Interval <string> > intervals) in suppIntervals)
{
intervalArrays[chromIndex] = new IntervalArray <string>(intervals.ToArray());
}
return(new NsiReader(assembly, version, jsonKey, reportFor, intervalArrays));
}
}
public JasixIndex(Stream stream) : this()
{
_stream = stream;
using (var reader = new ExtendedBinaryReader(stream))
{
int version = reader.ReadOptInt32();
if (version != JasixCommons.Version)
{
throw new InvalidDataException($"Invalid Jasix version: Observed {version}, expected{JasixCommons.Version}");
}
int count = reader.ReadOptInt32();
for (var i = 0; i < count; i++)
{
var chrIndex = new JasixChrIndex(reader);
_chrIndices[chrIndex.ReferenceSequence] = chrIndex;
}
int synonymCount = reader.ReadOptInt32();
for (var i = 0; i < synonymCount; i++)
{
string synonym = reader.ReadAsciiString();
string indexName = reader.ReadAsciiString();
_synonymToChrName[synonym] = indexName;
}
int sectionCount = reader.ReadOptInt32();
for (var i = 0; i < sectionCount; i++)
{
string sectionName = reader.ReadAsciiString();
long begin = reader.ReadOptInt64();
long end = reader.ReadOptInt64();
_sectionRanges[sectionName] = new FileRange(begin, end);
}
}
}
public override void Rebuild(string outputFolder)
{
var outputPath = System.IO.Path.Combine(outputFolder, RelativePath);
Directory.CreateDirectory(System.IO.Path.GetDirectoryName(outputPath));
var subtitles = GetSubtitles();
var encryptedInputData = System.IO.File.ReadAllBytes(Path);
var inputData = EncryptionManager.DecryptData(encryptedInputData);
byte[] outputData;
using (var msInput = new MemoryStream(inputData))
using (var input = new ExtendedBinaryReader(msInput, FileEncoding))
using (var msOutput = new MemoryStream())
using (var output = new ExtendedBinaryWriter(msOutput, FileEncoding))
{
while (input.Position + 2 <= input.Length)
{
var offset = input.Position;
var id = input.ReadUInt16();
var inputText = input.ReadString();
var subtitle = subtitles.First(x => x.Offset == offset);
var outputText = subtitle.Translation.ToFullWidthChars();
output.Write(id);
output.WriteString(outputText);
}
outputData = msOutput.ToArray();
}
var encryptedOutputData = EncryptionManager.EncryptData(outputData);
System.IO.File.WriteAllBytes(outputPath, encryptedOutputData);
}
public static void LoadLight(string filePath)
{
using (var fileStream = File.OpenRead(filePath))
{
var reader = new ExtendedBinaryReader(fileStream, true);
uint fileSize = reader.ReadUInt32();
uint rootNodeType = reader.ReadUInt32();
uint finalTableOffset = reader.ReadUInt32();
uint rootNodeOffset = reader.ReadUInt32();
uint finalTableOffsetAbs = reader.ReadUInt32();
uint padding = reader.ReadUInt32();
lightType = (LightType)reader.ReadUInt32();
XPos = reader.ReadSingle();
YPos = reader.ReadSingle();
ZPos = reader.ReadSingle();
ColorR = reader.ReadSingle();
ColorG = reader.ReadSingle();
ColorB = reader.ReadSingle();
// Print out Light information
Console.WriteLine($"Light type: {lightType}");
Console.WriteLine("");
Console.WriteLine($"ColorR is {ColorR}," + $" It should Be {ColorR/10000} after re-saving");
Console.WriteLine($"ColorG is {ColorG}," + $" It should Be {ColorG/10000} after re-saving");
Console.WriteLine($"ColorB is {ColorB}," + $" It should Be {ColorB/10000} after re-saving");
Console.WriteLine("");
// Read Omni-Specific Values if present.
