static void Main(string[] args)
{
linearEquation Linear = new linearEquation();
quadraticEquation Quadratic = new quadraticEquation();
Validations validations = new Validations();
LinearEquationOperations LinearOperations = new LinearEquationOperations();
QuadraticEquationOperations QuadraticOperations = new QuadraticEquationOperations();
limits <double> Roots = new limits <double>();
Linear.slope = 5;
Linear.y_intercept = 7;
Console.WriteLine(LinearOperations.GetRootLinearEquation(validations, Linear));
Quadratic.coefficient_a = 1;
Quadratic.coefficient_b = 4;
Quadratic.coefficient_c = 3;
Roots.minimLimit = -3;
Roots.maximLimit = -1;
Console.WriteLine(QuadraticOperations.GetValueQuadraticEquation(Quadratic, Roots));
}
public double GetValueQuadraticEquation(quadraticEquation Equation, limits <double> Roots)
{
double Result;
Result = ((Equation.coefficient_a * Math.Pow(Roots.minimLimit, 2) + (Equation.coefficient_b * Roots.maximLimit) + (Equation.coefficient_c)));
return(Result);
}
static void Main(string[] args)
{
linearEquation Linear = new linearEquation();
quadraticEquation Quadratic = new quadraticEquation();
Equations EquationsMethods = new Equations();
limits <double> Roots = new limits <double>();
Linear.slope = 5;
Linear.y_intercept = 7;
Console.WriteLine(EquationsMethods.GetRootLinearEquation(Linear));
Quadratic.coefficient_a = 1;
Quadratic.coefficient_b = 4;
Quadratic.coefficient_c = 3;
Roots.minimLimit = -3;
Roots.maximLimit = -1;
Console.WriteLine(EquationsMethods.GetValueQuadraticEquation(Quadratic, Roots));
}
/// <summary>
/// Reads a given set of selected scans of a given raw
/// </summary>
/// <param name="filePath">(string) directory path of the raws</param>
/// <param name="rawfile">(string) name of the raw to open</param>
/// <param name="scannumber">(int[]) set of MSMS id scans to read</param>
/// <param name="options">options selected to create the binStack</param>
/// <returns>(Comb.mzI[][]) spectrum of each selected scan</returns>
public Comb.mzI[][] ReadScanRaw(string filePath,
string rawfile,
int[] firstScan,
int[] peakStart,
int[] peakEnd,
double[] parentMassList,
BinStackOptions options,
Label _status,
ref object _parObject,
int _currNumFrame,
int _totNumFrames)
// string specType, string spectrumPosition)
{
int stepSearch;
quadraticEquation _par = new quadraticEquation();
switch (options.spectrumPos)
{
case spectrumPositions.previous:
stepSearch = -1;
break;
case spectrumPositions.next:
stepSearch = 1;
break;
default:
stepSearch = 0;
break;
}
if (filePath == null || filePath.Length == 0)
{
return(null);
}
if (rawfile == null || rawfile.Length == 0)
{
return(null);
}
Comb.mzI[][] scansRaw = new Comb.mzI[firstScan.GetUpperBound(0) + 1][];
//open the raw
try
{
int iMaxGeneration = GC.MaxGeneration;
long iTotalMem = GC.GetTotalMemory(true);
rawFilePath = filePath.ToString().Trim() + "\\" + rawfile.ToString().Trim();
}
catch
{
return(null);
}
rawStats frmReader = new rawStats();
//frmReader.Show();
frmReader.openRawFast(rawFilePath);
int nSpec = frmReader.lastSpectrumNumber();
frmReader.initialiseSpectrumTypes(nSpec);
//object a2 = frmReader.getSpectrum(1900);
#region mode: retention time (not used)
