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 void SingleFileMatching(object FileIDObj)
{
int FileID = (FileIDObj as IntArg).Arg;
//создаем список из
MGFFile File = Files[FileID];
List <MGFMatched> Matches = new List <MGFMatched>();
MGFMatched M;
for (int i = 0; i < File.Spectra.Count; i++)
{
M = new MGFMatched(File.Spectra[i]);
M.Index = i;
M.Origin = FileID;
Matches.Add(M);
}
//сортируем список по массам
Matches.Sort(new MGFMatched.MatchedByMass());
// пробегаемся по списку и матчим тех кто в пределах массы
for (int i = 0; i < Matches.Count; i++)
{
//отступаем
int First;
for (First = i; First >= 0; First--)
{
double Diff = (Math.Abs(Matches[First].Spectrum.mz - Matches[i].Spectrum.mz) /
Math.Max(Matches[First].Spectrum.mz, Matches[i].Spectrum.mz)) * 1000000.0;
if (Diff > PPMs)
{
break;
}
}
First++;
for (int j = First; j < Matches.Count; j++)
{
if (i == j)
{
continue;
}
if (Matches[i].Matched.Contains(Matches[j].Index) ||
Matches[j].Matched.Contains(Matches[i].Index))
{
continue;
}
double Diff = (Math.Abs(Matches[First].Spectrum.mz - Matches[j].Spectrum.mz) /
Math.Max(Matches[First].Spectrum.mz, Matches[j].Spectrum.mz)) * 1000000.0;
if (Diff > PPMs)
{
break;
}
MGFMatched IM = Matches[i];
MGFMatched JM = Matches[j];
int R = Match(ref IM, ref JM);
if (R > 0)
{
IM.Matched.Add(JM.Index);
}
if (R < 0)
{
JM.Matched.Add(IM.Index);
}
}
}
//Вытаскиваем за головку дерева. самые интенсивные - остальных уничтожаем
Matches.Sort(new MGFMatched.MatchedByWeight());
for (int i = 0; i < Matches.Count; i++)
{
if (Matches[i].Matched == null)
{
continue;
}
for (int j = i; j < Matches.Count; j++)
{
if (Matches[j].Matched == null)
{
continue;
}
if (Matches[i].Matched.Contains(Matches[j].Index))
{
Matches[i].Matched.AddRange(Matches[j].Matched);
Matches[j].Matched = null;
}
}
}
for (int i = Matches.Count - 1; i >= 0; i--)
{
if (Matches[i].Matched == null)
{
Matches.RemoveAt(i);
}
}
MatchedFiles[FileID] = Matches;
lock (ForCountLock){
ExecCount++;
}
return;
}
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);
}
private void DoWork()
{
//проверка параметров
try{
PPMs = Convert.ToDouble(Settings.Default.MassDev);
RTPerc = Convert.ToDouble(Settings.Default.RTDevProc);
RTMin = Convert.ToDouble(Settings.Default.RTDevMin);
MS2Acc = Convert.ToDouble(Settings.Default.MS2Da);
FrMatch = Convert.ToInt32(Settings.Default.MS2PeakMatches);
SpectraPerCluster = Convert.ToInt32(Settings.Default.SpecPerClust);
}catch {
MessageBox.Show("Parametrs must be set.");
}
//открываем себе файл для выборочного лога
//StreamWriter SW = new StreamWriter("log.log");
//загрузка данных
Files = new MGFFile[MGFlist.Items.Count];
FileCount = MGFlist.Items.Count;
ProgressMessage = "Loading data...";
for (int i = 0; i < FileCount; i++)
{
Files[i] = new MGFFile();
Files[i].MGFRead(MGFlist.Items[i].ToString());
Progress(i, FileCount);
//если есть информация по RT Apex - используем ее
for (int j = 0; j < Files[i].Spectra.Count; j++)
{
if (Files[i].Spectra[j].RTApex != 0.0)
{
Files[i].Spectra[j].RT = Files[i].Spectra[j].RTApex;
}
}
}
int WorkerThreads, IOThreads;
ThreadPool.GetMaxThreads(out WorkerThreads, out IOThreads);
WorkerThreads = Environment.ProcessorCount;
ThreadPool.SetMaxThreads(WorkerThreads, IOThreads);
//Очистка лишних сигналов
try{
MISignals = Convert.ToInt32(Settings.Default.MS2PeaksNumber);
}catch { MISignals = 0; }
SpectrabyRT sr = new SpectrabyRT();
for (int i = 0; i < FileCount; i++)
{
Files[i].Spectra.Sort(sr);
}
//Собираем консенсусный набор спектров
//матчинг спектров - нетранзитивен!!
