public AssemblyOS(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
OSPlatformID = ReadSize(4);
OSMajorVersion = ReadSize(4);
OSMinorVersion = ReadSize(4);
}
public Property(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Flags = (ushort)ReadSize(2);
Name = ReadSize(HeapSizes.String);
Type = ReadSize(HeapSizes.Blob);
}
public Param(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Flags = (ushort)ReadSize(2);
Sequence = (ushort)ReadSize(2);
Name = ReadSize(HeapSizes.String);
}
public TypeRef(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
ResolutionScope = ReadSize(IndexSizes[Index.ResolutionScope]);
TypeName = ReadSize(HeapSizes.String);
TypeNamespace = ReadSize(HeapSizes.String);
}
public AbstractTable(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset)
{
HeapSizes = heapSizes;
IndexSizes = indexSizes;
CurrentOffset = Offset;
}
private O18QuanEnvelope GetCorrespondingEnvelope(IRawFile rawFile, double theoreticalMz, int charge, double mzTolerance, int scan)
{
PeakList <Peak> pkl = rawFile.GetPeakList(scan);
if (pkl.ScanTimes.Count == 0)
{
pkl.ScanTimes.Add(new ScanTime(scan, rawFile.ScanToRetentionTime(scan)));
}
PeakList <Peak> O16 = pkl.FindEnvelopeDirectly(theoreticalMz, charge, mzTolerance, 4, () => new Peak());
PeakList <Peak> O181 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap1[charge], charge, mzTolerance, 2, () => new Peak());
for (int i = 2; i < 4; i++)
{
if (O16[i].Intensity < O181[i - 2].Intensity)
{
O16[i].Mz = O181[i - 2].Mz;
O16[i].Intensity = O181[i - 2].Intensity;
}
}
PeakList <Peak> O182 = pkl.FindEnvelopeDirectly(theoreticalMz + chargeGapMap2[charge], charge, mzTolerance, 2, () => new Peak());
O16.AddRange(O182);
return(new O18QuanEnvelope(O16));
}
public DeclSecurity(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Action = (ushort)ReadSize(2);
Parent = ReadSize(IndexSizes[Index.HasDeclSecurity]);
PermissionSet = ReadSize(HeapSizes.Blob);
}
public PeFile(IRawFile peFile)
{
RawFile = peFile;
_nativeStructureParsers = new NativeStructureParsers(RawFile);
if (ImageNtHeaders?.OptionalHeader?.DataDirectory != null)
{
if (ImageSectionHeaders != null)
{
_dataDirectoryParsers = new DataDirectoryParsers(
RawFile,
ImageNtHeaders.OptionalHeader.DataDirectory,
ImageSectionHeaders,
Is32Bit
);
}
}
_dotNetStructureParsers = new DotNetStructureParsers(
RawFile,
ImageComDescriptor,
ImageSectionHeaders
);
_authenticodeParser = new AuthenticodeParser(this);
}
public MetaDataStreamGuid(IRawFile peFile, long offset, uint size)
: base(peFile, offset)
{
_size = size;
GuidsAndIndices = ParseGuidsAndIndices();
Guids = GuidsAndIndices.Select(x => x.Item1).ToList();
}
public DataDirectoryParsers(
IRawFile peFile,
IEnumerable <ImageDataDirectory>?dataDirectories,
IEnumerable <ImageSectionHeader>?sectionHeaders,
bool is32Bit
)
{
_peFile = peFile;
_dataDirectories = dataDirectories.ToArray();
_sectionHeaders = sectionHeaders.ToArray();
_is32Bit = is32Bit;
// Init all parsers
_imageExportDirectoriesParser = InitImageExportDirectoryParser();
_runtimeFunctionsParser = InitRuntimeFunctionsParser();
_imageImportDescriptorsParser = InitImageImportDescriptorsParser();
_imageBaseRelocationsParser = InitImageBaseRelocationsParser();
_imageResourceDirectoryParser = InitImageResourceDirectoryParser();
_imageDebugDirectoryParser = InitImageDebugDirectoryParser();
_winCertificateParser = InitWinCertificateParser();
_exportedFunctionsParser = InitExportFunctionParser();
_importedFunctionsParser = InitImportedFunctionsParser();
_imageBoundImportDescriptorParser = InitBoundImportDescriptorParser();
_imageTlsDirectoryParser = InitImageTlsDirectoryParser();
