public void SaveLoad_16Bit()
{
Random rnd = new Random(0);
int size = 1024;
int stripSize = 32;
float[] data = new float[size];
for (int i = 0; i < size; i++)
{
data[i] = (float)rnd.Next(0, ushort.MaxValue) / (float)ushort.MaxValue;
}
try
{
RawFile.Save16Bit(fileName, data);
RawFile raw = new RawFile(fileName, 16, BYTE_ORDER.WINDOWS, stripSize);
Assert.AreEqual(fileName, raw.FileName);
Assert.AreEqual(size, raw.ElementCount, "Element count incorrect");
Assert.AreEqual(size * 2, raw.ByteCount, "Byte count incorrect");
Assert.AreEqual(stripSize, raw.StripSize, "Strip size incorrect");
Assert.AreEqual(16, raw.BitDepth);
Assert.AreEqual(BYTE_ORDER.WINDOWS, raw.ByteOrder);
CollectionAssert.AreEqual(data, ToArray(raw));
}
finally
{
File.Delete(fileName);
}
}
public void SaveLoad_8Bit()
{
Random rnd = new Random(0);
int size = 1024;
int stripSize = 32;
float[] data = new float[size];
for (int i = 0; i < size; i++)
{
data[i] = (float)rnd.Next(0, byte.MaxValue) / byte.MaxValue;
}
try
{
RawFile.Save8Bit(fileName, data);
RawFile raw = new RawFile(fileName, 8, BYTE_ORDER.WINDOWS, stripSize);
Assert.AreEqual(fileName, raw.FileName);
Assert.AreEqual(size, raw.ElementCount);
Assert.AreEqual(size, raw.ByteCount);
Assert.AreEqual(stripSize, raw.StripSize);
Assert.AreEqual(8, raw.BitDepth);
Assert.AreEqual(BYTE_ORDER.WINDOWS, raw.ByteOrder);
CollectionAssert.AreEqual(data, ToArray(raw));
}
finally
{
File.Delete(fileName);
}
}
public void Dispose()
{
if (RawFile != null && RawFile.IsOpen)
{
RawFile.Dispose();
}
}
public IActionResult CreateFile([FromForm] CreateExternalFileViewModel model) {
ApplicationUser user = userRepository.GetApplicationUserByUsername(User.Identity.Name);
Post post = postRepository.GetPostByPostId(model.PostId, true);
if(post == null) {
return NotFound();
}
if( user == null) {
return Unauthorized();
}
var time = DateTime.Now.ToBinary();
ExternalFile file = new ExternalFile() {
FileName = model.RawFile.FileName+time,
MIMEType = model.RawFile.ContentType,
PostId = post.PostId,
PostedTime = DateTime.Now
};
RawFile rawFile = new RawFile() {
Data = GetByteArrayFromFile(model.RawFile),
FileName = model.RawFile.FileName+time,
};
file.RawFile = rawFile;
try {
externalFileRepository.CreateExternalFile(file);
}
catch (Exception) {
return BadRequest();
}
return new OkObjectResult(Conversions.ExternalFileViewModelFromExternalFile(file));
}
public static object Contruct(Type type, RawFile reader)
{
object target = null;
return(target);
}
public async Task <RawFile> ProcessImage(RawFile rawImage)
{
rawImage.Content = await this.imageProcessor
.Resize(rawImage.Content, GlobalConstants.ResizedImageWidth);
rawImage.PreviewContent = await this.imageProcessor
.Resize(rawImage.Content, GlobalConstants.ResizedImageThumbnailWidth);
return(rawImage);
}
public static T Contruct <T>(RawFile reader)
{
T target = default(T);
var type = typeof(T);
var constructer = type.GetConstructor(new Type[0]);
return(target);
}
public void Save(string path, RawFile file)
{
try
{
fileIO.Save(path, file);
}
catch (Exception ex)
{
errorReporter.Add(ex);
}
}
float[] ToArray(RawFile raw)
{
int size = raw.ElementCount;
float[] data = new float[size];
for (int i = 0; i < size; i++)
{
data[i] = raw.Read(i);
}
return(data);
}
public async Task <T> SaveFileInfo <T>(RawFile file)
where T : FileInfo, new()
{
var processedFileName = string.Join(WhiteSpace.ToString(), file.OriginalFileName.Split(new[] { WhiteSpace }, StringSplitOptions.RemoveEmptyEntries));
var databaseFile = new T {
OriginalFileName = processedFileName, FileExtension = file.FileExtension
};
var filesContext = this.objectFactory.GetInstance <ShowcaseDbContext>();
filesContext.Set <T>().Add(databaseFile);
await filesContext.SaveChangesAsync();
databaseFile.UrlPath = databaseFile.Id.ToUrlPath();
await filesContext.SaveChangesAsync();
return(databaseFile);
}
public static RawFile ReadRaw(string dbFile, DBEntry entry)
{
// figure out what file version exists
string db2file = Path.ChangeExtension(dbFile, ".db2");
if (File.Exists(db2file))
{
dbFile = db2file;
}
else
{
dbFile = Path.ChangeExtension(dbFile, ".dbc");
}
using (var fs = new FileStream(dbFile, FileMode.Open, FileAccess.Read))
using (var br = new BinaryReader(fs, Encoding.UTF8))
{
DBHeader header = ReadHeader(br, "", 0);
if (!ValidationChecks(header, dbFile, out string error))
{
return(null);
}
RawFile rawFile = new RawFile()
{
Entry = entry
};
// stringtable stuff
long pos = br.BaseStream.Position;
long stringTableStart = br.BaseStream.Position += header.RecordCount * header.RecordSize;
rawFile.StringTable = ReadStringTable(br, stringTableStart); //Get stringtable
br.Scrub(pos);
// store data
rawFile.RawRecords = new List <byte[]>();
for (int i = 0; i < header.RecordCount; i++)
{
rawFile.RawRecords.Add(br.ReadBytes((int)header.RecordSize));
}
return(rawFile);
}
}
public ActionResult InsertFile(RawFile file_item)
{
Value temp_file = new Value();
temp_file = Session["TxtFile"] as Value;
if (file_item.file != null && file_item.file.ContentLength > 0)
{
var InputFileName = Path.GetFileName(date_ff);
var ServerSavePath = Path.Combine("D:/File/Topic/" + InputFileName);
file_item.file.SaveAs(ServerSavePath);
if (file_item.description == "null" || file_item.description == null)
{
file_item.description = " ";
}
M_Req.InsertFile(file_item.file, (long)Session["TopicID"], "Topic", file_item.description, Session["User"].ToString(), Session["TopicCode"].ToString(), Session["Department"].ToString());
}
return(Json((string)Session["TopicCode"]));
}
//[TestMethod]
public void BigFileTest()
{
string directory = "C:/Users/Justin/Desktop/Residuals/";
string fileName = directory + "YellowStone_5m_Ortho_8192_8_3.raw";
RawFileFormat fileFormat = new RawFileFormat();
fileFormat.bitDepth = 8;
fileFormat.byteOrder = BYTE_ORDER.WINDOWS;
fileFormat.fileName = fileName;
RawFile raw = new RawFile(fileFormat);
int count = raw.ElementCount;
for (int i = 0; i < count; i++)
{
raw.Read(i);
}
}
/// <summary>
/// Insert detail into Raw File detail table
/// </summary>
/// <param name="runId">Run number Id</param>
/// <param name="file">Raw File Name</param>
/// <param name="desLoc"></param>
/// <returns></returns>
public bool InsertRawFileDetails(int runId, string file, string desLoc)
{
try
{
using (IRawFileRepository objRawFileRepository = new RawFileRepository())
{
RawFile rawFile = new RawFile();
rawFile.RunNumberId = runId;
rawFile.FileName = Path.GetFileName(file);
rawFile.HotFolder = desLoc;
rawFile.Status = true;
objRawFileRepository.Save(rawFile);
}
}
catch (Exception ex)
{
throw new Exception("Error while inserting record in Raw file : " + ex);
}
return(true);
}
public bool IsValid()
{
if (RawFile != null)
{
Filename = Filename ?? RawFile.FileName;
using (var stream = new MemoryStream())
{
RawFile.CopyTo(stream);
FileBytes = stream.ToArray();
var data = Convert.ToBase64String(FileBytes);
var index = data.LastIndexOf("base64", StringComparison.Ordinal);
Data = index == -1 ? data : data.Substring(index + 7);
}
}
if (string.IsNullOrEmpty(FileType))
{
if (!string.IsNullOrEmpty(Filename))
{
FileType = Path.GetExtension(Filename).ToLower();
}
if (string.IsNullOrEmpty(FileType))
{
var match = Regex.Match(Data, "data:(.*?);");
if (!match.Success)
{
return(false);
}
FileType = match.Groups[1].Value;
}
}
if (string.IsNullOrEmpty(FileType))
{
return(false);
}
return(true);
}
public void StaticSaveLoad_32Bit()
