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);
}
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 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;
}