_imageDelayImportDescriptorParser = InitImageDelayImportDescriptorParser();
_imageLoadConfigDirectoryParser = InitImageLoadConfigDirectoryParser();
_imageCor20HeaderParser = InitImageComDescriptorParser();
_resourcesParser = InitResourcesParser();
}
protected override void DoWritePeakList(IRawFile rawReader, PeakList <Peak> pkl, string rawFileName, List <string> result)
{
var sw = GetStreamWriter(rawReader, pkl.ScanMode, pkl.MsLevel, rawFileName);
var scan = pkl.ScanTimes[0].Scan;
if (pkl.MsLevel == 1)
{
sw.Flush();
sw1Index.Write("{0}\t{1}\n", scan, sw.BaseStream.Position);
sw.Write("S\t{0}\t{0}\n", scan);
sw.Write("I\tRetTime\t{0:0.####}\n", pkl.ScanTimes[0].RetentionTime);
foreach (Peak p in pkl)
{
sw.Write("{0:0.#####} {1:0.#} {2}\n", p.Mz, p.Intensity, p.Charge);
}
}
else
{
sw.WriteLine("S\t{0}\t{1}\t{2}", scan, scan, pkl.PrecursorMZ);
int[] charges = 0 != pkl.PrecursorCharge ? new[] { pkl.PrecursorCharge } : new[] { 2, 3 };
foreach (var charge in charges)
{
sw.WriteLine("Z\t{0}\t{1:0.#####}", charge, PrecursorUtils.MzToMH(pkl.PrecursorMZ, charge, true));
}
foreach (var peak in pkl)
{
sw.WriteLine("{0:0.#####}\t{1:0.#}", peak.Mz, peak.Intensity);
}
}
}
public ClassLayout(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
PackingSize = (ushort)ReadSize(2);
ClassSize = ReadSize(4);
Parent = ReadSize(IndexSizes[Index.TypeDef]);
}
public MetaDataStreamUs(IRawFile peFile, long offset, uint size)
: base(peFile, offset)
{
_size = size;
UserStringsAndIndices = ParseUserStringsAndIndices();
UserStrings = UserStringsAndIndices.Select(x => x.Item1).ToList();
}
public MethodImpl(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Class = ReadSize(IndexSizes[Index.TypeDef]);
MethodBody = ReadSize(IndexSizes[Index.MethodDefOrRef]);
MethodDeclaration = ReadSize(IndexSizes[Index.MethodDefOrRef]);
}
private StreamWriter GetStreamWriter(IRawFile rawReader, string peakMode, int msLevel, string fileName)
{
string mgfFile = GetPeakModeFileName(rawReader, peakMode, msLevel, fileName) + ".tmp";
if (swMap.ContainsKey(mgfFile))
{
return(swMap[mgfFile]);
}
outputFiles.Add(mgfFile);
var result = new StreamWriter(mgfFile);
swMap[mgfFile] = result;
foreach (var comment in Writer.Comments)
{
result.WriteLine("###" + comment);
}
foreach (var comment in this.PeakListProcessor.ToString().Split('\n'))
{
result.WriteLine("###" + comment);
}
return(result);
}
public MethodSemantics(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Semantics = (ushort)ReadSize(2);
Method = ReadSize(IndexSizes[Index.MethodDef]);
Association = ReadSize(IndexSizes[Index.HasSemantics]);
}
public QuantificationChromotograph Build(IIdentifiedSpectrum mphit, IRawFile reader)
{
QuantificationChromotograph result = new QuantificationChromotograph();
var envelopes = builder.Build(mphit);
int startScan = mphit.Query.FileScan.FirstScan;
double mzTolerance = PrecursorUtils.ppm2mz(envelopes[0][0], ppmTolerance);
bool bFirst = true;
int firstScanNumber = reader.GetFirstSpectrumNumber();
int lastScanNumber = reader.GetLastSpectrumNumber();
//backward
for (int scan = startScan; scan >= firstScanNumber; scan--)
{
if (1 == reader.GetMsLevel(scan))
{
QuantificationScan qscan = reader.GetPeakList(scan).GetQuantificationScan(envelopes, mzTolerance);
if (!validate(qscan))
{
break;
}
if (bFirst)
{
qscan.IsIdentified = true;
bFirst = false;
}
result.Insert(0, qscan);
}
}
//forward
for (int scan = startScan + 1; scan <= lastScanNumber; scan++)
{
if (1 == reader.GetMsLevel(scan))
{
QuantificationScan qscan = reader.GetPeakList(scan).GetQuantificationScan(envelopes, mzTolerance);