{
Random rnd = new Random(0);
int size = 1024;
float[] data = new float[size];
for (int i = 0; i < size; i++)
{
data[i] = (float)rnd.NextDouble();
}
try
{
RawFile.Save32Bit(fileName, data);
CollectionAssert.AreEqual(data, RawFile.Load32Bit(fileName));
}
finally
{
File.Delete(fileName);
}
}
public void StaticSaveLoad_16Bit()
{
Random rnd = new Random(0);
int size = 1024;
float[] data = new float[size];
for (int i = 0; i < size; i++)
{
data[i] = (float)rnd.Next(0, ushort.MaxValue) / ushort.MaxValue;
}
try
{
RawFile.Save16Bit(fileName, data);
CollectionAssert.AreEqual(data, RawFile.Load16Bit(fileName, BYTE_ORDER.WINDOWS));
}
finally
{
File.Delete(fileName);
}
}
private int GetFileStats()
{
TextReader instream = null;
try
{
instream = (ReadStdin ? Console.In : new StreamReader(FilenameIn));
bool firstZero = true;
for (int row = 0; ; row++)
{
bool saveLine = true;
bool processLine = true;
string line = instream.ReadLine();
if (line == null)
{
break;
}
if (firstZero && row == 0 && Header == PrintHeaderType.PrintRow1)
{
row = -1;
HeaderLine = line;
saveLine = false;
// still process it
firstZero = false;
}
// if we still want to save it, it's not a header
if (saveLine && SkipRows > 0)
{
SkipRows--;
saveLine = false;
processLine = false;
}
if (processLine)
{
SaveFieldCount(line);
}
if (saveLine)
{
MaxReadLine++;
if (!UseTwoPassMethod)
{
RawFile.Add(line);
}
if (LineCountToPrint > 0)
{
LineCountToPrint--;
if (LineCountToPrint <= 0)
{
break;
}
}
}
}
int ret = ReadExternHeader();
if (ret > 0)
{
return(ret);
}
VerifyFieldLengths();
return(0);
}
finally
{
if (instream != null && instream != Console.In)
{
try { instream.Close(); }
catch { }
try { instream.Dispose(); }
catch { }
}
}
}
public QMatch FindBestScore(double MZ, int Charge, double IsoRatio, double MinRT, double MaxRT)
{
MSMatch First = null, Best = null;
QMatch Res = new QMatch();
Res.Clean();
Res.MSMatches = new List <MSMatch>();
double FirstIso = 0.0, SecondIso = 0.0;
double BestScore = 0.0, fs = 0.0;
int BestIndex = 0;
int Scan = 0;
double AveRT = (MinRT + MaxRT) / 2;
RawFile.ScanNumFromRT(AveRT, ref Scan);
Scan = ms2index[Scan];
//отступаем до минимального времени RT в массиве спектров
double LowMZ = (MZ * Charge + (float)1.007277) / (Charge + 1);
double HighMZ;
if (Charge > 1)
{
HighMZ = (MZ * Charge - 1.007277) / (Charge - 1);
}
else
{
HighMZ = 0.0;
}
while (Scan > 0 && RawSpectra[Scan].RT >= MinRT)
{
Scan = IndexRev[Scan];
}
//цикл поиска лучшего
while (Scan != -1 && RawSpectra[Scan].RT <= MaxRT)
{
if (Settings.Default.Deconvolution) //прихватываем другие зарядовые состояния
{
First = FindMatchwithCharges(Scan, MZ, Charge, LowMZ, HighMZ);
}
else
{
First = FindMatch(Scan, MZ, Charge);
}
//если не найден сам пик или его первый изотоп - сбрасываем
if (First.Score == 0.0 || First.SecondIsotope == 0.0)
{
Scan = IndexDir[Scan];
continue;
}
FirstIso = First.FirstIsotope +
(First.UpperCharges == null ? 0 : First.UpperCharges.FirstIsotope) +
(First.LowerCharges == null ? 0 : First.LowerCharges.FirstIsotope);
SecondIso = First.SecondIsotope +
(First.UpperCharges == null ? 0 : First.UpperCharges.SecondIsotope) +
(First.LowerCharges == null ? 0 : First.LowerCharges.SecondIsotope);
fs = SecondIso / FirstIso;
double CurrentScore = First.Score +
(First.UpperCharges == null ? 0 : First.UpperCharges.Score) +
(First.LowerCharges == null ? 0 : First.LowerCharges.Score);
//пик может распространяться за границы, но апекс должен быть внутри
if (CurrentScore > BestScore && fs > IsoRatio * 0.5 && fs < IsoRatio * 2)
{
BestScore = CurrentScore;
BestIndex = Scan;
Best = First;
}
//переходим к следующему full-ms
Scan = IndexDir[Scan];
}
if (BestScore == 0.0)
{
return(null);
}
//если хоть что-то нашли
//добавляем наибольшее
LowMZ = (Best.MZ * Charge + (float)1.007277) / (Charge + 1);
if (Charge > 1)
{
HighMZ = (MZ * Charge - 1.007277) / (Charge - 1);
}
else
{
HighMZ = 0.0;
}
Res.ApexRT = Best.RT;
Res.MSMatches.Add(Best);
//берем сплошную область вокруг Best - вперед
for (Scan = IndexDir[BestIndex]; Scan > 0; Scan = IndexDir[Scan])
{
if (Settings.Default.Deconvolution) //прихватываем другие зарядовые состояния
{
First = FindMatchwithCharges(Scan, Best.MZ, Charge, LowMZ, HighMZ);
}
else
{
First = FindMatch(Scan, Best.MZ, Charge);
}
if (First.Score == 0.0 || First.SecondIsotope == 0.0)
{
Res.MSMatches.Add(First);
break;
}
fs = First.SecondIsotope / First.FirstIsotope;
//включаем здесь контроль по соотношению изотопов
//if (fs < IsoRatio*0.5 || fs > IsoRatio * 2 ){
// break;
//}
Res.MSMatches.Add(First);
}
//берем сплошную область вокруг Best - назад
for (Scan = IndexRev[BestIndex]; Scan > 0; Scan = IndexRev[Scan])
{
if (Settings.Default.Deconvolution) //прихватываем другие зарядовые состояния
{
First = FindMatchwithCharges(Scan, Best.MZ, Charge, LowMZ, HighMZ);
}
else
{
First = FindMatch(Scan, Best.MZ, Charge);
}
if (First.Score == 0.0 || First.SecondIsotope == 0.0)
{
Res.MSMatches.Add(First);
break;
}
fs = First.SecondIsotope / First.FirstIsotope;
//включаем здесь контроль по соотношению изотопов
//if (fs < IsoRatio*0.5 || fs > IsoRatio * 2 ){
// break;
//}
Res.MSMatches.Insert(0, First);
}
Res.Estimate(IsoRatio);
Res.CleanUp();
return(Res);
}
/// <summary>
/// Remove a section from the PE file.
/// </summary>
/// <param name="name">Name of the section to remove.</param>
/// <param name="removeContent">Flag if the content should be removed or only the section header entry.</param>
public void RemoveSection(string name, bool removeContent = true)
{
var sectionToRemove = ImageSectionHeaders.First(s => s.Name == name);
// Remove section from list of sections
var newSections = ImageSectionHeaders.Where(s => s.Name != name).ToArray();
// Change number of sections in the file header
ImageNtHeaders !.FileHeader.NumberOfSections--;
if (removeContent)
{
// Reloc the physical address of all sections
foreach (var s in newSections)
{
if (s.PointerToRawData > sectionToRemove.PointerToRawData)
{
s.PointerToRawData -= sectionToRemove.SizeOfRawData;
}
}
// Remove section content
RawFile.RemoveRange(sectionToRemove.PointerToRawData, sectionToRemove.SizeOfRawData);
}
// Fix virtual size
for (var i = 1; i < newSections.Count(); i++)
{
if (newSections[i - 1].VirtualAddress < sectionToRemove.VirtualAddress)
{
newSections[i - 1].VirtualSize = newSections[i].VirtualAddress - newSections[i - 1].VirtualAddress;
}
}
// Replace old section headers with new section headers
var sectionHeaderOffset = ImageDosHeader !.E_lfanew + ImageNtHeaders !.FileHeader.SizeOfOptionalHeader + 0x18;
var sizeOfSection = 0x28;
var newRawSections = new byte[newSections.Count() * sizeOfSection];
for (var i = 0; i < newSections.Count(); i++)
{
Array.Copy(newSections[i].ToArray(), 0, newRawSections, i * sizeOfSection, sizeOfSection);
}
// Null the data directory entry if any available
var de = ImageNtHeaders
.OptionalHeader
.DataDirectory
.FirstOrDefault(d => d.VirtualAddress == sectionToRemove.VirtualAddress &&
d.Size == sectionToRemove.VirtualSize);
if (de != null)
{
de.Size = 0;
de.VirtualAddress = 0;
}
// Null the old section headers
RawFile.WriteBytes(sectionHeaderOffset, new byte[ImageSectionHeaders.Count() * sizeOfSection]);
// Write the new sections headers
RawFile.WriteBytes(sectionHeaderOffset, newRawSections);
// Reparse section header
_nativeStructureParsers.ReparseSectionHeaders();
}
/// <summary>
/// Add a new section to the PE file.