Aligners = new List <Aligner>();
//Матчинг внутри файла
MatchedFiles = new List <MGFMatched> [FileCount];
int LocalCount;
ProgressMessage = "Intermal Spectra Matching...";
ExecCount = 0;
for (int i = 0; i < FileCount; i++)
{
ThreadPool.QueueUserWorkItem(new WaitCallback(SingleFileMatching), new IntArg(i));
}
while (true)
{
lock (ForCountLock){
LocalCount = ExecCount;
}
Thread.Sleep(200);
Progress(LocalCount, Files.GetLength(0));
if (LocalCount >= Files.GetLength(0))
{
break;
}
}
/*for (int i = 0 ; i < FileCount ; i++ ){
* MatchedFiles[i] = SingleFileMatching(i);
* }*/
//соединяем и сортируем по времени выхода
for (int i = 0; i < FileCount; i++)
{
Merged.AddRange(MatchedFiles[i]);
}
Merged.Sort(new MGFMatched.MatchedByRT());
MaxRT = Merged[Merged.Count - 1].Spectrum.RT;
//сматчивем горизонтально в три прослойки (операционное поле, буфер спереди, буфер сзади)
ProgressMessage = "External Spectra Matching...";
int SliceCount = Convert.ToInt32(Math.Floor(MaxRT / RTMin)) + 1;
ExecCount = 0;
for (int i = 0; i < SliceCount; i += 3)
{
ThreadPool.QueueUserWorkItem(new WaitCallback(HorizontalMatching), new DoubleArg(RTMin * i));
}
while (true)
{
lock (ForCountLock){
LocalCount = ExecCount;
}
Thread.Sleep(200);
Progress(LocalCount, SliceCount);
if (LocalCount == ((SliceCount - 1) / 3) + 1)
{
break;
}
}
for (int i = 1; i < SliceCount; i += 3)
{
ThreadPool.QueueUserWorkItem(new WaitCallback(HorizontalMatching), new DoubleArg(RTMin * i));
}
while (true)
{
lock (ForCountLock){
LocalCount = ExecCount;
}
Thread.Sleep(200);
Progress(LocalCount, SliceCount);
if (LocalCount == (((SliceCount - 1) / 3) + 1) + ((SliceCount - 2) / 3 + 1))
{
break;
}
}
for (int i = 2; i < SliceCount; i += 3)
{
ThreadPool.QueueUserWorkItem(new WaitCallback(HorizontalMatching), new DoubleArg(RTMin * i));
}
while (true)
{
lock (ForCountLock){
LocalCount = ExecCount;
}
Thread.Sleep(200);
Progress(LocalCount, SliceCount);
if (LocalCount >= SliceCount)
{
break;
}
}
/* for(int i=0 ; i<SliceCount ; i+=3){
* HorizontalMatching(new DoubleArg(RTMin * i));
* }
* for(int i=1 ; i<SliceCount ; i+=3){
* HorizontalMatching(new DoubleArg(RTMin * i));
* }
* for(int i=2 ; i<SliceCount ; i+=3){
* HorizontalMatching(new DoubleArg(RTMin * i));
* }*/
Aligner Al;
for (int i = 0; i < Merged.Count; i++)
{
if (Merged[i] != null)
{
Al = new Aligner();
Al.Best = Merged[i].Spectrum;
Al.Origin = Merged[i].Origin;
Al.Indexes = new int[FileCount];
for (int j = 0; j < FileCount; j++)
{
Al.Indexes[j] = -1;
}
Al.Indexes[Al.Origin] = Merged[i].Index;
foreach (MGFMatched M in Merged[i].InterMatched)
{
Al.Indexes[M.Origin] = M.Index;
}
Al.SignChanged = false;
Aligners.Add(Al);
}
}
//собственно выравнивание
//??? - В каком порядке исходно стоят алигнеры
int Count;
//оцениваем расстояние и количество спектров
ProgressMessage = "Estimating spectra distance...";
ExecCount = 0;
for (int i = 0; i < Aligners.Count; i += 1000)
{
ThreadPool.QueueUserWorkItem(new WaitCallback(DistanceEst), new IntArg(i));
}
while (true)
{
lock (ForCountLock){
