static void Main(string[] args)
{
MSFileReader_XRawfile rawMSfile = new MSFileReader_XRawfile();
rawMSfile.Open("L:\\Davi\\_QE\\BSAs\\20150512_BSA_The-PEG-envelope.raw");
rawMSfile.SetCurrentController(0, 1); /* Controller type 0 means mass spec device; Controller 1 means first MS device */
int nms = 0; /* ref int usrd with GetNumSpectra */
int pbMSData=0;
int pnLastSpectrum=0;
rawMSfile.GetNumSpectra(ref nms);
rawMSfile.IsThereMSData(ref pbMSData);
rawMSfile.GetLastSpectrumNumber(ref pnLastSpectrum);
Debug.WriteLine("Total Spectra: " + nms);
Debug.WriteLine("MSdata: " + pbMSData);
Debug.WriteLine("Last MSdata: " + pnLastSpectrum);
double pkWidCentroid = 0.0;
object mzList = null;
object pkFlg = null;
int arrLen = 0;
for (int i = 1; i < 10; i++){
rawMSfile.GetMassListFromScanNum(i, null, 1, 0, 0, 0, ref pkWidCentroid, ref mzList, ref pkFlg, ref arrLen);
double[,] mslist = (double[,])mzList;
//for (int j = 0; j < 2; j++){
Debug.WriteLine("MSdata: " + mslist[0,i] + "MSdata: " + mslist[1,i] + "Scan:" + i);
//}
}
}
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 MSFileReader_XRawfile RawFile; //instance of LC-MS run
public override int LoadIndex(string FileName)
{
this.RawFileName = FileName;
RawFile = new MSFileReader_XRawfile();
RawFile.Open(FileName);
RawFile.SetCurrentController(0, 1);
Spectra = 0;
RawFile.GetNumSpectra(ref Spectra);
if (Spectra <= 0) //if there are no spectra available
{
return(0);
}
int i, LastFull = 0, Total = 0;
//there will be fake [0] spectra with no data and fake last spectra with no data
//it is made to make any chromatogram start and end with zero
IndexDir = new int[Spectra + 2];
IndexRev = new int[Spectra + 2];
RawSpectra = new RawSpectrum[Spectra + 2];
for (int j = 0; j <= Spectra + 1; j++)
{
RawSpectra[j] = new RawSpectrum();
}
TimeStamps = new double[Spectra + 2];
TimeCoefs = new double[Spectra + 2];
string Filter = null;
bool PosMode = false, NegMode = false;
LowRT = 0.0;
HighRT = 0.0;
int Progress = 0;
for (i = 1; i <= Spectra; i++)
{
if ((int)(100.0 * ((double)i / (double)Spectra)) > Progress) //report progress
{
Progress = (int)(100.0 * ((double)i / (double)Spectra));
RepProgress?.Invoke(Progress);
}
RawFile.GetFilterForScanNum(i, ref Filter); //to reveal spectra properties we parse filter string
if (Filter.Contains(" Full ") && Filter.Contains(" ms ") && Filter.Contains("FTMS")) //is a FULL MS
{
PosMode |= Filter.Contains(" + ");
NegMode |= Filter.Contains(" - ");
RawFile.RTFromScanNum(i, ref RawSpectra[i].RT);
RawSpectra[i].Scan = i;
TimeStamps[i] = RawSpectra[i].RT - RawSpectra[LastFull].RT;
IndexDir[LastFull] = i;
IndexRev[i] = LastFull;
LastFull = i;
Total++;
}
Filter = null;
}
IndexDir[LastFull] = Spectra + 1; //boundaries of navigation arrays
IndexDir[Spectra + 1] = -1;
IndexRev[Spectra + 1] = LastFull;
TotalRT = RawSpectra[LastFull].RT;
AverageTimeStamp = TotalRT / Total;
//time interval bias coefficients
for (i = IndexDir[0]; IndexDir[i] != -1; i = IndexDir[i])
{
TimeCoefs[i] = (TimeStamps[i] + TimeStamps[IndexDir[i]]) / (2.0 * AverageTimeStamp);
}
TimeCoefs[i] = 1.0;
//Fake spectra number 0 has to have reasonable RT
double FRT = RawSpectra[IndexDir[0]].RT; //First full spectra RT
double SRT = RawSpectra[IndexDir[IndexDir[0]]].RT; //Second full spectra RT
RawSpectra[0].RT = Math.Max(0, FRT - (SRT - FRT)); // 0 or make the same distance like between 1-st and 2-nd spectra
//Last spectra also has to have reasonable RT
FRT = RawSpectra[LastFull].RT; //the same for last spectra
SRT = RawSpectra[IndexRev[LastFull]].RT;
RawSpectra[Spectra + 1].RT = FRT + (FRT - SRT);
RawSpectra[Spectra + 1].Scan = RawSpectra[Spectra].Scan + 1;
RawSpectra[0].Data = new MZData[0];
RawSpectra[Spectra + 1].Data = new MZData[0];
if (PosMode && !NegMode)
{
Mode = 1;
}
if (!PosMode && NegMode)
{
Mode = -1;
}
return(Spectra);
}
public Form2(double[] Values, string flname)
{
InitializeComponent();
//this.SetStyle(ControlStyles.SupportsTransparentBackColor, true);
foreach (var item in Values)
{
Console.Write(item.ToString() + " ");
}
Console.WriteLine();
this.Text = flname;
TextBox t = new TextBox();
t.Text = "Spot Number: " + (Values[0]).ToString();
t.Location = new Point(15, 15);
this.Controls.Add(t);