// if (options.mode == adquisitionMode.RetentionTime)
// {
// double startTime = new double();
// double endTime = new double();
// double centralTime = new double();
// //short actualIndex = new short();
// //double actualRetentionTime = new double();
// int firstScan = new int();
// int lastScan = new int();
// centralTime = frmReader.getRTfromScanNumber(1900);
// startTime = frmReader.getRTfromScanNumber(1);
// endTime = frmReader.getRTfromScanNumber(frmReader.numSpectra());
// //_Spectra.IndexToRetentionTime(1, ref actualIndex, ref startTime);
// //_Spectra.IndexToRetentionTime(_Spectra.Count, ref actualIndex, ref endTime);
// for (int i = 0; i <= scannumber.GetUpperBound(0); i++)
// {
// double parentMass = 0;
// if (options.useParentalMass)
// {
// parentMass = parentMassList[i];
// }
// centralTime = frmReader.getRTfromScanNumber(scannumber[i, 0]);
// //_Spectra.IndexToRetentionTime((short)scannumber[i], ref actualIndex, ref centralTime);
// float timeMargin = options.retentionTime / (2 * 60);
// double startCheckingTime = centralTime - timeMargin;
// double stopCheckingTime = centralTime + timeMargin;
// if (startCheckingTime < startTime) { startCheckingTime = startTime; }
// if (stopCheckingTime > endTime) { stopCheckingTime = endTime; }
// firstScan = frmReader.retentionTimeToIndex(startCheckingTime);
// lastScan = frmReader.retentionTimeToIndex(stopCheckingTime);
// //_Spectra.RetentionTimeToIndex(startCheckingTime, ref actualRetentionTime, ref firstScan);
// //_Spectra.RetentionTimeToIndex(stopCheckingTime, ref actualRetentionTime, ref lastScan);
// try
// {
// for (int j = firstScan; j <= lastScan; j++)
// {
// int tentativeSpectrum = (int)j;
// spectrumTypes ff = frmReader.spectrumTypeFromScanNumber(j);
// //XCALIBURFILESLib.XFilter filt = (XCALIBURFILESLib.XFilter)_filter.ScanNumber(tentativeSpectrum);
// //string ff = filt.Text;
// //XCALIBURFILESLib.XSpectrumRead Xspec = new XCALIBURFILESLib.XSpectrumRead();
// double[,] specData = new double[10, 0];
// if (options.spectrumType == ff)
// {
// specData = (double[,])frmReader.getSpectrum(tentativeSpectrum);
// scansRaw = (Comb.mzI[][])newScansRaw(options, scansRaw, i, parentMass, specData).Clone();
// }
// //switch (options.spectrumType)
// //{
// // case spectrumTypes.Full:
// // if (ff == spectrumTypes.Full)
// // Xspec = (XCALIBURFILESLib.XSpectrumRead)frmReader.getSpectrum(tentativeSpectrum);
// // //Xspec = _Spectra.Item(tentativeSpectrum) as XCALIBURFILESLib.XSpectrumRead;
// // scansRaw = (Comb.mzI[][])newScansRaw(options, scansRaw, i, parentMass, Xspec).Clone();
// // break;
// // case spectrumTypes.MSMS:
// // if (ff == spectrumTypes.MSMS)
// // Xspec = (XCALIBURFILESLib.XSpectrumRead)frmReader.getSpectrum(tentativeSpectrum);
// // //Xspec = _Spectra.Item(tentativeSpectrum) as XCALIBURFILESLib.XSpectrumRead;
// // scansRaw = (Comb.mzI[][])newScansRaw(options, scansRaw, i, parentMass, Xspec).Clone();
// // break;
// // case spectrumTypes.ZoomScan:
// // if (ff == spectrumTypes.ZoomScan)
// // Xspec = (XCALIBURFILESLib.XSpectrumRead)frmReader.getSpectrum(tentativeSpectrum);
// // //Xspec = _Spectra.Item(tentativeSpectrum) as XCALIBURFILESLib.XSpectrumRead;
