private Comb.mzI[][] newScansRaw(BinStackOptions _options,
Comb.mzI[][] _scansRaw,
int _spectrumToQuantitate,
double _parentMass,
double[,] _specData)
{
double[,] data = _specData as double[, ];
double minMass = data[0, 0];
double maxMass = data[0, data.GetUpperBound(1)];
int minMassPos = 0;
int maxMassPos = data.GetUpperBound(1);
Comb.mzI[][] scansRaw = (Comb.mzI[][])_scansRaw.Clone();
//if (minMassPos == 0)
//{
// return scansRaw;
//}
if (_options.useParentalMass)
{
//Mass conversions (mz data in the raw file is expressed in Th)
switch (_options.parentalMassUnits)
{
case massUnits.Th:
minMass = _parentMass - _options.parentalMass / 2;
maxMass = _parentMass + _options.parentalMass / 2;
break;
case massUnits.mTh:
// Th = mTh * 1e3
minMass = _parentMass - _options.parentalMass * 1000 / 2;
maxMass = _parentMass + _options.parentalMass * 1000 / 2;
break;
case massUnits.ppm:
// Th = ppm * parentalMass * 1e-6
minMass = _parentMass - _options.parentalMass * _parentMass * 1e-6;
maxMass = _parentMass - _options.parentalMass * _parentMass * 1e-6;
break;
}
if (minMass < data[0, 0])
{
minMass = data[0, 0];
}
if (maxMass > data[0, data.GetUpperBound(1)])
{
maxMass = data[0, data.GetUpperBound(1)];
}
}
//determine index of minimum mass
for (int pos = 0; pos <= data.GetUpperBound(1); pos++)
{
if (data[0, pos] < minMass)
{
minMassPos = pos + 1;
}
else
{
break;
}
}
//determine index of maximum mass
for (int pos = data.GetUpperBound(1); pos >= 0; pos--)
{
if (data[0, pos] > maxMass)
{
maxMassPos = pos - 1;
}
else
{
break;
}
}
int diffPos = maxMassPos - minMassPos;
extData = new Comb.mzI[diffPos + 1];
int counter = 0;
for (int k = minMassPos; k <= maxMassPos; k++)
{
extData[counter].mz = data[0, k];
extData[counter].I = data[1, k];
counter++;
}
int i = 0;
try
{
if (scansRaw[_spectrumToQuantitate] == null)
{
scansRaw[_spectrumToQuantitate] = new Comb.mzI[1000];
}
switch (_options.mode)
{
case adquisitionMode.position:
scansRaw[_spectrumToQuantitate] = (Comb.mzI[])extData.Clone();
break;
case adquisitionMode.RetentionTime:
for (i = extData.GetLowerBound(0); i < extData.GetUpperBound(0); i++)
{
scansRaw[_spectrumToQuantitate][i].I = extData[i].I;
scansRaw[_spectrumToQuantitate][i].mz = extData[i].mz;
}
break;
}
}
catch
{
//blank spectrum
extData = new Comb.mzI[1];
//scansRaw[_spectrumToQuantitate] = (Comb.mzI[])extData.Clone();
scansRaw[_spectrumToQuantitate] = null;
//return null;
}
return(scansRaw);
}
private void createBinStackBtn_Click(object sender, EventArgs e)
{
options = new BinStackOptions();
if (tbxQuiXML.Text.Trim() == "")
{
MessageBox.Show("No QuiXML selected", "Error");
return;
}
int quiXMLlength = tbxQuiXML.Text.Trim().Length;
if (quiXMLlength > 251)
{
MessageBox.Show(String.Concat("QuiXML file path too long,",
"\nplease shorten it at least ",
(quiXMLlength - 251).ToString(),
" characters\nand paste it here again"), "Error");
return;
}
if (tbxSchema.Text.Trim() == "")
{
MessageBox.Show("No QuiXML schema (xsd) selected", "Error");
return;
}
if (tbxSpecFolder.Text.Trim() == "")
{
MessageBox.Show("No spectra folder selected", "Error");
return;
}
if (cbxSpecType.Text.Trim() == "")
{
MessageBox.Show("No spectrum type selected", "Error");
return;
}
if (cbxPosition.Text == "")
{
MessageBox.Show("No spectrum position selected", "Error");
return;
}
if (rbnImportParental.Checked && tbxParentalMZ.Text == "")
{
MessageBox.Show("No parental mass selected", "Error");
return;
}
if (rbnImportWindowBetween.Checked && (tbxWindowEnd.Text == "" || tbxWindowStart.Text == ""))
{
MessageBox.Show("No window selected", "Error");
return;
}
options.mode = adquisitionMode.position;
foreach (spectrumPositions sp in specPositionsChoose)
{
if (cbxPosition.Text == sp.ToString())
{
options.spectrumPos = sp;
break;
}
}