chart1.Series["MassSpectrum"].ChartType = System.Windows.Forms.DataVisualization.Charting.SeriesChartType.Line;
t.BringToFront();
int[,] sample = new int[2, 10];
MSFileReader_XRawfile rawfile = new MSFileReader_XRawfile();
rawfile.Open(flname);
rawfile.SetCurrentController(0, 1);
int ScanNumber = Convert.ToInt32(Values[0]);
double Centroid_Peak_Width = 0.0;
object Mass_List = null;
object Peak_Flags = null;
int Array_Size = 0;
rawfile.GetMassListFromScanNum(ref ScanNumber, null, 1, 0, 0, 0, ref Centroid_Peak_Width, ref Mass_List, ref Peak_Flags, ref Array_Size);
double[,] ms_list = (double[, ])Mass_List;
//Random rdn = new Random();
//chart1.Series.Add("Series2");
double[] found = new double[(Values.Length - 2) / 2];
//int start = 2;
for (int i = 0; i < ms_list.Length / 2; i++)
{
/*for(int j = start; j < Values.Length; j = j + 2)
* {
* if ((ms_list[0,i] > Values[j]-0.005) && (ms_list[0, i] < Values[j] + 0.005))
* {
* found[(j - 2) / 2] = ms_list[0, i];
* start = j + 2;
* }
* }*/
DataPoint dp2 = new DataPoint(ms_list[0, i], ms_list[1, i]);
chart1.Series["MassSpectrum"].Points.Add(dp2);
// (rdn.Next(0, 10), rdn.Next(0, 10));
}
for (int j = 2; j < Values.Length; j = j + 2)
{
//chart1.Series["MassSpectrum"].Points.FindByValue(found[j], "X").IsValueShownAsLabel = true; // = "("+Values[2*j+2]+", "+Values[2*j+3]+")";
DataPoint dtp = chart1.Series["MassSpectrum"].Points.Aggregate((x, y) => Math.Abs(x.XValue - Values[j]) < Math.Abs(y.XValue - Values[j]) ? x : y);
//DataPoint dtp = chart1.Series["MassSpectrum"].Points.FindByValue(found[j], "X");
double temp = new double();
temp = Math.Round(dtp.XValue, 2);
dtp.Label = temp.ToString(); //"(" + Values[2 * j + 2] + ", " + Values[2 * j + 3] + ")";
}
//chart1.Series["Series2"].Enabled = false;
//chart1.Series["Series2"].IsValueShownAsLabel = true;
chart1.Series["MassSpectrum"].Color = Color.Blue;
}
public int LoadIndex(string FileName)
{
this.RawFileName = FileName;
RawFile = new MSFileReader_XRawfile();
RawFile.Open(FileName);
RawFile.SetCurrentController(0, 1);
Spectra = 0;
RawFile.GetNumSpectra(ref Spectra);
if (Spectra <= 0)
{
return(0);
}
int i, lastfull = 0, total = 0;
double TotalEsi = 0.0;
ms2index = new int[Spectra + 1];
IndexDir = new int[Spectra + 1];
IndexRev = new int[Spectra + 1];
RawSpectra = new RawData[Spectra + 1];
for (int j = 0; j <= Spectra; j++)
{
RawSpectra[j] = new RawData();
}
Buf = new MZData[1000000];
ESICurrents = new double[Spectra + 1];
TimeStamps = new double[Spectra + 1];
TimeCoefs = new double[Spectra + 1];
string Filter = null;
LowRT = 0.0;
HighRT = 0.0;
int Progress = 0;
for (i = 1; i <= Spectra; i++)
{
if ((int)(100.0 * ((double)i / (double)Spectra)) > Progress)
{
Progress = (int)(100.0 * ((double)i / (double)Spectra));
if (RepProgress != null)
{
RepProgress(Progress);
}
}
RawFile.GetFilterForScanNum(i, ref Filter);
//YL - для спектров ms-only
//Заплатка для MSX спектров
if ((Filter.IndexOf(" ms ") != -1) && (Filter.IndexOf("FTMS") != -1)) //is a FULL MS
{
TimeStamps[i] = RawSpectra[lastfull].RT;
IndexDir[lastfull] = i;
IndexRev[i] = lastfull;
lastfull = i;
ms2index[i] = lastfull;
++total;
RawFile.RTFromScanNum(i, ref RawSpectra[i].RT);
RawSpectra[i].Filter = Filter;
TotalRT = RawSpectra[i].RT;
TimeStamps[i] = RawSpectra[i].RT - TimeStamps[i];
object Labels = null;
object Values = null;
int ArraySize = 0;
double RT = 0.0;
RawFile.GetStatusLogForScanNum(i, ref RT, ref Labels, ref Values, ref ArraySize);
for (int k = 0; k < ArraySize; k++)
{
if ((Labels as Array).GetValue(k).ToString().Contains("Source Current"))
{
ESICurrents[i] = Convert.ToDouble((Values as Array).GetValue(k).ToString());
TotalEsi += ESICurrents[i];
}
}
}
else
{
ms2index[i] = lastfull;
}
Filter = null;
}
IndexDir[lastfull] = -1;
TotalRT = RawSpectra[lastfull].RT;
AverageTimeStamp = TotalRT / total;
//пересчитаем временные коэффициэнты
for (i = IndexDir[0]; IndexDir[i] != -1; i = IndexDir[i])
{
TimeCoefs[i] = (TimeStamps[i] + TimeStamps[IndexDir[i]]) / (2.0 * AverageTimeStamp);
ESICurrents[i] = ESICurrents[i] / (TotalEsi / (double)total);
}
TimeCoefs[i] = 1.0;
return(Spectra);
}
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);
}
/// <summary>
/// Test the functionality of the reader - can we instantiate the MSFileReader Object?