if (lightType == LightType.Omni)
{
Unknown1 = reader.ReadUInt32();
Unknown2 = reader.ReadUInt32();
Unknown3 = reader.ReadUInt32();
OmniInnerRange = reader.ReadSingle();
OmniOuterRange = reader.ReadSingle();
}
}
}
public override void Load(ExtendedBinaryReader reader, bool keepOpen = false)
{
// Height of the character in pixels
CharacterHeight = reader.ReadInt32();
// The amount of characters defined
int characterCount = reader.ReadInt32();
// Unknown
WidthScale = reader.ReadSingle();
HeightScale = reader.ReadSingle();
for (int i = 0; i < characterCount; ++i)
{
var fontEntry = new FontEntry
{
Character = ReadReversedUTF8Char(reader), // The read UTF8 character
XScale = reader.ReadSingle(), // X position on the texture (Multiply by the textures width to get pixels)
YScale = reader.ReadSingle(), // Y position on the texture (Multiply by the textures height to get pixels)
Kerning = reader.ReadInt32(), // -X offset for positioning when rendering
Width = reader.ReadInt32() // The width of the character in pixels
};
Characters.Add(fontEntry);
}
}
public WriteToSinkEvent ReadWriteToSinkEvent(ExtendedBinaryReader reader)
{
var evt = new WriteToSinkEvent
{
RowUid = reader.Read7BitEncodedInt(),
ProcessInvocationUID = reader.Read7BitEncodedInt(),
SinkUID = reader.Read7BitEncodedInt()
};
var columnCount = reader.Read7BitEncodedInt();
if (columnCount > 0)
{
evt.Values = new KeyValuePair <string, object> [columnCount];
for (var i = 0; i < columnCount; i++)
{
var column = GetTextById(reader.Read7BitEncodedInt());
var value = reader.ReadObject();
evt.Values[i] = new KeyValuePair <string, object>(column, value);
}
}
return(evt);
}
protected override IList <Subtitle> GetSubtitles()
{
var result = new List <Subtitle>();
using (var fs = new FileStream(Path, FileMode.Open))
using (var input = new ExtendedBinaryReader(fs, FileEncoding))
{
var tableEnd = input.PeekUInt16();
while (input.Position < tableEnd)
{
var item = ReadItem(input);
item.Title.PropertyChanged += SubtitlePropertyChanged;
item.Description.PropertyChanged += SubtitlePropertyChanged;
result.Add(item.Title);
result.Add(item.Description);
}
}
LoadChanges(result);
return(result);
}
public NgaReader(Stream stream)
{
_nsaStream = stream;
// read the whole file. Currently they are well under 2MB
var compressedBytes = new byte[2 * 1024 * 1024];
var decompressedBytes = new byte[20 * 1024 * 1024];
var compressedSize = _nsaStream.Read(compressedBytes, 0, compressedBytes.Length);
var zstd = new Zstandard();
var decompressedSize = zstd.Decompress(compressedBytes, compressedSize, decompressedBytes, decompressedBytes.Length);
_memStream = new MemoryStream(decompressedBytes, 0, decompressedSize);
_reader = new ExtendedBinaryReader(_memStream);
Version = DataSourceVersion.Read(_reader);
JsonKey = _reader.ReadAsciiString();
_isArray = _reader.ReadBoolean();
ushort schemaVersion = _reader.ReadOptUInt16();
if (schemaVersion != SaCommon.SchemaVersion)
{
throw new UserErrorException($"Expected schema version: {SaCommon.SchemaVersion}, observed: {schemaVersion} for {JsonKey}");
}
}
public void TranscriptRegion_EndToEnd()
{
var expectedResults = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 13, 100, 200, 300, 400),
new TranscriptRegion(TranscriptRegionType.Gap, 0, 120, 230, 10, 20),
new TranscriptRegion(TranscriptRegionType.Intron, 14, 130, 230, 330, 430)
};
var observedResults = new ITranscriptRegion[expectedResults.Length];
using (var ms = new MemoryStream())
{
using (var writer = new ExtendedBinaryWriter(ms, Encoding.UTF8, true))
{
foreach (var region in expectedResults)
{
region.Write(writer);
}
}