/// </summary>
/// <param name="name">Name of the section to add. At max. 8 characters.</param>
/// <param name="size">Size in bytes of the new section.</param>
/// <param name="characteristics">Section characteristics.</param>
public void AddSection(string name, int size, ScnCharacteristicsType characteristics)
{
if (ImageNtHeaders is null)
{
throw new Exception("IMAGE_NT_HEADERS must not be null.");
}
if (ImageDosHeader is null)
{
throw new Exception("IMAGE_DOS_HEADER must not be null");
}
uint getNewSizeOfImage()
{
var factor = size / (double)ImageNtHeaders.OptionalHeader.SectionAlignment;
var additionalSize = (uint)Math.Ceiling(factor) * ImageNtHeaders !.OptionalHeader.SectionAlignment;
return(ImageNtHeaders.OptionalHeader.SizeOfImage + additionalSize);
}
uint getNewSecHeaderOffset()
{
var sizeOfSection = 0x28;
var x = (uint)ImageNtHeaders !.FileHeader.SizeOfOptionalHeader + 0x18;
var startOfSectionHeader = ImageDosHeader.E_lfanew + x;
return((uint)(startOfSectionHeader + (ImageNtHeaders.FileHeader.NumberOfSections * sizeOfSection)));
}
uint getNewSecVA()
{
var lastSec = ImageSectionHeaders.OrderByDescending(sh => sh.VirtualAddress).First();
var vaLastSecEnd = lastSec.VirtualAddress + lastSec.VirtualSize;
var factor = vaLastSecEnd / (double)ImageNtHeaders.OptionalHeader.SectionAlignment;
return((uint)(Math.Ceiling(factor) * ImageNtHeaders.OptionalHeader.SectionAlignment));
}
// Append new section to end of file
var paNewSec = RawFile.AppendBytes(new Byte[size]);
// Add new entry in section table
var newSection = new ImageSectionHeader(RawFile, getNewSecHeaderOffset(), ImageNtHeaders.OptionalHeader.ImageBase)
{
Name = name,
VirtualSize = (uint)size,
VirtualAddress = getNewSecVA(),
SizeOfRawData = (uint)size,
PointerToRawData = (uint)paNewSec,
PointerToRelocations = 0,
PointerToLinenumbers = 0,
NumberOfRelocations = 0,
NumberOfLinenumbers = 0,
Characteristics = characteristics
};
// Increase number of sections
ImageNtHeaders.FileHeader.NumberOfSections = (ushort)(ImageNtHeaders.FileHeader.NumberOfSections + 1);
// Adjust image size by image alignment
ImageNtHeaders.OptionalHeader.SizeOfImage = getNewSizeOfImage();
// Reparse section headers
_nativeStructureParsers.ReparseSectionHeaders();
}
public async Task <int> Add(
string title,
string autenticatedUserId,
string description,
bool isPrivate,
RawFile rawImage,
IEnumerable <Tag> imageTags = null,
IEnumerable <Album> imageAlbums = null)
{
var currentUser = this.Users
.All()
.FirstOrDefault(u => u.Id == autenticatedUserId && u.IsDeleted == false);
if (currentUser == null)
{
return(GlobalConstants.ItemNotFoundReturnValue);
}
var newImageInfo = new ImageInfo()
{
OriginalName = rawImage.OriginalFileName,
OriginalExtension = rawImage.FileExtension,
};
var newImage = new Image()
{
Title = title,
Author = currentUser,
Description = description,
IsPrivate = isPrivate,
UploadedOn = DateTime.Now,
ImageInfo = newImageInfo,
};
var guid = Guid.NewGuid().ToString();
newImage.Url = await this.webSrorageService
.UploadImageToCloud(
rawImage.Content,
guid,
rawImage.FileExtension,
currentUser.Id);
newImage.ThumbnailUrl = await this.webSrorageService
.UploadImageToCloud(
rawImage.PreviewContent,
guid + ThumbnailExtension,
rawImage.FileExtension,
currentUser.Id);
if (imageTags != null)
{
imageTags.ForEach(t =>
{
newImage.Tags.Add(t);
});
}
if (imageAlbums != null)
{
imageAlbums.ForEach(a =>
{
newImage.Albums.Add(a);
});
}
try
{
this.images.Add(newImage);
await this.images.SaveChangesAsync();
}
catch (Exception e)
{
var er = e.Message;
}
try
{
string notification = string.Format("{0} added picture {1}", currentUser.UserName, title);
this.notifier.Notify(notification);
}
catch (Exception ex)
{
throw new Exception(ex.Message);
}
return(newImage.Id);
}
private void WriteFile(string filepath)
{
onStartingFile(new FilepathEventArgs(filepath));
txt_outputs = new Dictionary<string, StreamWriter>();
mgf_outputs = new Dictionary<string, StreamWriter>();
SortedDictionary<string, int> spectrum_counts = new SortedDictionary<string, int>();
SortedDictionary<string, int> dta_counts = new SortedDictionary<string, int>();
SortedDictionary<int, double> retention_times = new SortedDictionary<int, double>();
SortedDictionary<int, double> scan_filter_mzs = new SortedDictionary<int, double>();
SortedDictionary<int, double> precursor_mzs = new SortedDictionary<int, double>();
SortedDictionary<int, double> precursor_intensities = new SortedDictionary<int, double>();
SortedDictionary<int, double> precursor_denormalized_intensities = new SortedDictionary<int, double>();
SortedDictionary<int, int> precursor_charge_states = new SortedDictionary<int, int>();
SortedDictionary<int, string> precursor_fragmentation_methods = new SortedDictionary<int, string>();
SortedDictionary<int, double> elapsed_scan_times = new SortedDictionary<int, double>();
SortedDictionary<int, double> ion_injection_times = new SortedDictionary<int, double>();
SortedDictionary<int, double?> precursor_sns = new SortedDictionary<int, double?>();
SortedDictionary<int, int> precursor_peak_depths = new SortedDictionary<int, int>();
using (RawFile raw = new RawFile(filepath))
{
// Open connection to the raw file
raw.Open();
// Can generate massive background spectrum here... to remove from all the other spectra
using (StreamWriter writer = new StreamWriter(Path.Combine(outputFolder, Path.GetFileNameWithoutExtension(filepath) + ".txt")))
{
int count = 0;
foreach (Spectrum msms in raw.GetNextMSMS())
{
// Clean the spectrum
CleanSpectrum(msms);
// Write the spectrum out
WriteSpectrumToFile(writer, msms);
// Change Progress
if (count > 100)
{
count = 0;
double progress = (double)(msms.ScanNumber - raw.FirstScanNumber + 1) / (raw.LastScanNumber - raw.FirstScanNumber + 1);
onUpdateProgress(new ProgressEventArgs((int)(progress * 100)));
}
count++;
}
}
}
// for (int scan_number = first_scan_number; scan_number <= last_scan_number; scan_number++)
// {
// string scan_filter = null;
// raw.GetFilterForScanNum(scan_number, ref scan_filter);
// if (scan_filter != null && scan_filter.Contains("@"))
// {
//* retention_times.Add(scan_number, time);
//* scan_filter_mzs.Add(scan_number, precursor_mz);
// if (!no_precursor_scan)
// {
// /
// int? precursor_index = null;
// int precusor_data_index = (int)RawLabelDataColumn.MZ;
// int min = precursor_data.GetLowerBound(1);
// int max = precursor_data.GetUpperBound(1);
// for (int i = min; i <= max; i++)
// {
// if (Math.Abs(precursor_data[precusor_data_index, i] - precursor_mz) <= PEAK_IDENTIFICATION_MASS_TOLERANCE)
// {
// if (!precursor_index.HasValue || precursor_data[(int)RawLabelDataColumn.Intensity, i] > precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value])
// {
// precursor_index = i;
// }
// }
// }
// if (!precursor_index.HasValue)
// {
// for (int i = precursor_data.GetLowerBound(1); i <= precursor_data.GetUpperBound(1); i++)
// {
// if (!precursor_index.HasValue || Math.Abs(precursor_data[(int)RawLabelDataColumn.MZ, i] - precursor_mz) < Math.Abs(precursor_data[(int)RawLabelDataColumn.MZ, precursor_index.Value] - precursor_mz))
// {
// precursor_index = i;
// }
// }
// }
// if (precursor_index.HasValue)
// {
// precursor_mz = precursor_data[(int)RawLabelDataColumn.MZ, precursor_index.Value];
// precursor_mzs.Add(scan_number, precursor_mz);
// precursor_intensities.Add(scan_number, precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value]);
// object precursor_header_labels = null;
// object precursor_header_values = null;
// int precursor_array_size = -1;
// raw.GetTrailerExtraForScanNum(precursor_scan_number, ref precursor_header_labels, ref precursor_header_values, ref precursor_array_size);
// string[] precursor_header_label_strings = (string[])precursor_header_labels;