// // scansRaw = (Comb.mzI[][])newScansRaw(options, scansRaw, i, parentMass, Xspec).Clone();
// // break;
// //}
// }
// }
// catch
// {
// //_Raw.Close();
// //_Detector = null;
// //_Spectra = null;
// //GC.Collect();
// //GC.WaitForPendingFinalizers();
// ////MessageBox.Show("Could not open selected raw file: " + e.Message);
// ////Application.DoEvents();
// //return null;
// }
// }
// }
#endregion
#region mode: position
if (!(options.averagingMethod == averagingMethod.mostIntense ||
options.averagingMethod == averagingMethod.none))
{
if (_parObject == "")
{
_par.rawFilePath = rawFilePath;
_par.hasBeenCalculated = false;
_parObject = (object)_par;
}
else
{
_par = (quadraticEquation)_parObject;
if (_par.rawFilePath != rawFilePath)
{
_par.rawFilePath = rawFilePath;
_par.hasBeenCalculated = false;
}
}
string filter = "FTMS + p NSI Full ms"; // filter for fulls
int totScans = firstScan.Length;
for (int i = 0; i < totScans; i++)
{
_status.Text = "Averaging scan " + (i + 1).ToString() + "/" + totScans.ToString() +
" (frame " + _currNumFrame.ToString() + "/" + _totNumFrames.ToString() + ")";
Application.DoEvents();
double[,] specData = new double[10, 0];
try
{
int maxNumberOfLateralZeros = 4;
double firstMz = 0;
double lastMz = 0;
if (!options.useParentalMass && !options.useWindow)
{
double[,] firstSpec = (double[, ])frmReader.getSpectrum(peakStart[i]);
getMinAndMaxMass(options, parentMassList[i], firstSpec, ref firstMz, ref lastMz);
}
if (options.useParentalMass)
{
getMinAndMaxMass(options, parentMassList[i], null, ref firstMz, ref lastMz);
}
if (options.useWindow)
{
firstMz = options.windowStart;
lastMz = options.windowEnd;
}
// fast but bad
switch (options.averagingMethod)
{
case averagingMethod.everything_ThermoMethod_noWidth:
{
// mostly fast but very bad
specData = (double[, ])frmReader.getAveragedSpectrumThermoFunction(peakStart[i],
peakEnd[i],
firstMz,
lastMz,
filter,
0);
break;
}
case averagingMethod.everything_ThermoMethod_Width0001:
{
// mostly fast but somewhat acceptable
double optimisedWidth = 0.0001;
specData = (double[, ])frmReader.getAveragedSpectrumThermoFunction(peakStart[i],
peakEnd[i],
firstMz,
lastMz,
filter,
optimisedWidth);
break;
}
case averagingMethod.everything_InlabMethod:
{
// slow but good
specData = (double[, ])frmReader.getAveragedSpectrum(peakStart[i],
peakEnd[i],
firstScan[i],
true, 0,
firstMz,
lastMz,
maxNumberOfLateralZeros,
ref _par,
_status);
_parObject = (object)_par;
break;
//msnPerFull.rawStats.saveIndividualSpectrum(specData, "jv");
}
case averagingMethod.mostIntenseAndInflections_InlabMethod:
{
specData = (double[, ])frmReader.getAveragedSpectrum(peakStart[i],
peakEnd[i],
firstScan[i],
true, 3,
firstMz,
lastMz,
maxNumberOfLateralZeros,
ref _par,
_status);
_parObject = (object)_par;
break;
}
case averagingMethod.fiveSpectra_InlabMethod:
{
specData = (double[, ])frmReader.getAveragedSpectrum(peakStart[i],
peakEnd[i],
firstScan[i],
false, 5,
firstMz,
lastMz,
maxNumberOfLateralZeros,
ref _par,
_status);
_parObject = (object)_par;
break;
}
}
//double[,] otherData = (double[,])frmReader.getSpectrum(firstScan[i]);
//msnPerFull.rawStats.saveIndividualSpectrum(specData, "thermo_width1-001");
}
catch
{