ms.Position = 0;
using (var reader = new ExtendedBinaryReader(ms))
{
for (int i = 0; i < expectedResults.Length; i++)
{
observedResults[i] = TranscriptRegion.Read(reader);
}
}
}
var comparer = new TranscriptRegionComparer();
Assert.Equal(expectedResults, observedResults, comparer);
}
public override void Rebuild(string outputFolder)
{
var outputPath = System.IO.Path.Combine(outputFolder, RelativePath);
Directory.CreateDirectory(System.IO.Path.GetDirectoryName(outputPath));
var subtitles = GetSubtitles();
var subs = subtitles.Select(subtitle => subtitle as SubtitleWithId).ToList();
var dictionary = new Dictionary <string, SubtitleWithId>(subs.Count);
foreach (SubtitleWithId subtitle in subs)
{
dictionary.Add(subtitle.Id, subtitle);
}
using (var fsInput = new FileStream(Path, FileMode.Open))
using (var input = new ExtendedBinaryReader(fsInput, FileEncoding))
using (var fsOutput = new FileStream(outputPath, FileMode.Create))
using (var output = new ExtendedBinaryWriter(fsOutput, FileEncoding))
{
var count = input.ReadInt32();
output.Write(count);
for (int i = 0; i < count; i++)
{
// UILabel
output.Write(input.ReadBytes(0x04));
output.Write(input.ReadBytes(0x08));
var strJap = input.ReadStringSerialized(0x04);
var strEng = input.ReadStringSerialized(0x04);
output.WriteStringSerialized(strJap, 0x04);
output.WriteStringSerialized(dictionary.TryGetValue((i + 1).ToString(), out SubtitleWithId subtitle) ? subtitle.Translation : strEng, 0x04);
}
}
}
protected override IList <Subtitle> GetSubtitles()
{
var result = new List <Subtitle>();
using (var fs = new FileStream(Path, FileMode.Open))
using (var input = new ExtendedBinaryReader(fs, FileEncoding, Endianness.BigEndian))
{
input.Seek(0x20, SeekOrigin.Begin);
var pointer = input.ReadInt32();
if (pointer > -1)
{
input.Seek(pointer, SeekOrigin.Begin);
var subtitle = ReadSubtitle(input);
subtitle.PropertyChanged += SubtitlePropertyChanged;
result.Add(subtitle);
}
input.Seek(0x24, SeekOrigin.Begin);
pointer = input.ReadInt32();
if (pointer > -1)
{
input.Seek(pointer, SeekOrigin.Begin);
var subtitle = ReadSubtitle(input);
subtitle.PropertyChanged += SubtitlePropertyChanged;
result.Add(subtitle);
}
}
LoadChanges(result);
return(result);
}
public void ReadWriteTests()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
var regulatoryFeature1 = new RegulatoryElement(2, 100, 200, CompactId.Convert("1"), RegulatoryElementType.promoter);
var regulatoryFeature2 = new RegulatoryElement(3, 100, 200, CompactId.Convert("2"), RegulatoryElementType.enhancer);
var regulatoryFeature3 = new RegulatoryElement(4, 105, 201, CompactId.Convert("3"), RegulatoryElementType.CTCF_binding_site);
using (var writer = new ExtendedBinaryWriter(FileUtilities.GetCreateStream(randomPath)))
{
regulatoryFeature1.Write(writer);
regulatoryFeature2.Write(writer);
regulatoryFeature3.Write(writer);
}
using (var reader = new ExtendedBinaryReader(FileUtilities.GetReadStream(randomPath)))
{
Assert.Equal(regulatoryFeature1, RegulatoryElement.Read(reader));
Assert.Equal(regulatoryFeature2, RegulatoryElement.Read(reader));
Assert.Equal(regulatoryFeature3, RegulatoryElement.Read(reader));
}
File.Delete(randomPath);
}
protected virtual void LoadChanges(TableData data)
{
if (HasChanges)
{
using (var fs = new FileStream(ChangesFile, FileMode.Open))
using (var input = new ExtendedBinaryReader(fs, Encoding.Unicode))
{
var version = input.ReadInt32();
if (version != ChangesFileVersion)
{
//System.IO.File.Delete(ChangesFile);
return;
}
foreach (var column in data.Columns)
{
column.PropertyChanged -= SubtitlePropertyChanged;
column.LoadChanges(input);