// string[] precursor_header_value_strings = (string[])precursor_header_values;
// if (precursor_header_label_strings != null && precursor_header_value_strings != null)
// {
// for (int header_i = precursor_header_label_strings.GetLowerBound(0); header_i <= precursor_header_label_strings.GetUpperBound(0); header_i++)
// {
// if (precursor_header_label_strings[header_i].StartsWith("Ion Injection Time (ms)"))
// {
// precursor_denormalized_intensities.Add(scan_number, precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value] * double.Parse(precursor_header_value_strings[header_i]) / 1000.0);
// }
// }
// }
// if (precursor_data.GetLength(0) > 2)
// {
// precursor_sns.Add(scan_number, (precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value] - precursor_data[(int)RawLabelDataColumn.NoiseBaseline, precursor_index.Value]) / precursor_data[(int)RawLabelDataColumn.NoiseLevel, precursor_index.Value]);
// }
// else
// {
// precursor_sns.Add(scan_number, null);
// }
// int peak_depth = 1;
// int precursor_data_index = (int)RawLabelDataColumn.Intensity;
// double prec_value = precursor_data[precursor_data_index, precursor_index.Value];
// min = precursor_data.GetLowerBound(1);
// max = precursor_data.GetUpperBound(1);
// for (int i = min; i <= max; i++)
// {
// if (precursor_data[precursor_data_index, i] > prec_value && i != precursor_index.Value)
// {
// peak_depth++;
// }
// }
// precursor_peak_depths.Add(scan_number, peak_depth);
// }
// }
// object header_labels = null;
// object header_values = null;
// int array_size = -1;
// raw.GetTrailerExtraForScanNum(scan_number, ref header_labels, ref header_values, ref array_size);
// string[] header_label_strings = (string[])header_labels;
// string[] header_value_strings = (string[])header_values;
// int charge = 0;
// if (header_label_strings != null && header_value_strings != null)
// {
// for (int header_i = header_label_strings.GetLowerBound(0); header_i <= header_label_strings.GetUpperBound(0); header_i++)
// {
// if (header_label_strings[header_i].StartsWith("Charge"))
// {
// charge = int.Parse(header_value_strings[header_i]);
// if (scan_filter.Contains(" - "))
// {
// charge = -charge;
// }
// precursor_charge_states.Add(scan_number, charge);
// }
// else if (header_label_strings[header_i].StartsWith("Elapsed Scan Time (sec)"))
// {
// elapsed_scan_times.Add(scan_number, double.Parse(header_value_strings[header_i]));
// }
// else if (header_label_strings[header_i].StartsWith("Ion Injection Time (ms)"))
// {
// ion_injection_times.Add(scan_number, double.Parse(header_value_strings[header_i]));
// }
// }
// }
// object labels = null;
// object flags = null;
// raw.GetLabelData(ref labels, ref flags, ref scan_number);
// double[,] data = (double[,])labels;
// if (data.Length == 0)
// {
// double centroid_peak_width = -1.0;
// labels = null;
// flags = null;
// int mass_list_array_size = -1;
// raw.GetMassListFromScanNum(ref scan_number, null, 0, 0, 0, 1, ref centroid_peak_width, ref labels, ref flags, ref mass_list_array_size);
// data = (double[,])labels;
// }
// double total_ion_current = 0.0;
// double base_peak_mz = -1.0;
// double base_peak_intensity = -1.0;
// for (int data_i = data.GetLowerBound(1); data_i <= data.GetUpperBound(1); data_i++)
// {
// total_ion_current += data[(int)RawLabelDataColumn.Intensity, data_i];
// if (base_peak_mz < 0.0 ||
// data[(int)RawLabelDataColumn.Intensity, data_i] > base_peak_intensity)
// {
// base_peak_mz = data[(int)RawLabelDataColumn.MZ, data_i];
// base_peak_intensity = data[(int)RawLabelDataColumn.Intensity, data_i];
// }
// }
// List<int> charges = new List<int>();
// if (charge == 0 || no_precursor_scan)
// {
// for (int assumed_charge_state = minimumAssumedPrecursorChargeState; assumed_charge_state <= maximumAssumedPrecursorChargeState; assumed_charge_state++)
// {
// charges.Add(assumed_charge_state);
// }
// }
// else
// {
// charges.Add(charge);
// }
// string mass_analyzer = scan_filter.Substring(0, 4).ToUpper();
// if (!mass_analyzer.Contains("MS"))
// {
// mass_analyzer = "TQMS";
// }
// string fragmentation_method = null;
// if (groupByActivationEnergyTime)
// {
// foreach (int i in AllIndicesOf(scan_filter, '@'))
// {
// string temp_scan_filter = scan_filter.Substring(i + 1);
// temp_scan_filter = temp_scan_filter.Substring(0, temp_scan_filter.IndexOf(' '));
// fragmentation_method += temp_scan_filter.ToUpper() + '-';
// }
// }
// else
// {
// foreach (int i in AllIndicesOf(scan_filter, '@'))
// {
// fragmentation_method += scan_filter.Substring(i + 1, 3).ToUpper() + '-';
// }
// }
// fragmentation_method = fragmentation_method.Substring(0, fragmentation_method.Length - 1);
// string base_output_filename = Path.GetFileNameWithoutExtension(filepath) + '_' + mass_analyzer + '_' + fragmentation_method;
// precursor_fragmentation_methods.Add(scan_number, fragmentation_method);
// if (!spectrum_counts.ContainsKey(mass_analyzer))
// {
// spectrum_counts.Add(mass_analyzer, 0);
// }
// spectrum_counts[mass_analyzer]++;
// if (!dta_counts.ContainsKey(mass_analyzer))
// {
// dta_counts.Add(mass_analyzer, 0);
// }
// dta_counts[mass_analyzer] += charges.Count;
// if (!spectrum_counts.ContainsKey(fragmentation_method))
// {
// spectrum_counts.Add(fragmentation_method, 0);
// }
// spectrum_counts[fragmentation_method]++;
// if (!dta_counts.ContainsKey(fragmentation_method))
// {
// dta_counts.Add(fragmentation_method, 0);
// }
// dta_counts[fragmentation_method] += charges.Count;
// if (!spectrum_counts.ContainsKey(mass_analyzer + ' ' + fragmentation_method))
// {
// spectrum_counts.Add(mass_analyzer + ' ' + fragmentation_method, 0);
// }
// spectrum_counts[mass_analyzer + ' ' + fragmentation_method]++;
// if (!dta_counts.ContainsKey(mass_analyzer + ' ' + fragmentation_method))
// {
// dta_counts.Add(mass_analyzer + ' ' + fragmentation_method, 0);
// }
// dta_counts[mass_analyzer + ' ' + fragmentation_method] += charges.Count;
// if (sequestDtaOutput || omssaTxtOutput || mascotMgfOutput)
// {
// List<MSPeak> all_peaks = new List<MSPeak>();
// for (int data_i = data.GetLowerBound(1); data_i <= data.GetUpperBound(1); data_i++)
// {
// double mz = data[(int)RawLabelDataColumn.MZ, data_i];
// all_peaks.Add(new MSPeak(mz, data[(int)RawLabelDataColumn.Intensity, data_i]));
// }
// foreach (int charge_i in charges)
// {
// double retention_time_min = double.NaN;
// raw.RTFromScanNum(scan_number, ref retention_time_min);
// double retention_time_s = retention_time_min * 60;
// string dta_filepath = Path.GetFileNameWithoutExtension(filepath) +
// '.' + mass_analyzer + '.' + fragmentation_method +
// '.' + scan_number.ToString() + '.' +
// scan_number.ToString() + '.' +
// charge_i.ToString() + '.' +
// "RT_" + retention_time_min.ToString("0.000") + "_min_" + retention_time_s.ToString("0.0") + "_s" +
// ".dta";
// double precursor_mass = MassFromMZ(precursor_mz, charge_i);
// StringBuilder dta_content_sb = new StringBuilder();
// StringBuilder mgf_content_sb = new StringBuilder();
// dta_content_sb.AppendLine((precursor_mass + PROTON_MASS).ToString("0.00000") + ' ' + charge_i.ToString());
// mgf_content_sb.AppendLine("BEGIN IONS");
// mgf_content_sb.AppendLine("Title=" + Path.GetFileNameWithoutExtension(dta_filepath));
// mgf_content_sb.AppendLine("SCANS=" + scan_number.ToString());
// mgf_content_sb.AppendLine("RTINSECONDS=" + retention_time_s.ToString());
// mgf_content_sb.AppendLine("PEPMASS=" + precursor_mz.ToString("0.00000"));
// mgf_content_sb.AppendLine("CHARGE=" + charge_i.ToString("0+;0-"));
// List<MSPeak> peaks = new List<MSPeak>(all_peaks);
// bool isHCD = fragmentation_method.StartsWith("HCD");