foreach (spectrumTypes spt in spectrumTypesChoose)
{
if (cbxSpecType.Text == spt.ToString())
{
options.spectrumType = spt;
break;
}
}
if (rbnImportParental.Checked)
{
options.useParentalMass = true;
options.useWindow = false;
foreach (massUnits mu in massUnitsChoose)
{
if (cbxUnits.Text == mu.ToString())
{
options.units = mu;
break;
}
}
try
{
options.parentalMass = float.Parse(tbxParentalMZ.Text.Trim());
}
catch
{
MessageBox.Show("Parental mass is not valid (not a number)", "Error");
return;
}
}
if (rbnImportWindowBetween.Checked)
{
options.useWindow = true;
options.useParentalMass = false;
foreach (massUnits mu in massUnitsChoose)
{
if (cbxUnits.Text == mu.ToString())
{
options.units = mu;
break;
}
}
try
{
options.windowStart = float.Parse(tbxWindowStart.Text.Trim());
options.windowEnd = float.Parse(tbxWindowEnd.Text.Trim());
}
catch
{
MessageBox.Show("Parental mass is not valid (not a number)", "Error");
return;
}
}
if (chbAverageSpectra.Checked)
{
options.averageSpectra = true;
/*Everything between inflection points
* Maximum + inflection points (not implemented yet)
* Three most intense (not implemented yet)*/
string methodName = cbxAverageMethod.Text.Split(':')[0];
switch (methodName)
{
case "THERMO WIDTH": //Everything between inflection points (Thermo method, width = 0.0001)
options.averagingMethod = averagingMethod.everything_ThermoMethod_Width0001;
break;
case "LAB ALL": // Everything between inflection points (Thermo method, no width specified)
options.averagingMethod = averagingMethod.everything_ThermoMethod_noWidth;
break;
case "THERMO ALL": // Everything between inflection points (averaging extrapolations)
options.averagingMethod = averagingMethod.everything_InlabMethod;
break;
case "LAB INFLECMAX": // Most intense + inflection points (averaging extrapolations)
options.averagingMethod = averagingMethod.mostIntenseAndInflections_InlabMethod;
break;
case "LAB5": // Five spectra within the chromatographic peak (averaging extrapolations)
options.averagingMethod = averagingMethod.fiveSpectra_InlabMethod;
break;
case "Three most intense (not implemented yet)":
options.averagingMethod = averagingMethod.mostIntense;
break;
default: options.averagingMethod = averagingMethod.none;
break;
}
}
else
{
options.averageSpectra = false;
options.averagingMethod = averagingMethod.none;
}
this.lblStatus.Text = "Generating binaries stack... loading quiXML...";
this.lblStatus.Visible = true;
genStack(tbxSpecFolder.Text.Trim(), options);
}
/// <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[] scannumber,
double[] parentMassList,
BinStackOptions options)
// string specType, string spectrumPosition)
{
int stepSearch;
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[scannumber.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);
}
QuiXoT.Forms.frmInvisible frmReader = new QuiXoT.Forms.frmInvisible();
//frmReader.Show();
frmReader.openRaw(rawFilePath);
int nSpec = frmReader.numSpectra();
//object a2 = frmReader.getSpectrum(1900);
#region mode: retention time
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.indexToRetentionTime(1900);
startTime = frmReader.indexToRetentionTime(1);
endTime = frmReader.indexToRetentionTime(frmReader.spectrumCount());
//_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.indexToRetentionTime(scannumber[i]);
//_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.mode == adquisitionMode.position)
{
//for each identified spectrum (~each row of the QuiXML)
for (int i = 0; i <= scannumber.GetUpperBound(0); i++)
{
bool spectrumFound = false;
double parentMass = 0;
if (options.useParentalMass)
{
parentMass = parentMassList[i];
}
try
{
int tentativeSpectrum = (int)(scannumber[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 > frmReader.spectrumCount())