column.PropertyChanged += SubtitlePropertyChanged;
}
}
}
}
public void LoadChromosome(string ucscReferenceName)
{
IsInitialized = false;
if (_saDirectory == null || ucscReferenceName == _currentReferenceName)
{
return;
}
_currentReferenceName = ucscReferenceName;
_currentIntervalIndex = -1;
_phylopIntervals.Clear();
// load the appropriate phyloP file
var stream = PhylopCommon.GetStream(_saDirectory, ucscReferenceName);
if (stream == null)
{
_reader = null;
return;
}
_reader = new ExtendedBinaryReader(stream);
LoadHeader();
}
private static SetObjectTransform ReadTransform(
ExtendedBinaryReader reader, bool readLocalSpace)
{
var transform = new SetObjectTransform();
// World Space
transform.Position = reader.ReadVector3();
transform.Rotation = new Quaternion(reader.ReadVector3(), true);
// Local Space
if (readLocalSpace)
{
transform.Position += reader.ReadVector3();
// TODO: Convert euler angles rotation to quaternion and multiply.
var localRotation = reader.ReadVector3();
if (localRotation.X != 0 || localRotation.Y != 0 || localRotation.Z != 0)
{
Console.WriteLine("Local rotation {0} is not zero!", localRotation);
}
}
return(transform);
}
public static ISaDataSource Read(ExtendedBinaryReader reader)
{
var keyName = reader.ReadString();
var vcfkeyName = reader.ReadString();
var altAllele = reader.ReadString();
var flags = reader.ReadByte();
var matchByAllele = (flags & 1) != 0;
var isArray = (flags & 2) != 0;
var vcfString = reader.ReadString();
var numJsonStrings = reader.ReadOptInt32();
string[] jsonStrings = null;
if (numJsonStrings > 0)
{
jsonStrings = new string[numJsonStrings];
for (int i = 0; i < numJsonStrings; i++)
{
jsonStrings[i] = reader.ReadString();
}
}
return(new SaDataSource(keyName, vcfkeyName, altAllele, matchByAllele, isArray, vcfString, jsonStrings));
}
// ReSharper disable once UnusedParameter.Local
private static void ReadFromBlockStream(ICompressionAlgorithm compressionAlgorithm, Stream ms, string expectedRandomString)
{
// grab the header
var header = DemoHeader.Read(ms);
Assert.Equal(ExpectedAssembly, header.Assembly);
using (var blockStream = new BlockStream(compressionAlgorithm, ms, CompressionMode.Decompress))
using (var reader = new ExtendedBinaryReader(blockStream))
{
CheckWriteException(blockStream);
// sequential string check
CheckString(reader, expectedRandomString);
CheckString(reader, SmallString);
CheckString(reader, FinalString);
// random access string check
blockStream.SetBlockPosition(header.Custom.FileOffset, header.Custom.InternalOffset);
//reader.Reset();
CheckString(reader, SmallString);
}
}
protected override void LoadChanges(IList <Subtitle> subtitles)
{
if (HasChanges)
{
using (var fs = new FileStream(ChangesFile, FileMode.Open))
using (var input = new ExtendedBinaryReader(fs, System.Text.Encoding.Unicode))
{
var version = input.ReadInt32();
if (version != ChangesFileVersion)
{
//System.IO.File.Delete(ChangesFile);
return;
}
input.Skip(128 * 4);
var subtitleCount = input.ReadInt32();
for (var i = 0; i < subtitleCount; i++)
{
var offset = input.ReadInt64();
var text = input.ReadString();
var subtitle = subtitles.FirstOrDefault(x => x.Offset == offset);
if (subtitle != null)
{
subtitle.PropertyChanged -= SubtitlePropertyChanged;
subtitle.Translation = text;
subtitle.Loaded = subtitle.Translation;
subtitle.PropertyChanged += SubtitlePropertyChanged;
}
}
}
}
}
public void ExonReadWriteTests()
{
var randomPath = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
var exon1 = new CdnaCoordinateMap(100, 200, 10, 20);
var exon2 = new CdnaCoordinateMap(100, 200, 11, 21);