/// </summary>
/// <returns></returns>
public bool CheckFunctionality()
{
// I have a feeling this doesn't actually work, and will always return True
try
{
// ReSharper disable once UnusedVariable
var objXRawFile = new MSFileReader_XRawfile();
// If we get here, all is fine
return true;
}
catch (Exception)
{
return false;
}
}
private void Form1_Load(object sender, EventArgs e)
{
int loop_num = 0;
this.grid.CellMouseClick += new System.Windows.Forms.DataGridViewCellMouseEventHandler(this.grid_CellMouseClick);
grid.Anchor = (AnchorStyles.Top | AnchorStyles.Left | AnchorStyles.Bottom | AnchorStyles.Right);
grid.Show();
// To Do
IEnumerable <string> sample_files = Directory.GetFiles(fldrpath, "*.raw").OrderBy(f => f);
string one_file = sample_files.First();
MSFileReader_XRawfile rawfile = new MSFileReader_XRawfile();
rawfile.Open(one_file);
rawfile.SetCurrentController(0, 1);
int last_scan = 0;
rawfile.GetLastSpectrumNumber(ref last_scan);
//
for (int i = 0; i < last_scan; i++)
{
grid.Columns.Add("column" + i.ToString(), i.ToString());
grid.Columns[i].MinimumWidth = 4;
}
Color[] colorSet = { Color.Green, Color.Blue, Color.Aqua, Color.Yellow, Color.Orange, Color.Purple, Color.LightSeaGreen };
//foreach (string file in Directory.EnumerateFiles(fldrpath, "*.raw"))
foreach (string file in Directory.GetFiles(fldrpath, "*.raw").OrderBy(f => f))
{
bool flag = Analytics.analytics(mass_ratio, file);
while (flag != true)
{
continue;
}
string text_file = file.Remove(file.Length - 4);
list.Add(text_file);
//int n = TotalLines(text_file+".txt"); // 50 scans in a file :)
int rowId = grid.Rows.Add();
DataGridViewRow row = grid.Rows[rowId];
grid.Rows[rowId].MinimumHeight = 2;
System.Collections.Generic.IEnumerable <String> lines = File.ReadLines(text_file + ".txt");
//Button[] buttArray = new Button[n];
int i = 0;
foreach (string l in lines)
{
char[] delimiterChars = { ' ' };
string[] words = l.Split(delimiterChars);
//Console.WriteLine(words[1]);
if (Int32.Parse(words[1]) == 0)
{
grid.Rows[rowId].Cells[i].Style.BackColor = Color.Red;
}
else
{
grid.Rows[rowId].Cells[i].Style.BackColor = colorSet[Int32.Parse(words[1])];
}
i++;
}
loop_num++;
//if (loop_num >= 2) break;
}
//Console.WriteLine(loop_num);
this.WindowState = System.Windows.Forms.FormWindowState.Maximized;
grid.Dock = DockStyle.Fill;
this.grid.AutoSizeColumnsMode = DataGridViewAutoSizeColumnsMode.Fill;
grid.Columns[grid.ColumnCount - 1].MinimumWidth = 8;
grid.CurrentCell.Selected = false;
sw.Stop();
//Console.WriteLine(sw.ElapsedMilliseconds);
//Console.WriteLine(this.Height);
//grid.AutoResizeRows(DataGridViewAutoSizeRowsMode.AllCells);
}
public int LoadIndex(string FileName)
{
this.RawFileName = FileName;
RawFile = new MSFileReader_XRawfile();
RawFile.Open(FileName);
RawFile.SetCurrentController(0, 1);
Spectra = 0;
RawFile.GetNumSpectra(ref Spectra);
if( Spectra <= 0)
return 0;
int i, lastfull = 0, total = 0;
double TotalEsi = 0.0;
ms2index = new int[Spectra+1];
IndexDir = new int[Spectra+1];
IndexRev = new int[Spectra+1];
RawSpectra = new RawData[Spectra+1];
for(int j = 0 ; j <= Spectra ; j++){
RawSpectra[j] = new RawData();
}
Buf = new MZData[1000000];
ESICurrents = new double[Spectra+1];
TimeStamps = new double[Spectra+1];
TimeCoefs = new double[Spectra+1];
string Filter = null;
LowRT = 0.0;
HighRT = 0.0;
int Progress = 0;
for(i = 1; i <= Spectra; i++){
if ((int)(100.0*((double)i/(double)Spectra)) > Progress) {
Progress = (int)(100.0*((double)i/(double)Spectra));
if (RepProgress != null){
RepProgress(Progress);