// bool isETD = fragmentation_method.StartsWith("ETD") || fragmentation_method.StartsWith("ECD");
// // FOR AARON
//#if Aaron_Experiment
// isETD = isETD || scan_filter.Contains("hcd0.5") || scan_filter.Contains("hcd1.5");
//#endif
// //
// if (neutralLossesIncluded)
// {
// List<KeyValuePair<double, double>> mzs = new List<KeyValuePair<double, double>>();
// foreach (double nl_mass in this.neutralLosses)
// {
// double mz = precursor_mz - MZFromMass(nl_mass, charge_i);
// double min = mz - LOW_PRECURSOR_CLEANING_WINDOW_MZ;
// double max = mz + HIGH_PRECURSOR_CLEANING_WINDOW_MZ;
// mzs.Add(new KeyValuePair<double, double>(min, max));
// }
// int p = 0;
// while (p < peaks.Count)
// {
// double mz = peaks[p].MZ;
// if (mz >= precursor_mz)
// {
// break;
// }
// bool removed = false;
// foreach (KeyValuePair<double, double> minmax in mzs)
// {
// if (mz >= minmax.Key && mz <= minmax.Value)
// {
// peaks.RemoveAt(p);
// removed = true;
// break;
// }
// }
// if (!removed)
// {
// p++;
// }
// }
// }
// // ETD pre-processing
// if (enableEtdPreProcessing && isETD)
// {
// // negative ETD
// if (scan_filter.Contains(" - "))
// {
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// bool clean = false;
// for (int reduced_precursor_charge = -2; reduced_precursor_charge >= charge_i + 1; reduced_precursor_charge--)
// {
// if (mz >= MZFromMass(precursor_mass - NETD_LOW_NEUTRAL_LOSS_CLEANING_WINDOW_DA, reduced_precursor_charge) &&
// mz <= MZFromMass(precursor_mass + NETD_HIGH_NEUTRAL_LOSS_CLEANING_WINDOW_DA, reduced_precursor_charge))
// {
// clean = true;
// break;
// }
// if (mz >= MZFromMass(precursor_mass + NETD_ADDUCT_CLEANING_WINDOW_DA, reduced_precursor_charge) - NETD_ADDUCT_LOW_CLEANING_WINDOW_MZ &&
// mz <= MZFromMass(precursor_mass + NETD_ADDUCT_CLEANING_WINDOW_DA, reduced_precursor_charge) + NETD_ADDUCT_LOW_CLEANING_WINDOW_MZ)
// {
// clean = true;
// break;
// }
// }
// if (!clean)
// {
// if (mz >= MZFromMass(precursor_mass, -1) - NETD_SINGLY_CHARGED_LOW_NEUTRAL_LOSS_CLEANING_WINDOW_MZ)
// {
// clean = true;
// }
// }
// if (clean)
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// // positive ETD
// else
// {
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// bool clean = false;
// for (int reduced_precursor_charge = 1; reduced_precursor_charge <= charge_i - 1; reduced_precursor_charge++)
// {
// if (mz >= MZFromMass(precursor_mass - LOW_NEUTRAL_LOSS_CLEANING_WINDOW_DA, reduced_precursor_charge) &&
// mz < MZFromMass(precursor_mass, reduced_precursor_charge) + HIGH_PRECURSOR_CLEANING_WINDOW_MZ)
// {
// clean = true;
// break;
// }
// }
// if (clean)
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// // TMT duplex cleaning
// if (cleanTmtDuplex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_duplex_tag_cleaning_mz = precursor_mz * reduced_charge_i - TMT_DUPLEX_CAD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_DUPLEX_CAD_REPORTER_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_DUPLEX_CAD_REPORTER_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_DUPLEX_CAD_TAG_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_DUPLEX_CAD_TAG_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_duplex_tag_cleaning_mz - TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_duplex_tag_cleaning_mz + TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// else if (fragmentation_method.StartsWith("ETD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_duplex_reporter_loss_cleaning_mz = precursor_mz * charge_i - TMT_DUPLEX_ETD_REPORTER_LOSS_DA / reduced_charge_i;
// double precursor_tmt_duplex_tag_loss_cleaning_mz = precursor_mz * charge_i - TMT_DUPLEX_ETD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_DUPLEX_ETD_REPORTER_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_DUPLEX_ETD_REPORTER_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_DUPLEX_ETD_TAG_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_DUPLEX_ETD_TAG_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_duplex_reporter_loss_cleaning_mz - TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_duplex_reporter_loss_cleaning_mz + TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_duplex_tag_loss_cleaning_mz - TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_duplex_tag_loss_cleaning_mz + TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// }
// // iTRAQ 4-plex cleaning
// if (cleanItraq4Plex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// double precursor_itraq_4plex_tag_cleaning_mz = precursor_mz * charge_i - ITRAQ_4PLEX_CAD_TAG_LOSS_DA;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_ITRAQ_4PLEX_CAD_REPORTER_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_ITRAQ_4PLEX_CAD_REPORTER_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= ITRAQ_4PLEX_CAD_TAG_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= ITRAQ_4PLEX_CAD_TAG_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_tag_cleaning_mz - ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_tag_cleaning_mz + ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// else if (fragmentation_method.StartsWith("ETD"))
// {
// double precursor_itraq_4plex_reporter_loss_cleaning_mz = precursor_mz * charge_i - ITRAQ_4PLEX_ETD_REPORTER_LOSS_DA;
// double precursor_itraq_4plex_tag_loss_cleaning_mz = precursor_mz * charge_i - ITRAQ_4PLEX_ETD_TAG_LOSS_DA;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_ITRAQ_4PLEX_ETD_REPORTER_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_ITRAQ_4PLEX_ETD_REPORTER_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= ITRAQ_4PLEX_ETD_TAG_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= ITRAQ_4PLEX_ETD_TAG_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_reporter_loss_cleaning_mz - ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_reporter_loss_cleaning_mz + ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_tag_loss_cleaning_mz - ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_tag_loss_cleaning_mz + ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// // TMT 6-plex cleaning
// if (cleanTmt6Plex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_6plex_tag_cleaning_mz = precursor_mz * reduced_charge_i - TMT_6PLEX_CAD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_6PLEX_CAD_REPORTER_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_6PLEX_CAD_REPORTER_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_6PLEX_CAD_TAG_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_6PLEX_CAD_TAG_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_6plex_tag_cleaning_mz - TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_6plex_tag_cleaning_mz + TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// else if (fragmentation_method.StartsWith("ETD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_6plex_reporter_loss_cleaning_mz = precursor_mz * charge_i - TMT_6PLEX_ETD_REPORTER_LOSS_DA / reduced_charge_i;
// double precursor_tmt_6plex_tag_loss_cleaning_mz = precursor_mz * charge_i - TMT_6PLEX_ETD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_6PLEX_ETD_REPORTER_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_6PLEX_ETD_REPORTER_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_6PLEX_ETD_TAG_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_6PLEX_ETD_TAG_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_6plex_reporter_loss_cleaning_mz - TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_6plex_reporter_loss_cleaning_mz + TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_6plex_tag_loss_cleaning_mz - TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_6plex_tag_loss_cleaning_mz + TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// }
// // iTRAQ 8-plex cleaning