var exon3 = new CdnaCoordinateMap(105, 201, 12, 15);
using (var writer = new ExtendedBinaryWriter(FileUtilities.GetCreateStream(randomPath)))
{
exon1.Write(writer);
exon2.Write(writer);
exon3.Write(writer);
}
using (var reader = new ExtendedBinaryReader(FileUtilities.GetReadStream(randomPath)))
{
Assert.Equal(exon1, CdnaCoordinateMap.Read(reader));
Assert.Equal(exon2, CdnaCoordinateMap.Read(reader));
Assert.Equal(exon3, CdnaCoordinateMap.Read(reader));
}
File.Delete(randomPath);
}
public JasixChrIndex(ExtendedBinaryReader reader) : this("")
{
ReferenceSequence = reader.ReadAsciiString();
int count = reader.ReadOptInt32();
for (var i = 0; i < count; i++)
{
_nodes.Add(new JasixNode(reader));
}
int intervalCount = reader.ReadOptInt32();
if (intervalCount == 0)
{
return;
}
for (var i = 0; i < intervalCount; i++)
{
_largeVariants.Add(ReadInterval(reader));
}
_intervalArray = new IntervalArray <long>(_largeVariants.ToArray());
}
public static BootstrapInfoBox FromBase64String(string s)
{
var stream = new MemoryStream(System.Convert.FromBase64String(s));
using (var br = new ExtendedBinaryReader(stream))
{
BootstrapInfoBox bib = new BootstrapInfoBox();
bib.Parse(br);
return bib;
}
}
public override void Parse(ExtendedBinaryReader br)
{
base.Parse(br);
Version = br.ReadByte();
Flags = br.ReadUInt24();
BootstrapinfoVersion = br.ReadUInt32();
var b = br.ReadByte();
Profile = (new byte[] { 0x80, 0x40 }).Select(i => (i & b) != 0).ToArray();
Live = (0x02 & b) != 0;
Update = (0x01 & b) != 0;
Reserved = (new byte[] { 0x08, 0x04, 0x02, 0x01 }).Select(i => (i & b) != 0).ToArray();
TimeScale = br.ReadUInt32();
CurrentMediaTime = br.ReadUInt64();
SmpteTimeCodeOffset = br.ReadUInt64();
MovieIdentifier = br.ReadNullTerminatedString();
ServerEntryCount = br.ReadByte();
ServerEntryTable = new ServerEntry[ServerEntryCount];
for (int i = 0; i < ServerEntryCount; i++)
ServerEntryTable[i] = ServerEntry.Parse(br);
QualityEntryCount = br.ReadByte();
QualityEntryTable = new QualityEntry[QualityEntryCount];
for (int i = 0; i < QualityEntryCount; i++)
QualityEntryTable[i] = QualityEntry.Parse(br);
DrmData = br.ReadNullTerminatedString();
MetaData = br.ReadNullTerminatedString();
SegmentRunTableCount = br.ReadByte();
SegmentRunTableEntries = new SegmentRunTableBox[SegmentRunTableCount];
for (int i = 0; i < SegmentRunTableCount; i++)
{
SegmentRunTableEntries[i] = new SegmentRunTableBox();
SegmentRunTableEntries[i].Parse(br);
}
FragmentRunTableCount = br.ReadByte();
FragmentRunTableEntries = new FragmentRunTableBox[FragmentRunTableCount];
for (int i = 0; i < FragmentRunTableCount; i++)
{
FragmentRunTableEntries[i] = new FragmentRunTableBox();
FragmentRunTableEntries[i].Parse(br);
}
}
/// <summary>
/// returns a collection of bytes from a Url
/// </summary>
/// <param name="url">The URL to retrieve</param>
public void GetUrlData(string url)
{
Uri uri = new Uri(url);
if (!uri.IsFile)
throw new UriFormatException("url is not a local file");
FileWebRequest request = WebRequest.Create(url) as FileWebRequest;
if (request == null)
{
this.Clear();
return;
}
request.Method = "GET";
// download the target URL
FileWebResponse response = (FileWebResponse) request.GetResponse();
// convert response stream to byte array
using (Stream stream = response.GetResponseStream())
{
ExtendedBinaryReader extReader = new ExtendedBinaryReader(stream);
_ResponseBytes = extReader.ReadToEnd();
}
// For local operations, we consider the data are never compressed. Else, the "Content-Encoding" field
// in the headers would be "gzip" or "deflate". This could be handled quite easily with SharpZipLib for instance.