}
}
RawFile.GetFilterForScanNum(i, ref Filter);
//YL - для спектров ms-only
//Заплатка для MSX спектров
if((Filter.IndexOf(" ms ") != -1) && (Filter.IndexOf("FTMS") != -1)) { //is a FULL MS
TimeStamps[i] = RawSpectra[lastfull].RT;
IndexDir[lastfull] = i;
IndexRev[i] = lastfull;
lastfull = i;
ms2index[i] = lastfull;
++total;
RawFile.RTFromScanNum(i, ref RawSpectra[i].RT);
RawSpectra[i].Filter = Filter;
TotalRT = RawSpectra[i].RT;
TimeStamps[i] = RawSpectra[i].RT - TimeStamps[i];
object Labels = null;
object Values = null;
int ArraySize = 0;
double RT = 0.0;
RawFile.GetStatusLogForScanNum(i, ref RT, ref Labels, ref Values , ref ArraySize);
for (int k = 0 ; k < ArraySize ; k++ ){
if ((Labels as Array).GetValue(k).ToString().Contains("Source Current")){
ESICurrents[i] = Convert.ToDouble((Values as Array).GetValue(k).ToString());
TotalEsi+=ESICurrents[i];
}
}
}
else {
ms2index[i] = lastfull;
}
Filter = null ;
}
IndexDir[lastfull] = -1;
TotalRT = RawSpectra[lastfull].RT;
AverageTimeStamp = TotalRT/total;
//пересчитаем временные коэффициэнты
for (i = IndexDir[0] ; IndexDir[i] != -1 ; i = IndexDir[i]) {
TimeCoefs[i] = (TimeStamps[i]+TimeStamps[IndexDir[i]])/(2.0*AverageTimeStamp);
ESICurrents[i] = ESICurrents[i]/(TotalEsi/(double)total);
}
TimeCoefs[i] = 1.0;
return Spectra;
}
private void SleepT()
{
if (filedirectory_array.Length != 0)
{
#region
for (int i_filedirectory = 0; i_filedirectory < pathway.Items.Count; i_filedirectory++)
{
SetTextMessage_rawfile_num(i_filedirectory + 1);
//Utilize the MSFileReader to obtain the information from the DIA data;
filedirectory = (string)pathway.Items[i_filedirectory];
MSFileReader_XRawfile rawfile = new MSFileReader_XRawfile();
IXRawfile5 rawfile5 = (IXRawfile5) new MSFileReader_XRawfile();
string rawpath = filedirectory;
rawfile.Open(rawpath);
rawfile.SetCurrentController(0, 1);
string rawpath5 = filedirectory;
rawfile5.Open(rawpath5);
rawfile5.SetCurrentController(0, 1);
string filename = Path.GetFileName(filedirectory);
string newfilepath = Path.GetDirectoryName(filedirectory);
#region
if (extracttype == "MS1MS2Data")
{
//creat the output file names
string outfilems1 = newfilepath + "\\" + "MS1Data_" + filename + ".txt";
StreamWriter swms1 = File.AppendText(outfilems1);
string outfilems2 = newfilepath + "\\" + "MS2Data_" + filename + ".txt";
StreamWriter swms2 = File.AppendText(outfilems2);
//write the 9 columns information in the .txt file
swms1.Write("ScanNum\tMSOrder\tPeakNumber\tPeakNumberAfter\tRT\tm/z\tIntensity\tNoise\tBaseline\n");
swms2.Write("ScanNum\tMSOrder\tPeakNumber\tPeakNumberAfter\tRT\tm/z\tIntensity\tNoise\tBaseline\n");
int specnum = 0;
rawfile5.GetNumSpectra(ref specnum);
for (int i = 1; i <= specnum; i++)
{
System.Threading.Thread.Sleep(0);
SetTextMessage(100 * i / specnum);
int nOrder = 0;
rawfile5.GetMSOrderForScanNum(i, ref nOrder);
double scanRT = 0;
rawfile5.RTFromScanNum(i, ref scanRT);
object varlabels = null;
object varflags = null;
rawfile5.GetLabelData(ref varlabels, ref varflags, ref i);
var labels = (double[, ])varlabels;
int dim = labels.GetLength(1);
double massNeutron = 1.00335; // massC13 - massC12
double mztol = Convert.ToDouble(ionmtoltextbox.Text);
double mzdecontol = Convert.ToDouble(ionmtoltextbox.Text);
double ms1sonthreshold = Convert.ToDouble(ms1sontextbox.Text);
double ms2sonthreshold = Convert.ToDouble(ms2sontextbox.Text);
double ms1resolutiontol = Convert.ToDouble(ms1unitoltextbox.Text);
double ms2resolutiontol = Convert.ToDouble(ms2unitoltextbox.Text);
if (nOrder == 1)