// if (cleanItraq8Plex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// double precursor_itraq_4plex_tag_cleaning_mz = precursor_mz * charge_i - ITRAQ_8PLEX_CAD_TAG_LOSS_DA;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_ITRAQ_8PLEX_CAD_REPORTER_MZ - ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_ITRAQ_8PLEX_CAD_REPORTER_MZ + ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= ITRAQ_8PLEX_CAD_TAG_MZ - ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= ITRAQ_8PLEX_CAD_TAG_MZ + ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_tag_cleaning_mz - ITRAQ_8PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_tag_cleaning_mz + ITRAQ_8PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// MSPeak base_peak = null;
// foreach (MSPeak peak in peaks)
// {
// if (base_peak == null || peak.Intensity > base_peak.Intensity)
// {
// base_peak = peak;
// }
// }
// //if (omssaTxtOutput)
// //{
// //foreach (MSPeak peak in peaks)
// //{
// // dta_content_sb.AppendFormat(" {0:0.00000} {1:0.000}", peak.MZ, peak.Intensity).AppendLine();
// //dta_content_sb.AppendLine(string.Format(" {0:0.00000} {1:0.00}", peak.MZ, peak.Intensity));
// //}
// //}
// if (mascotMgfOutput)
// {
// foreach (MSPeak peak in peaks)
// {
// mgf_content_sb.AppendLine(string.Format("{0:0.00000} {1:0.00}", peak.MZ, peak.Intensity));
// }
// }
// if (sequestDtaOutput)
// {
// StreamWriter dta = new StreamWriter(Path.Combine(outputFolder, dta_filepath));
// if (dta_content_sb.Length > 0)
// {
// dta.Write(dta_content_sb.ToString());
// }
// dta.Close();
// }
// if (omssaTxtOutput)
// {
// string txt_filepath = Path.Combine(outputFolder,
// base_output_filename + ".txt");
// if (!txt_outputs.ContainsKey(txt_filepath))
// {
// txt_outputs.Add(txt_filepath, new StreamWriter(txt_filepath));
// }
// StreamWriter txt = txt_outputs[txt_filepath];
// txt.WriteLine("<dta id=\"" + scan_number.ToString() + "\" name=\"" + dta_filepath + "\">");
// txt.WriteLine();
// foreach (MSPeak peak in peaks)
// {
// txt.WriteLine(" {0:0.00000} {1:0.000}", peak.MZ, peak.Intensity);
// // dta_content_sb.AppendFormat(" {0:0.00000} {1:0.000}", peak.MZ, peak.Intensity).AppendLine();
// //dta_content_sb.AppendLine(string.Format(" {0:0.00000} {1:0.00}", peak.MZ, peak.Intensity));
// }
// // if(dta_content_sb.Length > 0)
// // {
// // txt.Write(dta_content_sb.ToString());
// // }
// txt.WriteLine();
// txt.WriteLine();
// }
// if (mascotMgfOutput)
// {
// string mgf_filepath = Path.Combine(outputFolder,
// base_output_filename + ".mgf");
// if (!mgf_outputs.ContainsKey(mgf_filepath))
// {
// mgf_outputs.Add(mgf_filepath, new StreamWriter(mgf_filepath));
// }
// StreamWriter mgf = mgf_outputs[mgf_filepath];
// if (mgf_content_sb.Length > 0)
// {
// mgf.Write(mgf_content_sb.ToString());
// }
// mgf.WriteLine("END IONS");
// mgf.WriteLine();
// }
// }
// }
// }
// // Perform update progress every 100 scans so not to slow down with all the callbacks
// if (scan_number % 100 == 0)
// {
// double progress = (double)(scan_number - first_scan_number + 1) / (last_scan_number - first_scan_number + 1);
// onUpdateProgress(new ProgressEventArgs((int)(progress * 100)));
// }
//}
//raw.Close();
//if (txt_outputs != null)
//{
// foreach (StreamWriter sw in txt_outputs.Values)
// {
// if (sw != null)
// {
// sw.Close();
// }
// }
//}
//if (mgf_outputs != null)
//{
// foreach (StreamWriter sw in mgf_outputs.Values)
// {
// if (sw != null)
// {
// sw.Close();
// }
// }
//}
//using (StreamWriter log = new StreamWriter(Path.Combine(LogFolder, Path.GetFileNameWithoutExtension(filepath) + "_log.txt")))
//{
// log.WriteLine("DTA Generator PARAMETERS");
// log.WriteLine("Assumed Precursor Charge State Range: " + minimumAssumedPrecursorChargeState.ToString() + '-' + maximumAssumedPrecursorChargeState.ToString());
// log.WriteLine("Clean Precursor: " + cleanPrecursor.ToString());
// log.WriteLine("Enable ETD Pre-Processing: " + enableEtdPreProcessing.ToString());
// log.WriteLine("Clean TMT Duplex: " + cleanTmtDuplex.ToString());
// log.WriteLine("Clean iTRAQ 4-Plex: " + cleanItraq4Plex.ToString());
// log.WriteLine("Clean TMT 6-Plex: " + cleanTmt6Plex.ToString());
// log.WriteLine("Clean iTRAQ 8-Plex: " + cleanItraq8Plex.ToString());
// log.WriteLine();
// log.WriteLine("Spectrum Type\tNumber of Scans");
// foreach (KeyValuePair<string, int> kvp in spectrum_counts)
// {
// log.WriteLine(kvp.Key + '\t' + kvp.Value.ToString());
// }
// log.WriteLine();
// log.WriteLine("Spectrum Type\tNumber of DTAs");
// foreach (KeyValuePair<string, int> kvp in dta_counts)
// {
// log.WriteLine(kvp.Key + '\t' + kvp.Value.ToString());
// }
// log.WriteLine();
// double? min_elapsed = null;
// double? max_elapsed = null;
// double mean_elapsed = 0.0;
// foreach (double elapsed_scan_time in elapsed_scan_times.Values)
// {
// if (!min_elapsed.HasValue || elapsed_scan_time < min_elapsed)
// {
// min_elapsed = elapsed_scan_time;
// }
// if (!max_elapsed.HasValue || elapsed_scan_time > max_elapsed)
// {
// max_elapsed = elapsed_scan_time;
// }
// mean_elapsed += elapsed_scan_time;
// }
// mean_elapsed /= elapsed_scan_times.Count;
// if (min_elapsed.HasValue)
// {
// log.WriteLine("Minimum Fragmentation Elapsed Scan Time (sec): " + min_elapsed.Value.ToString());
// }
// if (max_elapsed.HasValue)
// {
// log.WriteLine("Maximum Fragmentation Elapsed Scan Time (sec): " + max_elapsed.Value.ToString());
// }
// if (!Double.IsNaN(mean_elapsed))
// {
// log.WriteLine("Average Fragmentation Elapsed Scan Time (sec): " + mean_elapsed.ToString());
// }
// log.WriteLine();
// double? min_injection = null;
// double? max_injection = null;
// double mean_injection = 0.0;
// foreach (double ion_injection_time in ion_injection_times.Values)
// {
// if (!min_injection.HasValue || ion_injection_time < min_injection)
// {
// min_injection = ion_injection_time;
// }
// if (!max_injection.HasValue || ion_injection_time > max_injection)
// {
// max_injection = ion_injection_time;
// }
// mean_injection += ion_injection_time;
// }
// mean_injection /= ion_injection_times.Count;
// if (min_injection.HasValue)
// {
// log.WriteLine("Minimum Fragmentation Ion Injection Time (msec): " + min_injection.Value.ToString());
// }
// if (max_injection.HasValue)
// {
// log.WriteLine("Maximum Fragmentation Ion Injection Time (msec): " + max_injection.Value.ToString());
// }
// if (!Double.IsNaN(mean_injection))
// {
// log.WriteLine("Average Fragmentation Ion Injection Time (msec): " + mean_injection.ToString());
// }
// log.WriteLine();
// log.WriteLine("Fragmentation Scan Summary");
// log.Write("Fragmentation Scan Number\t");
// log.Write("Retention Time (min.)\t");
// log.Write("Scan Filter m/z\t");
// log.Write("Precursor m/z\t");
// log.Write("Precursor Intensity\t");
// log.Write("Precursor Denormalized Intensity\t");
// log.Write("Precursor Charge State\t");
// log.Write("Precursor S/N Ratio\t");
// log.Write("Precursor Peak Depth\t");
// log.Write("Fragmentation Method\t");
// log.Write("Elapsed Scan Time (sec)\t");
// log.Write("Ion Injection Time (msec)");
// log.WriteLine();
// foreach (int sn2 in retention_times.Keys)
// {
// log.Write(sn2.ToString() + '\t');
// log.Write(retention_times[sn2].ToString("0.00") + '\t');
// log.Write(scan_filter_mzs[sn2].ToString("0.00") + '\t');
// log.Write((precursor_mzs.ContainsKey(sn2) ? precursor_mzs[sn2].ToString("0.00000") : "n/a") + '\t');
// log.Write((precursor_intensities.ContainsKey(sn2) ? precursor_intensities[sn2].ToString("0.0") : "n/a") + '\t');
// log.Write((precursor_denormalized_intensities.ContainsKey(sn2) ? precursor_denormalized_intensities[sn2].ToString("0.0") : "n/a") + '\t');
// log.Write((precursor_charge_states.ContainsKey(sn2) ? precursor_charge_states[sn2].ToString() : "n/a") + '\t');