// sometimes URL is indeterminate, eg, "http://website.com/myfolder"
// in that case the folder and file resolution MUST be done on
// the server, and returned to the client as ContentLocation
_ContentLocation = response.Headers["Content-Location"];
if (_ContentLocation == null)
_ContentLocation = "";
// if we have string content, determine encoding type
// (must cast to prevent null)
// HACK We determine the content type based on the uri extension,
// as the header returned by the FileWebResponse is always "application/octet-stream" (hard coded in .NET!!)
// text/html
string ext = Path.GetExtension(uri.LocalPath).TrimStart(new char[]{'.'});
switch (ext)
{
// What's important here is to identify TEXT mime types. Because, the default will resort to binary file.
case "htm":
case "html": _DetectedContentType = "text/html"; break;
case "css": _DetectedContentType = "text/css"; break;
case "csv": _DetectedContentType = "text/csv"; break;
case "rtf": _DetectedContentType = "text/rtf"; break;
case "aspx":
case "xsl":
case "xml": _DetectedContentType = "text/xml"; break;
case "bmp": _DetectedContentType = "image/bmp"; break;
case "gif": _DetectedContentType = "image/gif"; break;
case "ico": _DetectedContentType = "image/x-icon"; break;
case "jpg":
case "jpeg": _DetectedContentType = "image/jpeg"; break;
case "png": _DetectedContentType = "image/png"; break;
case "tif":
case "tiff": _DetectedContentType = "image/tiff"; break;
case "js": _DetectedContentType = "application/x-javascript"; break;
default:
// Line commented: we don't change it
_DetectedContentType = response.Headers["Content-Type"]; // Always "application/octet-stream" ...
break;
}
if (_DetectedContentType == null)
_DetectedContentType = "";
if (ResponseIsBinary)
_DetectedEncoding = null;
else if (_ForcedEncoding == null)
_DetectedEncoding = DetectEncoding(_DetectedContentType, _ResponseBytes);
}
public static ServerEntry Parse(ExtendedBinaryReader br)
{
return new ServerEntry
{
ServerBaseURL = br.ReadNullTerminatedString()
};
}
/// <param name="valueFixup"> /// Because reference types may not be read yet, the deserialization is fixed up when it becomes /// available /// </param> public abstract void Deserialize(ExtendedBinaryReader reader, Action <T> valueFixup);
public object Deserialize(Type classType, ExtendedBinaryReader br, object obj = null)
{
if (!Attribute.IsDefined(classType, typeof(UnitySerializableAttribute)))
{
throw new UnitySerializationException("Not deserializable type : " + classType.FullName);
}
if (obj == null)
{
obj = Activator.CreateInstance(classType);
}
// Deserialize base type first because Type.GetFields() returns base fields last
if (Attribute.IsDefined(classType.BaseType, typeof(UnitySerializableAttribute)))
{
Deserialize(classType.BaseType, br, obj);
}
var fieldArray = classType.GetFields();
foreach (var field in fieldArray)
{
if (!field.DeclaringType.Equals(classType))
{
continue;
}
if (field.IsLiteral || field.IsInitOnly)
{
continue;
}
Type fieldType = field.FieldType;
if (Attribute.IsDefined(field, typeof(UnityMinVersionAttribute)))
{
var minAttrib = Attribute.GetCustomAttribute(field, typeof(UnityMinVersionAttribute)) as UnityMinVersionAttribute;