LocalCount = ExecCount;
}
Thread.Sleep(200);
Progress(LocalCount, (Aligners.Count - 1) / 1000 + 1);
if (LocalCount >= (Aligners.Count - 1) / 1000 + 1)
{
break;
}
}
//подвид пузырьковой сортировки
//нарезаем кусочки по RTMin
Slices = new int[SliceCount];
Count = 0;
for (int i = 0; i < Aligners.Count; i++)
{
if (Aligners[i].Best.RT >= ((double)(Count) * RTMin))
{
Slices[Count] = i;
Count++;
}
}
ProgressMessage = "Aligning spectra...";
int UpperIndex, LowerIndex;
for (int i = 0; i < SliceCount; i++) //максимальная процедура - на квадрат
{
bool flag = true;
Count = 0;
ExecCount = 0;
for (int j = i % 2; j < SliceCount; j += 2)
{
UpperIndex = Slices[j];
if (j + 2 < SliceCount)
{
LowerIndex = Slices[j + 2];
}
else
{
LowerIndex = Aligners.Count;
}
int k;
for (k = UpperIndex; k < LowerIndex; k++)
{
if (!Aligners[k].SignChanged)
{
break;
}
}
if (k < LowerIndex)
{
ThreadPool.QueueUserWorkItem(new WaitCallback(Arrange), new IntArg(j));
//Arrange(new IntArg(j));
Count++;
flag = false;
}
}
while (true)
{
lock (ForCountLock){
LocalCount = ExecCount;
}
Thread.Sleep(200);
Progress(SliceCount - Count, SliceCount);
if (LocalCount >= Count)
{
break;
}
}
if (flag)
{
break;
}
}
ProgressMessage = "Writing spectra...";
Progress(0, 100);
//Меняем FSN в Title - сообразно новому порядку
for (int i = 0; i < Aligners.Count; i++)
{
string Title = Aligners[i].Best.Title;
if (Title.Contains("Origin")) //затычка на повторное включение спектра в коллекцию
{
Aligners[i].Best.Title = null;
continue;
}
Title = Title.Replace("FinneganScanNumber:",
String.Format("Origin: {0} Order: {1} FinneganScanNumber:",
Path.GetFileName(MGFlist.Items[Aligners[i].Origin].ToString()), i));
Aligners[i].Best.Title = Title;
Aligners[i].Best.Data.Sort(new ChildbyMass());
}
//выводим конечную коллекцию
//for (SpectraPerCluster = 1 ; SpectraPerCluster<48 ; SpectraPerCluster++){
MGFFile OutFile = new MGFFile();
for (int i = 0; i < Aligners.Count; i++)
{
if (Aligners[i].Best.Title == null)
{
continue;
}
//считаем наличные индексы
int IndexCount = 0;
for (int j = 0; j < FileCount; j++)
{
if (Aligners[i].Indexes[j] != -1)
{
IndexCount++;
}
}
if (IndexCount >= SpectraPerCluster)
{
OutFile.Spectra.Add(Aligners[i].Best);
}
}
//формируем комментарий
string Comment = Text + "; Consensus MGF aligned from :";
for (int i = 0; i < FileCount; i++)
{
Comment += MGFlist.Items[i].ToString() + ", ";
}
OutFile.MGFComments.Add(Text);
OutFile.MGFComments.Add(String.Format("MS Tol.: {0} ppm, MS/MS Tol: {1} Da, RT Deviation {2} min., Minimum {3} peaks of top {4} matched.",
MassDevBox.Text, MS2DaBox.Text, RTMinBox.Text, textBox8.Text, MS2PeaksBox.Text));
OutFile.MGFComments.Add("Source files:");
for (int i = 0; i < FileCount; i++)
{
OutFile.MGFComments.Add(MGFlist.Items[i].ToString());
}
OutFile.MGFComments.Add(String.Format("Consensus MGF aligned from {0} files", FileCount));
OutFile.MGFWrite(OutMgfBox.Text /*+SpectraPerCluster.ToString()*/);
//}
Progress(100, 100);
//SW.Close();
ProgressMessage = "Processing completed...";
SystemSounds.Beep.Play();
}