// log.Write((precursor_sns.ContainsKey(sn2) && precursor_sns[sn2].HasValue ? precursor_sns[sn2].Value.ToString() : "n/a") + '\t');
// log.Write((precursor_peak_depths.ContainsKey(sn2) ? precursor_peak_depths[sn2].ToString() : "n/a") + '\t');
// log.Write((precursor_fragmentation_methods.ContainsKey(sn2) ? precursor_fragmentation_methods[sn2] : "n/a") + '\t');
// log.Write((elapsed_scan_times.ContainsKey(sn2) ? elapsed_scan_times[sn2].ToString() : "n/a") + '\t');
// log.Write((ion_injection_times.ContainsKey(sn2) ? ion_injection_times[sn2].ToString() : "n/a") + '\t');
// log.WriteLine();
// }
//}
onFinishedFile(new FilepathEventArgs(filepath));
}
public ValueOrError<Ticker> Read(RawFile rawTicker)
{
return executor.SafeExecute<Ticker>(engine => engine.GetVariable("Read")(rawTicker));
}
static double MZError = 10; //ppm
static int Main(string[] args)
{
//Параметры соответствуют вводу в форму RawtoMGF
//args[0] - имя Raw-файла
//args[1] - имя MGF-файла
//args[2] - minimal MZ
//args[3] - maximal MZ
//args[4] - minimal RT
//args[5] - maximal RT
//args[6] - minimal Charge
//args[7] - maximal Charge
//args[8] - number of top peaks
//args[9] - CleanETD:yes / CleanETD:no
//args[10] - Instrument:yes / Instrument:no
//дополнительно (к версии 2.0.6)
//args[11] - CheckSpectra:yes / CheckSpectra:no
try{
Console.ReadLine();
//Thread.Sleep(30000);
string InFileName = args[0];
string OutFileName = args[1];
double MinMZ = Convert.ToDouble(args[2]);
double MaxMZ = Convert.ToDouble(args[3]);
double MinRT = Convert.ToDouble(args[4]);
double MaxRT = Convert.ToDouble(args[5]);
int MinCharge = Convert.ToInt32(args[6]);
int MaxCharge = Convert.ToInt32(args[7]);
int MaxPeakNumber = Convert.ToInt32(args[8]);
bool CleanETD = args[9].Contains("CleanETD:yes");
bool MarkInstrtument = args[10].Contains("Instrument:yes");
bool CheckSpectra = args[11].Contains("CheckSpectra:yes");
bool RTApex = args[12].Contains("RTApex:yes");
string[] Refs = { "@cid", "@hcd", "@etd", "@ecd", "FTMS", "ITMS" };
MSFileReader_XRawfile RawFile;
int Spectra, LocalCount = 0;
string Filter;
MGFFile MGF;
MGFSpectrum ms;
Childs ch;
ChildbyIntensity ci = new ChildbyIntensity();
ChildbyMass cm = new ChildbyMass();
int ArraySize = 0;
Object MassList, EmptyRef;
Object Labels, Values;
double temp = 0.0;
int Progress = 0;
int MSCount = 0;
int MSMSCount = 0;
if (RTApex)
{
MSFileBox = new RawFileBox();
MSFileBox.LoadIndex(InFileName);
RawFileBox.RepProgress = RepProgress;
RawFile = MSFileBox.RawFile;
}
else
{
RawFile = new MSFileReader_XRawfile();
RawFile.Open(InFileName);
RawFile.SetCurrentController(0, 1);
}
Spectra = 0;
RawFile.GetNumSpectra(ref Spectra);
if (Spectra == 0)
{
throw new Exception("Cannot get spectra from the file " + InFileName + ", File is invalid, broken or empty");
}
MGF = new MGFFile();
for (int j = 1; j <= Spectra; j++)
{
Filter = null;
RawFile.GetFilterForScanNum(j, ref Filter);
if (Filter.IndexOf("ms2") == -1)
{
MSCount++;
if (!CheckSpectra)
{
continue;
}
else
{
ArraySize = 0;
MassList = null;
EmptyRef = null;
temp = 0.0;
try {
RawFile.GetMassListFromScanNum(ref j, null, 0, 0, 0, 0,
ref temp, ref MassList, ref EmptyRef, ref ArraySize);
continue;
}catch {
Exception e = new Exception(string.Format("Scan #{0} cannot be loaded, probably RAW file is corrupted!", j));
throw e;
}
}
}
MSMSCount++;
ms = new MGFSpectrum();
//определяем родительскую массу, заряд и RT
Labels = null;
Values = null;
ArraySize = 0;
LocalCount++;
RawFile.GetTrailerExtraForScanNum(j, ref Labels, ref Values, ref ArraySize);
for (int k = 0; k < ArraySize; k++)
{
if ((Labels as Array).GetValue(k).ToString().Contains("Mono"))
{
ms.mz = Convert.ToDouble((Values as Array).GetValue(k).ToString());
}
if ((Labels as Array).GetValue(k).ToString().Contains("Charge State"))
{
ms.Charge = Convert.ToInt32((Values as Array).GetValue(k).ToString());
}
}
//Если не нашли в labels - берем из фильтра
if (ms.mz == 0.0)
{
string part = Filter.Substring(0, Filter.IndexOf('@'));
ms.mz = Convert.ToDouble(part.Substring(part.LastIndexOf(' ')));
}
Labels = null;
Values = null;
ArraySize = 0;
double RT = 0;
RawFile.GetStatusLogForScanNum(j, ref RT, ref Labels, ref Values, ref ArraySize);
RawFile.RTFromScanNum(j, ref ms.RT);
ms.ScanNumber = j;
//Фильтры
if (ms.Charge < MinCharge)
{
continue;
}
if (ms.Charge > MaxCharge)
{
continue;
}
if (ms.RT < MinRT)
{
continue;
}
if (MaxRT != 0.0 && ms.RT > MaxRT)
{
continue;
}
if (ms.mz < MinMZ)
{
continue;
}
if (MaxMZ != 0.0 && ms.mz > MaxMZ)
{
continue;
}
//забираем сам спектр
MassList = null;
EmptyRef = null;
ArraySize = 0;
temp = 0.0;
try{
if (Filter.IndexOf("FTMS") != -1)
{
//извлекаем FTMS данные
(RawFile as IXRawfile2).GetLabelData(ref MassList, ref EmptyRef, ref j);
ArraySize = (MassList as Array).GetLength(1);
for (int k = 0; k < ArraySize; k++)
{
ch = new Childs();
ch.Mass = (double)(MassList as Array).GetValue(0, k);
ch.Intensity = (double)(MassList as Array).GetValue(1, k);
ms.Data.Add(ch);
}
}
else
{
//извлекаем ITMS данные
RawFile.GetMassListFromScanNum(ref j, null, 0, 0, 0, 1, ref temp, ref MassList, ref EmptyRef, ref ArraySize);
ArraySize = (MassList as Array).GetLength(1);
for (int k = 0; k < ArraySize; k++)
{
ch = new Childs();
ch.Mass = (double)(MassList as Array).GetValue(0, k);
ch.Intensity = (double)(MassList as Array).GetValue(1, k);
ms.Data.Add(ch);
}
}
}catch {
Exception e = new Exception(string.Format("Scan #{0} cannot be loaded, probably RAW file is corrupted!", j));
throw e;
}
if (RTApex)
{
ms.RTApex = CheckRTApex(ms.RT, ms.mz);
}
if (MarkInstrtument)
{
if (Filter.Contains("ecd") || Filter.Contains("etd"))
{
ms.Instrument = "ETD-TRAP";
}
else
{
ms.Instrument = "ESI-FTICR";
}
}
//очистить ETD если был такой запрос
if (CleanETD)
{
if (Filter.Contains("ecd") || Filter.Contains("etd"))
{
FilterETD(ref ms, Filter.Contains("FTMS"));
}
}
//сбросить лишние сигналы
if (MaxPeakNumber > 0 && ms.Data.Count > MaxPeakNumber)
{
ms.Data.Sort(ci);
ms.Data.RemoveRange(0, ms.Data.Count - MaxPeakNumber);
ms.Data.Sort(cm);
}
//сформировать TITLE
if (RTApex)
{
ms.Title = String.Format("Elution from: {0:f4} to {0:f4} RT Apex: {1:f2} FinneganScanNumber: {2}",
ms.RT, ms.RTApex, ms.ScanNumber);
}
else
{
ms.Title = String.Format("Elution from: {0:f4} to {0:f4} FinneganScanNumber: {1}",
ms.RT, ms.ScanNumber);
}
MGF.Spectra.Add(ms);
// рапортовать прогресс
GC.Collect(2);
if ((int)(((double)j / (double)Spectra) * 100.0) > Progress)
{
Progress = (int)(((double)j / (double)Spectra) * 100.0);
Console.WriteLine("{0}%... {1} {2}", Progress, MSCount, MSMSCount);
}
//backgroundWorker1.ReportProgress((int)(((double)LocalCount/(double)SpCount)*100.0));
}
MGF.MGFComments.Add(String.Format("Created by RawToMGF 2.1.3; Spectra obtained from {0}", InFileName));
MGF.MGFComments.Add(String.Format("Filters: Parent m/z from {0} Th to {1} Th;", MinMZ, MaxMZ));
MGF.MGFComments.Add(String.Format(" RT from {0} min. to {1} min.;", MinRT, MaxRT));
MGF.MGFComments.Add(String.Format(" Charge state of parent ions minimum {0}, maximum {1};", MinCharge, MaxCharge));
MGF.MGFComments.Add(String.Format(" Max number of peaks in MS/MS spectra - {0}", MaxPeakNumber));
if (CleanETD)
{
MGF.MGFComments.Add(" ETD spectra cleaned from precursors and neutral losses");
}
MGF.MGFWrite(OutFileName, true);
}catch (Exception e) {
Console.Write("Error:");
Console.Write(e.Message);
Console.WriteLine("STACKINFO:" + e.StackTrace);
//Console.ReadKey();
return(1);
}
Console.WriteLine("Completed");
Console.ReadLine();
return(0);
}
public static void Contruct(string typeName, RawFile reader)
{
var t = Type.GetType(typeName);
}
public void addFile(int index, RawFile toAdd)
{
throw new NotImplementedException();
}
/// <summary>
/// Add imports to the PE file.