if (minAttrib.version > version)
{
field.SetValue(obj, GetDefault(fieldType));
continue;
}
}
if (Attribute.IsDefined(field, typeof(UnityMaxVersionAttribute)))
{
var maxAttrib = Attribute.GetCustomAttribute(field, typeof(UnityMaxVersionAttribute)) as UnityMaxVersionAttribute;
if (maxAttrib.version < version)
{
field.SetValue(obj, GetDefault(fieldType));
continue;
}
}
object value = null;
bool doNotAlign = Attribute.IsDefined(field, typeof(UnityDoNotAlignAttribute));
if (!doNotAlign)
{
br.AlignStream();
}
if (fieldType.IsEnum)
{
var enumType = Enum.GetUnderlyingType(fieldType);
value = ReadValueType(enumType, br);
}
else if (fieldType.IsValueType)
{
value = ReadValueType(fieldType, br);
}
else if (fieldType.IsArray && fieldType.GetElementType().IsValueType) // Value type array
{
value = ReadValueArray(fieldType.GetElementType(), br);
}
else if (fieldType == typeof(string))
{
value = br.ReadAlignedString();
}
else if (fieldType.IsClass || Attribute.IsDefined(fieldType, typeof(UnitySerializableAttribute)))
{
if (fieldType.IsArray)
{
var elementType = fieldType.GetElementType();
value = ReadArray(elementType, br);
}
else if (fieldType.IsGenericType && fieldType.GetGenericTypeDefinition() == typeof(List <>))
{
var elementType = fieldType.GetGenericArguments()[0];
object array;
if (elementType.IsValueType)
{
array = ReadValueArray(elementType, br);
}
else
{
array = ReadArray(elementType, br);
}
value = Activator.CreateInstance(fieldType, (IEnumerable)array);
}
else
{
value = Deserialize(fieldType, br);
}
}
else
{
throw new IOException("Failed to deserialize, unknown type : " + fieldType.ToString());
}
field.SetValue(obj, value);
}
return(obj);
}
public BoxParser(ExtendedBinaryReader br)
{
this.br = br;
currentHeader = null;
}
private static byte[] GetTwoBitBuffer(ExtendedBinaryReader reader)
{
int numBytes = reader.ReadOptInt32();
return(reader.ReadBytes(numBytes));
}
public override void Parse(ExtendedBinaryReader br)
{
base.Parse(br);
Version = br.ReadByte();
Flags = br.ReadUInt24();
TimeScale = br.ReadUInt32();
QualityEntryCount = br.ReadByte();
QualitySegmentUrlModifiers = Enumerable.Range(0, QualityEntryCount).Select(i => br.ReadNullTerminatedString()).ToArray();
FragmentRunEntryCount = br.ReadUInt32();
FragmentRunEntryTable = new FragmentRunEntry[FragmentRunEntryCount];
for (uint i = 0; i < FragmentRunEntryCount; i++)
FragmentRunEntryTable[i] = FragmentRunEntry.Parse(br);
}
/// <summary>
/// returns a collection of bytes from a Url
/// </summary>
/// <param name="Url">URL to retrieve</param>
public void GetUrlData(string Url, DateTime ifModifiedSince)
{
if (!string.IsNullOrEmpty(Url))
{
HttpWebRequest wreq = (HttpWebRequest)WebRequest.Create(Url);
//-- do we need to use a proxy to get to the web?
if (!string.IsNullOrEmpty(_ProxyUrl))
{
WebProxy wp = new WebProxy(_ProxyUrl);
if (_ProxyAuthenticationRequired)
{
if (!string.IsNullOrEmpty(_ProxyUser) & !string.IsNullOrEmpty(_ProxyPassword))
{
wp.Credentials = new NetworkCredential(_ProxyUser, _ProxyPassword);
}
else
{
wp.Credentials = CredentialCache.DefaultCredentials;
}
wreq.Proxy = wp;
}
}
//-- does the target website require credentials?