//this catch prevents from non existing scans
}
if (specData == null)
{
_status.Text = "Raw file error found.";
return(null);
}
try
{
double parentMass = 0;
if (options.useParentalMass)
{
parentMass = parentMassList[i];
}
scansRaw = (Comb.mzI[][])newScansRaw(options, scansRaw, i, parentMass, specData).Clone();
}
catch
{
//this catch prevents from empty scans
}
}
}
else
{
if (options.mode == adquisitionMode.position)
{
//for each identified spectrum (~each row of the QuiXML)
for (int i = 0; i <= firstScan.GetUpperBound(0); i++)
{
bool spectrumFound = false;
double parentMass = 0;
if (options.useParentalMass)
{
parentMass = parentMassList[i];
}
try
{
int tentativeSpectrum = (int)(firstScan[i] + stepSearch);
int spectrumToQuantitate = 0;
if (options.spectrumPos == spectrumPositions.same)
{
spectrumFound = true;
spectrumToQuantitate = tentativeSpectrum;
}
while (!spectrumFound)
{
if (tentativeSpectrum < 0)
{
MessageBox.Show("Error: reached lower bound for scans.");
return(null);
}
if (tentativeSpectrum > nSpec)
{
MessageBox.Show("Error: reached upper bound for scans.");
return(null);
}
try
{
//XCALIBURFILESLib.XFilter filt = (XCALIBURFILESLib.XFilter)_filter.ScanNumber(tentativeSpectrum); //(short)scannumber[i]
spectrumTypes st = frmReader.spectrumTypeFromScanNumber(tentativeSpectrum);
//string ff = "";// filt.Text;
if (options.spectrumType == st)
{
spectrumFound = true;
spectrumToQuantitate = tentativeSpectrum;
}
}
catch
{
GC.Collect();
GC.WaitForPendingFinalizers();
//MessageBox.Show("Could not open selected raw file: " + e.Message);
//Application.DoEvents();
return(null);
}
tentativeSpectrum = (int)(tentativeSpectrum + stepSearch);
}
if (spectrumFound)
{
double[,] specData = new double[10, 0];
try
{
specData = (double[, ])frmReader.getSpectrum(spectrumToQuantitate);
}
catch
{
//this catch prevents from non existing scans
}
try
{
scansRaw = (Comb.mzI[][])newScansRaw(options, scansRaw, i, parentMass, specData).Clone();
}
catch
{
//this catch prevents from empty scans
}
}
//XCALIBURFILESLib.XSpectrumRead Xspec = frmReader.getSpectrum(spectrumToQuantitate) as XCALIBURFILESLib.XSpectrumRead;
//XCALIBURFILESLib.XSpectrumRead Xspec = _Spectra.Item(spectrumToQuantitate) as XCALIBURFILESLib.XSpectrumRead;
#region not-useful
//try
//{
// XCALIBURFILESLib.XParentScans XparentScans = Xspec.ParentScans as XCALIBURFILESLib.XParentScans;
// short prScansCount = XparentScans.Count;
// short numOfSpectra = _Spectra.Count;
// string[] fll = new string[_filter.Count];
// for (int k=0; k<_filter.Count;k++)
// {
// XCALIBURFILESLib.XFilter fil= (XCALIBURFILESLib.XFilter)_filter.Item(1);
// fll[k] = fil.Text;
// //fil.Validate
// }
//}
//catch { }
//Get the instrument name
//XCALIBURFILESLib.XInstrument instrument = _Detector.Instrument as XCALIBURFILESLib.XInstrument;
//instrumentName = instrument.Name;
//instrument = null;
// spectrum data
#endregion
//***scansRaw = (Comb.mzI[][])newScansRaw(options, scansRaw, i, parentMass, Xspec);
}
catch
{
GC.Collect();
GC.WaitForPendingFinalizers();
//MessageBox.Show("Could not open selected raw file: " + e.Message);
//Application.DoEvents();
return(null);
}
}
}
}
#endregion
GC.Collect();
frmReader.closeRaw();
return(scansRaw);
}