/// </summary>
/// <param name="additionalImports">List with additional imports.</param>
public void AddImports(List <AdditionalImport> additionalImports)
{
if (ImageNtHeaders is null || ImageSectionHeaders is null || _dataDirectoryParsers is null)
{
throw new Exception("NT Headers, Section Headers and Data Directory must not be null.");
}
const int sizeOfImpDesc = 0x14;
var sizeOfThunkData = Is32Bit ? 4 : 8;
var numAddImpDescs = additionalImports.Count;
var importRva = ImageNtHeaders.OptionalHeader.DataDirectory[(int)DataDirectoryType.Import].VirtualAddress;
var importSize = ImageNtHeaders.OptionalHeader.DataDirectory[(int)DataDirectoryType.Import].Size;
ImageSectionHeader GetImportSection()
=> ImageSectionHeaders.First(sh => sh.VirtualAddress + sh.VirtualSize >= importRva);
int EstimateAdditionalNeededSpace()
=> additionalImports.Select(ai => ai.Functions).Count() * 64;
var impSection = GetImportSection();
var newUnalignedRawSecSize = EstimateAdditionalNeededSpace();
// First copy the current import descriptor array to the start of the new section to have enough space to
// add additional import descriptors.
AddSection(".addImp", (int)(impSection !.SizeOfRawData + newUnalignedRawSecSize), (ScnCharacteristicsType)0xC0000000);
var newImpSec = ImageSectionHeaders.First(sh => sh.Name == ".addImp");
var oldImpDescBytes = RawFile.AsSpan(importRva.RvaToOffset(ImageSectionHeaders), importSize);
RawFile.WriteBytes(newImpSec.PointerToRawData, oldImpDescBytes);
// Set the import data directory to the new import section and adjust the size
ImageNtHeaders.OptionalHeader.DataDirectory[(int)DataDirectoryType.Import].VirtualAddress = newImpSec.VirtualAddress;
ImageNtHeaders.OptionalHeader.DataDirectory[(int)DataDirectoryType.Import].Size = (uint)(importSize + (sizeOfImpDesc * numAddImpDescs));
var newImportRva = ImageNtHeaders.OptionalHeader.DataDirectory[(int)DataDirectoryType.Import].VirtualAddress;
var newImportSize = ImageNtHeaders.OptionalHeader.DataDirectory[(int)DataDirectoryType.Import].Size;
var paAdditionalSpace = newImpSec.PointerToRawData + newImportSize;
// Update import descriptors and imported functions to reflect the new
// position in the new section.
_dataDirectoryParsers.ReparseImportDescriptors(ImageSectionHeaders);
_dataDirectoryParsers.ReparseImportedFunctions();
uint AddModName(ref uint offset, string module)
{
var tmp = Encoding.ASCII.GetBytes(module);
var mName = new byte[tmp.Length + 1];
Array.Copy(tmp, mName, tmp.Length);
var paName = offset;
RawFile.WriteBytes(offset, mName);
offset = (uint)(offset + mName.Length);
return(paName);
}
List <uint> AddImpByNames(ref uint offset, List <string> funcs)
{
var adrList = new List <uint>();
foreach (var f in funcs)
{
var ibn = new ImageImportByName(RawFile, offset)
{
Hint = 0,
Name = f
};
adrList.Add(offset);
offset += (uint)ibn.Name.Length + 2;
}
// Add zero DWORD to end array
RawFile.WriteUInt(offset + 1, 0);
offset += 5;
return(adrList);
}
uint AddThunkDatas(ref uint offset, List <uint> adrList)
{
var paThunkStart = offset;
foreach (var adr in adrList)
{
_ = new ImageThunkData(RawFile, offset, Is64Bit)
{
AddressOfData = adr.OffsetToRva(ImageSectionHeaders !)
};
offset += (uint)sizeOfThunkData;
}
// End array with empty thunk data
_ = new ImageThunkData(RawFile, offset, Is64Bit)
{
AddressOfData = 0
};
offset += (uint)sizeOfThunkData;
return(paThunkStart);
}
void AddImportWithNewImpDesc(ref uint tmpOffset, ref long paIdesc, AdditionalImport ai)
{
var paName = AddModName(ref tmpOffset, ai.Module);
var funcAdrs = AddImpByNames(ref tmpOffset, ai.Functions);
var thunkAdrs = AddThunkDatas(ref tmpOffset, funcAdrs);
_ = new ImageImportDescriptor(RawFile, paIdesc)
{
Name = paName.OffsetToRva(ImageSectionHeaders),
OriginalFirstThunk = 0,
FirstThunk = thunkAdrs.OffsetToRva(ImageSectionHeaders),
ForwarderChain = 0,
TimeDateStamp = 0
};
paIdesc += (uint)sizeOfImpDesc;
}
var paIdesc = newImportRva.RvaToOffset(ImageSectionHeaders) + ImageImportDescriptors !.Length * sizeOfImpDesc;
var tmpOffset = paAdditionalSpace;
// Add new imports
foreach (var ai in additionalImports)
{
AddImportWithNewImpDesc(ref tmpOffset, ref paIdesc, ai);
}
// End with zero filled idesc
_ = new ImageImportDescriptor(RawFile, paIdesc)
{
Name = 0,
OriginalFirstThunk = 0,
FirstThunk = 0,
ForwarderChain = 0,
TimeDateStamp = 0
};
// Reparse imports
_dataDirectoryParsers.ReparseImportDescriptors(ImageSectionHeaders);
_dataDirectoryParsers.ReparseImportedFunctions();
}
}
public RawFile SaveAsZipArchive(string fileName)
{
var lstCleanUp = new List <string>(_attachments.Count + 1);
//If the filename does not include the zip extension add it
if (!fileName.EndsWith(".zip"))
{
fileName += ".zip";
}
var obj = new RawFile
{
FileName = fileName
};
//Get a temporary path to work with
var path = Path.Combine(Path.GetTempPath(), Path.GetRandomFileName());
//Get a separate directory so that the zip file can be created to avoid IO access exceptions
var pathZip = path + "zip";
//Create base working directory
Directory.CreateDirectory(path);
//Create directory for zip file
Directory.CreateDirectory(pathZip);
//Save to / Save as zip file
var zipFilePath = Path.Combine(pathZip, fileName);
lstCleanUp.Add(zipFilePath);
//For each attachment
foreach (var a in _attachments)
{
//Decode the base 64 string into a byte array
var bytes = Base64Decode(a.AttachmentBase64);
//Save as
var filePath = Path.Combine(path, a.Name);
//Write byte array to temp path with original name
File.WriteAllBytes(filePath, bytes);
lstCleanUp.Add(filePath);
}
//Archive everything into a zip file in the temp path
ZipFile.CreateFromDirectory(
path,
zipFilePath,
CompressionLevel.Optimal,
false);
//Create a byte array from the zip file
obj.Contents = File.ReadAllBytes(zipFilePath);
//Delete all files created
lstCleanUp.ForEach(File.Delete);
//Delete the working directories created
Directory.Delete(path);
Directory.Delete(pathZip);
return(obj);
}
public void replaceFile(string filename, RawFile toReplace)
{
int index = afsList.FindIndex(file => file.fileName == filename);
replaceFile(index, new MemoryStream(toReplace.fileContents));
}