if (_AuthenticationRequired)
{
if (!string.IsNullOrEmpty(_AuthenticationUser) & !string.IsNullOrEmpty(_AuthenticationPassword))
{
wreq.Credentials = new NetworkCredential(_AuthenticationUser, _AuthenticationPassword);
}
else
{
wreq.Credentials = CredentialCache.DefaultCredentials;
}
}
wreq.Method = "GET";
wreq.Timeout = _RequestTimeoutMilliseconds;
wreq.UserAgent = _HttpUserAgent;
wreq.Headers.Add("Accept-Encoding", _AcceptedEncodings);
//-- note that, if present, this will trigger a 304 exception
//-- if the URL being retrieved is not newer than the specified
//-- date/time
if (ifModifiedSince != DateTime.MinValue)
{
wreq.IfModifiedSince = ifModifiedSince;
}
//-- sometimes we need to transfer cookies to another URL;
//-- this keeps them around in the object
if (KeepCookies)
{
if (_PersistedCookies == null)
{
_PersistedCookies = new CookieContainer();
}
wreq.CookieContainer = _PersistedCookies;
}
//-- download the target URL into a byte array
HttpWebResponse wresp = (HttpWebResponse)wreq.GetResponse();
//-- convert response stream to byte array
ExtendedBinaryReader ebr = new ExtendedBinaryReader(wresp.GetResponseStream());
_ResponseBytes = ebr.ReadToEnd();
//-- determine if body bytes are compressed, and if so,
//-- decompress the bytes
HttpContentEncoding ContentEncoding = default(HttpContentEncoding);
if (wresp.Headers["Content-Encoding"] == null)
{
ContentEncoding = HttpContentEncoding.None;
}
else
{
switch (wresp.Headers["Content-Encoding"].ToLower())
{
case "gzip":
ContentEncoding = HttpContentEncoding.Gzip;
break;
case "deflate":
ContentEncoding = HttpContentEncoding.Deflate;
break;
default:
ContentEncoding = HttpContentEncoding.Unknown;
break;
}
_ResponseBytes = Decompress(_ResponseBytes, ContentEncoding);
}
//-- sometimes URL is indeterminate, eg, "http://website.com/myfolder"
//-- in that case the folder and file resolution MUST be done on
//-- the server, and returned to the client as ContentLocation
_ContentLocation = wresp.Headers["Content-Location"];
if (_ContentLocation == null)
{
_ContentLocation = "";
}
//-- if we have string content, determine encoding type
//-- (must cast to prevent Nothing)
_DetectedContentType = wresp.Headers["Content-Type"];
if (_DetectedContentType == null)
{
_DetectedContentType = "";
}
if (ResponseIsBinary)
{
_DetectedEncoding = null;
}
else
{
if (_ForcedEncoding == null)
{
_DetectedEncoding = DetectEncoding(_DetectedContentType, _ResponseBytes);
}
}
}
}
public virtual void Deserialize(ExtendedBinaryReader reader, Action <object> valueFixup)
{
Deserialize(reader, (Action <T>)(value => valueFixup(value)));
}
public static QualityEntry Parse(ExtendedBinaryReader br)
{
return new QualityEntry
{
QualitySegmentUrlModifier = br.ReadNullTerminatedString()
};
}
public override object Read(ExtendedBinaryReader reader) => Lookup(reader.ReadSByte());
public static FLVTag Parse(ExtendedBinaryReader br)
{
var b = br.ReadByte();
var tag = new FLVTag
{
Reserved = (byte)(b & 0xc0),
Filter = (b & 0x20) == 0,
TagType = (TagType)(b & 0x1f),
DataSize = br.ReadUInt24(),
TimeStamp = br.ReadUInt24(),
TimestampExtended = br.ReadByte(),
StreamID = br.ReadUInt24()
};
tag.HeaderAndBody = br.ReadBytes((tag.TimestampExtended << 24) + (int)tag.TimeStamp);
return tag;
}