{
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.Close();
return(scansRaw);
}
private void genStack(string rawPath,
BinStackOptions options)
{
Application.DoEvents();
try
{
this.lblStatus.Text = "Generating binaries stack... Creating index...";
this.lblStatus.Visible = true;
string idFileXml = this.tbxQuiXML.Text.Trim();
string idSchema = this.tbxSchema.Text.Trim();
string stackIndexFolder = idFileXml.Substring(0, idFileXml.LastIndexOf(@"\")) + "\\binStack\\";
string stackIndexFile = stackIndexFolder + "index.idx";
if (!Directory.Exists(stackIndexFolder))
{
Directory.CreateDirectory(stackIndexFolder);
}
//scans by frame
int scbyframe = 100;
//load the XML file to a DataSet object
DataSet quiXML = new DataSet();
quiXML.ReadXmlSchema(idSchema);
quiXML.ReadXml(idFileXml, XmlReadMode.Auto);
DataView quiXMLv = new DataView(quiXML.Tables["peptide_match"]);
if (!(options.averagingMethod == averagingMethod.mostIntense ||
options.averagingMethod == averagingMethod.none))
{
if (!quiXMLv.Table.Columns.Contains("PeakStart") ||
!quiXMLv.Table.Columns.Contains("PeakEnd"))
{
MessageBox.Show("This QuiXML file does not seem" +
"to contain PeakStart / PeakEnd columns,\n" +
"did you forget to use QuiXtoQuiX to get the inflection points?");
lblStatus.Text = "Error: no inflection points in QuiXML.";
return;
}
}
//calculate number of frames
//int inumFrames = binStack.countFrames(idFileXml, scbyframe);
int inumFrames = binStack.countFrames(quiXMLv, scbyframe);
//generate index
object parObject = "";
binStack[] stackIndex = binStack.genIndex(quiXMLv,
rawPath,
scbyframe,
options);
//generate and save frames
for (int i = 1; i <= inumFrames; i++)
{
Application.DoEvents();
this.lblStatus.Text = "Generating binaries stack... generating frame " + i.ToString() + "/" + inumFrames.ToString();
binFrame currFrame = binStack.genFrame(stackIndex,
i, scbyframe, rawPath, options, this.lblStatus, ref parObject, i, inumFrames);
if (currFrame == null)
{
return;
}
string frameFile = stackIndexFolder + currFrame.frame.ToString() + ".bfr";
FileStream qFr = new FileStream(frameFile, FileMode.Create, FileAccess.Write);
BinaryFormatter bFr = new BinaryFormatter();
bFr.Serialize(qFr, currFrame);
qFr.Close();
}
//save index
//WARNING: very dangerous change, but necessary to maintain old binstacks: in currFrame
// we swap the values of scanNumber by spectrumIndex (once we have obtained the desired
// spectrum, we use the unique index (spectrumIndex).
for (int i = stackIndex.GetLowerBound(0); i <= stackIndex.GetUpperBound(0); i++)
{
for (int j = stackIndex[i].scan.GetLowerBound(0); j <= stackIndex[i].scan.GetUpperBound(0); j++)
{
int scanNumber_t = stackIndex[i].scan[j].FirstScan;
stackIndex[i].scan[j].FirstScan = stackIndex[i].scan[j].spectrumIndex;
//this is not necessary, but I want to maintain the scanNumber elsewhere...
stackIndex[i].scan[j].spectrumIndex = scanNumber_t;
}
}
FileStream q = new FileStream(stackIndexFile, FileMode.Create, FileAccess.Write);
BinaryFormatter b = new BinaryFormatter();
b.Serialize(q, stackIndex);
q.Close();
string bsXml = Path.GetDirectoryName(idFileXml) + "\\" +
Path.GetFileNameWithoutExtension(idFileXml) + "_bs.xml";
//Save the quiXML changes (spectrumIndex is now written)
quiXML.WriteXml(bsXml);
MessageBox.Show("In order to preserve the old QuiXML, " +
"the new QuiXML containing the spectrumIndex has been saved to:\n\n" +
bsXml + "\n\n" + "Please, remember to use this new QuiXML or its derivations in further analysis.");
}
catch (System.Data.DataException e)
{
MessageBox.Show("Unable to generate binaries stack. System Data Exception thrown : " + e.Message);
}
catch
{
MessageBox.Show("Unable to generate binaries stack");
}
this.lblStatus.Text = "";
this.lblStatus.Visible = false;
}