if (!validate(qscan))
{
break;
}
result.Add(qscan);
}
}
if (result.Count > 0)
{
result.IdentifiedSpectra.Add(mphit);
}
return(result);
}
public static List <ScanLevel> GetScanLevels(IRawFile rawFile)
{
var levels = new List <ScanLevel>();
FillScanLevels(levels, rawFile);
BuildScanLevels(levels);
return(levels);
}
public TxLog(IRawFile data)
{
_data = data;
if (data == null)
{
throw new ArgumentNullException("data");
}
}
public Constant(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Type = (byte)ReadSize(1);
CurrentOffset += 1; // Padding after "Type"
Parent = ReadSize(IndexSizes[Index.HasConstant]);
Value = ReadSize(HeapSizes.Blob);
}
public MetaDataStreamBlobParser(
IRawFile peFile,
long offset,
uint size)
: base(peFile, offset)
{
_size = size;
}
public SymbolMapColumn(int columnID, int partitionID, IRawFile data, IRawFile datak, IRawFile datar,
IRawFile symd, IRawFile symi,
IRawFile symk, IRawFile symr,
string propertyName, int capacity, long recordCountHint, int maxLen) : this(columnID, partitionID, data, symd, symi, symk, symr, propertyName, capacity, maxLen)
{
_datarIndex = new IndexColumn(datak, datar, capacity, recordCountHint);
_isIndexed = true;
}
public ImplMap(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
MappingFlags = (ushort)ReadSize(2);
MemberForwarded = ReadSize(IndexSizes[Index.MemberForwarded]);
ImportName = ReadSize(HeapSizes.String);
ImportScope = ReadSize(IndexSizes[Index.ModuleRef]);
}
public BinaryColumn(IRawFile data, IRawFile index,
int maxSize, string propertyName)
{
PropertyName = propertyName;
_data = data;
_maxSize = maxSize;
_index = index;
}
public ExportedType(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Flags = ReadSize(4);
TypeDefId = ReadSize(IndexSizes[Index.TypeDef]);
TypeName = ReadSize(HeapSizes.String);
TypeNamespace = ReadSize(HeapSizes.String);
}
public ManifestResource(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Offset = ReadSize(4);
Flags = ReadSize(4);
Name = ReadSize(HeapSizes.String);
Implementation = ReadSize(IndexSizes[Index.Implementation]);
}
public GenericParam(IRawFile peFile, long offset, HeapSizes heapSizes, IndexSize indexSizes)
: base(peFile, offset, heapSizes, indexSizes)
{
Number = (ushort)ReadSize(2);
Flags = (ushort)ReadSize(2);
Owner = ReadSize(IndexSizes[Index.TypeOrMethodDef]);
Name = ReadSize(HeapSizes.String);
}
protected override void DoFinalize(bool bReadAgain, IRawFile rawReader, string rawFileName, List <string> result)
{
foreach (var sw in swMap.Values)
{
sw.Close();
}
if (!Progress.IsCancellationPending() && !IsLoopStopped && !bReadAgain)
{
if (outputFiles.Count == 1 && (options.GroupByMode || options.GroupByMsLevel))
{
var resultFile = GetResultFile(rawReader, rawFileName);
if (!resultFile.Equals(outputFiles[0]))
{
if (File.Exists(resultFile))
{
File.Delete(resultFile);
}
File.Move(outputFiles[0], resultFile);
}
result.Add(resultFile);
}
else
{
foreach (var mgf in outputFiles)
{
if (mgf.EndsWith(".tmp"))
{
var res = FileUtils.ChangeExtension(mgf, "");
if (File.Exists(res))
{
File.Delete(res);
}
File.Move(mgf, res);
result.Add(res);
}
else
{
result.Add(mgf);
}
}
}
}
else
{
foreach (var m in outputFiles)
{
try
{
File.Delete(m);
}
catch (Exception)
{
}
}
}
}
public ImageBaseRelocationsParser(
IRawFile peFile,
uint offset,
uint directorySize
)
: base(peFile, offset)
{
_directorySize = directorySize;
}
internal NativeStructureParsers(IRawFile peFile)
{
_peFile = peFile;
// Init all parsers
_imageDosHeaderParser = InitImageDosHeaderParser();
_imageNtHeadersParser = InitNtHeadersParser();
_imageSectionHeadersParser = InitImageSectionHeadersParser();
}
