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;
}
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);
}