{
swms1.Write("{0}\t", i);
swms1.Write("{0}\t", nOrder);
swms1.Write("{0}\t", dim);
List <double> ms1mzlist = new List <double>();
List <double> ms1intensitylist = new List <double>();
List <double> ms1chargelist = new List <double>();
List <double> ms1noiselist = new List <double>();
List <double> ms1baselinelist = new List <double>();
for (int inx = 0; inx < dim; inx++)
{
double dMassjms1 = labels[0, inx];
double dInms1 = labels[1, inx];
double dBasems1 = labels[3, inx];
double dNoisems1 = labels[4, inx];
double dChams1 = labels[5, inx];
double sonms1 = 0;
if (ms1rms_checkbox == "ms1rms")
{
//if checked, the S/N is changed to RMS S/N(root mean square signal over noise);
sonms1 = (dInms1 - dBasems1) / (dNoisems1 - dBasems1);
}
else
{
sonms1 = dInms1 / dNoisems1;
}
if (sonms1 >= ms1sonthreshold)
{
ms1chargelist.Add(dChams1);
ms1mzlist.Add(dMassjms1);
ms1intensitylist.Add(dInms1);
ms1noiselist.Add(dNoisems1);
ms1baselinelist.Add(dBasems1);
}
else
{
//if the S/N is too low, set their values to zero
ms1chargelist.Add(0);
ms1mzlist.Add(0);
ms1intensitylist.Add(0);
ms1noiselist.Add(0);
ms1baselinelist.Add(0);
}
}
//remove the peaks, whose values of (m/z, intensity, charge, noise, baseline) are equal to zero;
List <int> ms1mzzeroindex = new List <int>();
for (int izero = 0; izero < ms1mzlist.Count; izero++)
{
if (ms1mzlist[izero] == 0)
{
ms1mzzeroindex.Add(izero);
}
}
for (int izero1 = 0; izero1 < ms1mzzeroindex.Count(); izero1++)
{
ms1mzlist.RemoveAt(ms1mzzeroindex[izero1] - izero1);
ms1intensitylist.RemoveAt(ms1mzzeroindex[izero1] - izero1);
ms1baselinelist.RemoveAt(ms1mzzeroindex[izero1] - izero1);
ms1noiselist.RemoveAt(ms1mzzeroindex[izero1] - izero1);
ms1chargelist.RemoveAt(ms1mzzeroindex[izero1] - izero1);
}
//keep only one peak in a tolerance;
for (int ims1reso = 0; ims1reso < ms1mzlist.Count; ims1reso++)
{
if (ms1mzlist[ims1reso] != 0)
{
double ms1mzreso = ms1mzlist[ims1reso] * ms1intensitylist[ims1reso];
double ms1intensityreso = ms1intensitylist[ims1reso];
double ms1baselinereso = ms1baselinelist[ims1reso];
for (int jms1reso = ims1reso + 1; jms1reso < ms1mzlist.Count; jms1reso++)
{
double ms1resodiff = ms1mzlist[jms1reso] - ms1mzlist[jms1reso - 1];
if (ms1resodiff > ms1resolutiontol)
{
break;
}
if (ms1resodiff <= ms1resolutiontol)
{
ms1mzreso = ms1mzreso + ms1mzlist[jms1reso] * ms1intensitylist[jms1reso];
ms1intensityreso = ms1intensityreso + ms1intensitylist[jms1reso];
ms1intensitylist[jms1reso] = 0;
}
}
ms1mzlist[ims1reso] = ms1mzreso / ms1intensityreso;
ms1intensitylist[ims1reso] = ms1intensityreso;
}
}
List <int> ms1intensityzeroafterresoindex = new List <int>();
for (int izero = 0; izero < ms1mzlist.Count; izero++)
{
if (ms1intensitylist[izero] == 0)
{
ms1intensityzeroafterresoindex.Add(izero);
}
}
for (int izero1 = 0; izero1 < ms1intensityzeroafterresoindex.Count(); izero1++)
{
ms1mzlist.RemoveAt(ms1intensityzeroafterresoindex[izero1] - izero1);
ms1intensitylist.RemoveAt(ms1intensityzeroafterresoindex[izero1] - izero1);
ms1baselinelist.RemoveAt(ms1intensityzeroafterresoindex[izero1] - izero1);
ms1noiselist.RemoveAt(ms1intensityzeroafterresoindex[izero1] - izero1);
ms1chargelist.RemoveAt(ms1intensityzeroafterresoindex[izero1] - izero1);
}
//if checked, the peaks are deisotoped, which could remove the isotope peaks;
if (deisotope_checkbox == "deisotope")
{
List <int> ms1deisotopindexbefore = new List <int>();
for (int ims1 = 0; ims1 < ms1mzlist.Count; ims1++)
{
if (ms1chargelist[ims1] != 0)
{
for (int jms1 = ims1 + 1; jms1 < ms1mzlist.Count; jms1++)
{
double ms1mzdiff = ms1mzlist[jms1] - ms1mzlist[ims1];
double ms1tolvalue = Math.Abs(massNeutron / ms1chargelist[ims1] - ms1mzdiff);
if (ms1tolvalue < mztol && ms1intensitylist[jms1] < ms1intensitylist[ims1])
{
ms1deisotopindexbefore.Add(jms1);
}
}
}
}
List <int> ms1deisotopindex = new List <int>();
foreach (int ms1deiso in ms1deisotopindexbefore)
{
if (!ms1deisotopindex.Contains(ms1deiso))
{
ms1deisotopindex.Add(ms1deiso);
}
}
ms1deisotopindex.Sort();
for (int ide1 = 0; ide1 < ms1deisotopindex.Count; ide1++)
{
ms1mzlist.RemoveAt(ms1deisotopindex[ide1] - ide1);
ms1intensitylist.RemoveAt(ms1deisotopindex[ide1] - ide1);
ms1baselinelist.RemoveAt(ms1deisotopindex[ide1] - ide1);
ms1noiselist.RemoveAt(ms1deisotopindex[ide1] - ide1);
ms1chargelist.RemoveAt(ms1deisotopindex[ide1] - ide1);
}
}
//if checked, the peaks are deconvoluted to one charge;
if (deconvolution_checkbox == "deconvolution")
{
for (int idems1 = 0; idems1 < ms1mzlist.Count; idems1++)
{
if (ms1chargelist[idems1] != 0)
{
ms1mzlist[idems1] = ms1mzlist[idems1] * ms1chargelist[idems1] - ms1chargelist[idems1] * 1.0079;
}
}
List <int> ms1deconvolutionindexbefore = new List <int>();
for (int ideconms1 = 0; ideconms1 < ms1mzlist.Count; ideconms1++)
{
if (ms1mzlist[ideconms1] != 0)
{
double ms1mzdecon = ms1mzlist[ideconms1];
double ms1intensitydecon = ms1intensitylist[ideconms1];
double ms1baselinedecon = ms1baselinelist[ideconms1];
int ims1deconcount = 1;
for (int jdeconms1 = ideconms1 + 1; jdeconms1 < ms1mzlist.Count; jdeconms1++)
{
double ms1mzdecondiff = Math.Abs(ms1mzlist[jdeconms1] - ms1mzlist[ideconms1]);
if (ms1mzdecondiff <= mzdecontol)
{
ms1deconvolutionindexbefore.Add(jdeconms1);
ms1mzdecon = ms1mzdecon + ms1mzlist[jdeconms1];
ms1intensitydecon = ms1intensitydecon + ms1intensitylist[jdeconms1];
ims1deconcount++;
}
}
ms1mzlist[ideconms1] = ms1mzdecon / ims1deconcount;
ms1intensitylist[ideconms1] = ms1intensitydecon;
}
}
List <int> ms1deconvolutionindex = new List <int>();
foreach (int ms1deiso in ms1deconvolutionindexbefore)
{
if (!ms1deconvolutionindex.Contains(ms1deiso))
{
ms1deconvolutionindex.Add(ms1deiso);
}
}
ms1deconvolutionindex.Sort();
for (int ide1 = 0; ide1 < ms1deconvolutionindex.Count; ide1++)
{
ms1mzlist.RemoveAt(ms1deconvolutionindex[ide1] - ide1);
ms1intensitylist.RemoveAt(ms1deconvolutionindex[ide1] - ide1);
ms1baselinelist.RemoveAt(ms1deconvolutionindex[ide1] - ide1);
ms1noiselist.RemoveAt(ms1deconvolutionindex[ide1] - ide1);
ms1chargelist.RemoveAt(ms1deconvolutionindex[ide1] - ide1);
}
}
//write the data into the .txt file;
swms1.Write("{0}\t", ms1mzlist.Count);
swms1.Write("{0}\t", scanRT);
for (int ims1mz = 0; ims1mz < ms1mzlist.Count; ims1mz++)
{
swms1.Write("{0};", ms1mzlist[ims1mz]);
}
swms1.Write("\t");
for (int ims1in = 0; ims1in < ms1intensitylist.Count; ims1in++)
{
swms1.Write("{0};", ms1intensitylist[ims1in]);
}
swms1.Write("\t");
for (int ims1in = 0; ims1in < ms1noiselist.Count; ims1in++)
{
swms1.Write("{0};", ms1noiselist[ims1in]);
}
swms1.Write("\t");
for (int ims1base = 0; ims1base < ms1baselinelist.Count; ims1base++)
{
swms1.Write("{0};", ms1baselinelist[ims1base]);
}
swms1.Write("\n");
}
else //extract the ms/ms data, the process is similar with above;
{
swms2.Write("{0}\t", i);
swms2.Write("{0}\t", nOrder);
swms2.Write("{0}\t", dim);
List <double> ms2mzlist = new List <double>();
List <double> ms2intensitylist = new List <double>();
List <double> ms2noiselist = new List <double>();
List <double> ms2chargelist = new List <double>();
List <double> ms2baselinelist = new List <double>();
for (int inx = 0; inx < dim; inx++)
{
double dMassjms2 = labels[0, inx];
double dInms2 = labels[1, inx];
double dBasems2 = labels[3, inx];
double dNoisems2 = labels[4, inx];
double dChams2 = labels[5, inx];
double sonms2 = 0;
if (ms2rms_checkbox == "ms2rms")
{
sonms2 = (dInms2 - dBasems2) / (dNoisems2 - dBasems2);
}
else
{
sonms2 = dInms2 / dNoisems2;
}
if (sonms2 >= ms2sonthreshold)
{
ms2chargelist.Add(dChams2);
ms2mzlist.Add(dMassjms2);
ms2intensitylist.Add(dInms2);
ms2noiselist.Add(dNoisems2);
ms2baselinelist.Add(dBasems2);
}
else
{
ms2chargelist.Add(0);
ms2mzlist.Add(0);
ms2intensitylist.Add(0);
ms2noiselist.Add(0);
ms2baselinelist.Add(0);
}
}
List <int> ms2mzzeroindex = new List <int>();
for (int izero = 0; izero < ms2mzlist.Count; izero++)
{
if (ms2mzlist[izero] == 0)
{
ms2mzzeroindex.Add(izero);
}
}
for (int izero1 = 0; izero1 < ms2mzzeroindex.Count(); izero1++)
{
ms2mzlist.RemoveAt(ms2mzzeroindex[izero1] - izero1);
ms2intensitylist.RemoveAt(ms2mzzeroindex[izero1] - izero1);
ms2baselinelist.RemoveAt(ms2mzzeroindex[izero1] - izero1);
ms2noiselist.RemoveAt(ms2mzzeroindex[izero1] - izero1);
ms2chargelist.RemoveAt(ms2mzzeroindex[izero1] - izero1);
}
for (int ims2reso = 0; ims2reso < ms2mzlist.Count; ims2reso++)
{
if (ms2mzlist[ims2reso] != 0)
{
double ms2mzreso = ms2mzlist[ims2reso] * ms2intensitylist[ims2reso];
double ms2intensityreso = ms2intensitylist[ims2reso];
double ms2baselinereso = ms2baselinelist[ims2reso];
int iresocount = 1;
for (int jms2reso = ims2reso + 1; jms2reso < ms2mzlist.Count; jms2reso++)
{
double ms2resodiff = ms2mzlist[jms2reso] - ms2mzlist[jms2reso - 1];
if (ms2resodiff > ms2resolutiontol)
{
break;
}
if (ms2resodiff <= ms2resolutiontol)
{
ms2mzreso = ms2mzreso + ms2mzlist[jms2reso] * ms2intensitylist[jms2reso];
ms2intensityreso = ms2intensityreso + ms2intensitylist[jms2reso];
ms2intensitylist[jms2reso] = 0;
iresocount++;
}
}
ms2mzlist[ims2reso] = ms2mzreso / ms2intensityreso;
ms2intensitylist[ims2reso] = ms2intensityreso;
}
}
List <int> ms2intensityzeroafterresoindex = new List <int>();
for (int izero = 0; izero < ms2mzlist.Count; izero++)
{
if (ms2intensitylist[izero] == 0)
{
ms2intensityzeroafterresoindex.Add(izero);
}
}
for (int izero1 = 0; izero1 < ms2intensityzeroafterresoindex.Count(); izero1++)
{
ms2mzlist.RemoveAt(ms2intensityzeroafterresoindex[izero1] - izero1);
ms2intensitylist.RemoveAt(ms2intensityzeroafterresoindex[izero1] - izero1);
ms2baselinelist.RemoveAt(ms2intensityzeroafterresoindex[izero1] - izero1);
ms2noiselist.RemoveAt(ms2intensityzeroafterresoindex[izero1] - izero1);
ms2chargelist.RemoveAt(ms2intensityzeroafterresoindex[izero1] - izero1);
}
if (deisotope_checkbox == "deisotope")
{
List <int> ms2deisotopindexbefore = new List <int>();
for (int ims2 = 0; ims2 < ms2mzlist.Count(); ims2++)
{
if (ms2chargelist[ims2] != 0)
{
for (int jms2 = ims2 + 1; jms2 < ms2mzlist.Count(); jms2++)
{
double ms2mzdiff = ms2mzlist[jms2] - ms2mzlist[ims2];
double ms2tolvalue = Math.Abs(massNeutron / ms2chargelist[ims2] - ms2mzdiff);
if (ms2tolvalue <= mztol && ms2intensitylist[jms2] < ms2intensitylist[ims2])
{
ms2deisotopindexbefore.Add(jms2);
}
}
}
}
List <int> ms2deisotopindex = new List <int>();
foreach (int ms2deiso in ms2deisotopindexbefore)
{
if (!ms2deisotopindex.Contains(ms2deiso))
{
ms2deisotopindex.Add(ms2deiso);
}
}
ms2deisotopindex.Sort();
for (int ide2 = 0; ide2 < ms2deisotopindex.Count(); ide2++)
{
ms2mzlist.RemoveAt(ms2deisotopindex[ide2] - ide2);
ms2intensitylist.RemoveAt(ms2deisotopindex[ide2] - ide2);
ms2noiselist.RemoveAt(ms2deisotopindex[ide2] - ide2);
ms2baselinelist.RemoveAt(ms2deisotopindex[ide2] - ide2);
ms2chargelist.RemoveAt(ms2deisotopindex[ide2] - ide2);
}
}
if (deconvolution_checkbox == "deconvolution")
{
for (int idems2 = 0; idems2 < ms2mzlist.Count; idems2++)
{
if (ms2chargelist[idems2] != 0)
{
ms2mzlist[idems2] = ms2mzlist[idems2] * ms2chargelist[idems2] - (ms2chargelist[idems2] - 1) * 1.0079;
}
}
List <int> ms2deconvolutionindexbefore = new List <int>();
for (int ideconms2 = 0; ideconms2 < ms2mzlist.Count; ideconms2++)
{
if (ms2mzlist[ideconms2] != 0)
{
double ms2mzdecon = ms2mzlist[ideconms2];
double ms2intensitydecon = ms2intensitylist[ideconms2];
int ims2deconcount = 1;
for (int jdeconms2 = ideconms2 + 1; jdeconms2 < ms2mzlist.Count; jdeconms2++)
{
double ms2mzdecondiff = Math.Abs(ms2mzlist[jdeconms2] - ms2mzlist[ideconms2]);
if (ms2mzdecondiff <= mzdecontol)
{
ms2deconvolutionindexbefore.Add(jdeconms2);
ms2mzdecon = ms2mzdecon + ms2mzlist[jdeconms2];
ms2intensitydecon = ms2intensitydecon + ms2intensitylist[jdeconms2];
ims2deconcount++;
}
}
ms2mzlist[ideconms2] = ms2mzdecon / ims2deconcount;
ms2intensitylist[ideconms2] = ms2intensitydecon;
}
}
List <int> ms2deconvolutionindex = new List <int>();
foreach (int ms2deiso in ms2deconvolutionindexbefore)
{
if (!ms2deconvolutionindex.Contains(ms2deiso))
{
ms2deconvolutionindex.Add(ms2deiso);
}
}
ms2deconvolutionindex.Sort();
for (int ide2 = 0; ide2 < ms2deconvolutionindex.Count; ide2++)
{
ms2mzlist.RemoveAt(ms2deconvolutionindex[ide2] - ide2);
ms2intensitylist.RemoveAt(ms2deconvolutionindex[ide2] - ide2);
ms2baselinelist.RemoveAt(ms2deconvolutionindex[ide2] - ide2);
ms2noiselist.RemoveAt(ms2deconvolutionindex[ide2] - ide2);
ms2chargelist.RemoveAt(ms2deconvolutionindex[ide2] - ide2);
}
}
swms2.Write("{0}\t", ms2mzlist.Count);
swms2.Write("{0}\t", scanRT);
for (int ims2mz = 0; ims2mz < ms2mzlist.Count; ims2mz++)
{
swms2.Write("{0};", ms2mzlist[ims2mz]);
}
swms2.Write("\t");
for (int ims2in = 0; ims2in < ms2intensitylist.Count; ims2in++)
{
swms2.Write("{0};", ms2intensitylist[ims2in]);
}
swms2.Write("\t");
for (int ims2noise = 0; ims2noise < ms2noiselist.Count; ims2noise++)
{
swms2.Write("{0};", ms2noiselist[ims2noise]);
}
swms2.Write("\t");
for (int ims2base = 0; ims2base < ms2baselinelist.Count; ims2base++)
{
swms2.Write("{0};", ms2baselinelist[ims2base]);
}
swms2.Write("\n");
}
}
swms1.Flush();
swms1.Close();
swms2.Flush();
swms2.Close();
}
#endregion
#region
else if (extracttype == "LocalData(SMPR)")
{
// creat a new file name for "LocalData(SMPR)";
string outfile = newfilepath + "\\" + "LocalData(SMPR)_" + filename + ".txt";
StreamWriter sw = File.AppendText(outfile);
sw.Write("ScanNum\tMSOrder\tPeakNumber\tRT\n");
int specnum = 0;
rawfile.GetNumSpectra(ref specnum);
for (int i = 1; i <= specnum; i++)
{
System.Threading.Thread.Sleep(0);
SetTextMessage(100 * i / specnum);
int nOrder = 0;
rawfile5.GetMSOrderForScanNum(i, ref nOrder);
double scanRT = 0;
rawfile.RTFromScanNum(i, ref scanRT);
sw.Write("{0}\t", i);
sw.Write("{0}\t", nOrder);
object varlabels = null;
object varflags = null;
rawfile5.GetLabelData(ref varlabels, ref varflags, ref i);
var labels = (double[, ])varlabels;
int dim = labels.GetLength(1);
sw.Write("{0}\t", dim);
sw.Write("{0}\n", scanRT);
}
sw.Flush();
sw.Close();
}
//
else
{
MessageBox.Show("Please Select a type below!");
}
#endregion
}
MessageBox.Show("Extract Done!");
}
else
{
MessageBox.Show("Please Select a File!");
}
#endregion
}
