public SpectrumDisplayInfo(SpectrumInfo spectrumInfo, string replicateName,
MsDataFileUri filePath, int fileOrder, double?retentionTime, bool isBest)
{
_spectrumInfo = spectrumInfo;
ReplicateName = replicateName;
FilePath = filePath;
FileOrder = fileOrder;
RetentionTime = retentionTime;
IsBest = isBest;
}
private static DbRefSpectra MakeRefSpectrum(SpectrumInfo spectrum, string peptideSeq, string modifiedPeptideSeq, double precMz, int precChg)
{
var refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = precMz,
PrecursorCharge = precChg,
PeptideModSeq = modifiedPeptideSeq
};
MakeRefSpectrum(spectrum, refSpectra);
return(refSpectra);
}
private static void MakeRefSpectrum(SpectrumInfo spectrum, DbRefSpectra refSpectra)
{
short copies = (short)spectrum.SpectrumHeaderInfo.GetRankValue(LibrarySpec.PEP_RANK_COPIES);
var peaksInfo = spectrum.SpectrumPeaksInfo;
refSpectra.Copies = copies;
refSpectra.NumPeaks = (ushort)peaksInfo.Peaks.Length;
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
}
private static string GenerateThermoScanFilter(SpectrumInfo spectrumInfo)
{
string activationMethod;
float collisionEnergy;
if (spectrumInfo is SpectrumInfoMzXML mzXmlSpectrum)
{
activationMethod = mzXmlSpectrum.ActivationMethod;
collisionEnergy = mzXmlSpectrum.CollisionEnergy;
if (!string.IsNullOrWhiteSpace(mzXmlSpectrum.FilterLine))
{
return(mzXmlSpectrum.FilterLine);
}
}
else
{
activationMethod = "xxx";
collisionEnergy = 0;
}
var centroidOrProfile = spectrumInfo.Centroided ? "c" : "p";
// ReSharper disable once ConvertIfStatementToSwitchExpression
// ReSharper disable once ConvertIfStatementToSwitchStatement
if (spectrumInfo.MSLevel == 1)
{
return(string.Format("{0} {1} Full ms [{2}-{3}]",
spectrumInfo.Polarity, centroidOrProfile, spectrumInfo.MzRangeStart, spectrumInfo.MzRangeEnd));
}
if (spectrumInfo.MSLevel > 1)
{
return(string.Format("{0} {1} Full ms{2} {3}@{4}{5:F2} [{6}-{7}]",
spectrumInfo.Polarity,
centroidOrProfile,
spectrumInfo.MSLevel,
spectrumInfo.ParentIonMZ,
activationMethod,
collisionEnergy,
spectrumInfo.MzRangeStart,
spectrumInfo.MzRangeEnd));
}
return("Invalid value for MSLevel: " + spectrumInfo.MSLevel);
}
public SpectrumDisplayInfo(SpectrumInfo spectrumInfo)
{
_spectrumInfo = spectrumInfo;
IsBest = true;
}
/// <summary>
/// This function trigges when an interpretation is double clicked.
/// It prepares the annotation and spectrum viewer panels.
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
public void triggerSpectrumViewer(object sender, EventArgs e)
{
// Get the current row
DataGridViewRow row = spectraGrid.CurrentRow;
if (row != null)
{
// Get the result and variant objects associated with this row
Object[] tags = row.Tag as Object[];
SpectrumInfo spectrum = tags[0] as SpectrumInfo;
VariantInfo variant = tags[1] as VariantInfo;
if (spectrum != null && currentSpectraGridSelection != row)
{
try {
// Resolve the spectrum source
var source = Path.GetFileNameWithoutExtension(spectrum.id.source.name);
var paths = Properties.Settings.Default.SourcePath.Split(";".ToCharArray());
var matches = Util.FindFileInSearchPath(source, new string[] { "mzXML", "mzML", "mgf", "RAW" }, paths.ToArray(), true);
if (matches.Length == 0)
{
MessageBox.Show("Can't find source. Set the source folder path.");
}
else
{
// Convert the interpretation for seems compatibility
var interpetation = variant.ToSimpleString();
interpetation = interpetation.Replace('(', '[');
interpetation = interpetation.Replace(')', ']');
splitContainer4.Panel2.Hide();
splitContainer1.Panel2.Hide();
splitContainer5.Panel1.Hide();
splitContainer5.Panel2.Hide();
Application.DoEvents();
UniqueSpectrumID uniqueSpectrumID;
// Create a spectrum viewer and add its components
if (spectrum.nativeID != null && spectrum.nativeID.Length > 0)
{
currentSpectrumViewer = new SpectrumViewer(matches[0], spectrum.nativeID, interpetation);
uniqueSpectrumID = new UniqueSpectrumID(source, spectrum.nativeID, spectrum.id.charge);
}
else
{
currentSpectrumViewer = new SpectrumViewer(matches[0], spectrum.id.index, interpetation);
uniqueSpectrumID = new UniqueSpectrumID(source, spectrum.id.index, spectrum.id.charge);
}
splitContainer4.Panel2.Controls.Clear();
splitContainer4.Panel2.Controls.Add(currentSpectrumViewer.annotationPanel);
splitContainer5.Panel1.Controls.Clear();
splitContainer5.Panel1.Controls.Add(currentSpectrumViewer.spectrumPanel);
splitContainer5.Panel2.Controls.Clear();
splitContainer5.Panel2.Controls.Add(currentSpectrumViewer.fragmentationPanel);
splitContainer5.Panel2.AutoScroll = true;
splitContainer1.Panel2.Controls.Add(splitContainer5);
splitContainer1.Panel2.Show();
splitContainer4.Panel2.Show();
splitContainer5.Panel1.Show();
splitContainer5.Panel2.Show();
Application.DoEvents();
// If we have a seconday result associated with this spectrum,
// set the mechanism in spectrum viewer to see it.
if (alternativeInterpretations != null)
{
if (alternativeInterpretations.Contains(uniqueSpectrumID))
{
VariantInfo alt = alternativeInterpretations[uniqueSpectrumID];
interpetation = alt.ToSimpleString();
interpetation = interpetation.Replace('(', '[');
interpetation = interpetation.Replace(')', ']');
currentSpectrumViewer.setSecondarySequence(interpetation);
}
}
currentSpectraGridSelection = row;
}
} catch (Exception exp) {
MessageBox.Show(exp.StackTrace);
MessageBox.Show("Failed to show spectrum. Check raw data path.");
}
}
}
}
private static void ValidateScanInfo(IReadOnlyDictionary <int, string> expectedScanInfo, SpectrumInfo spectrumInfo)
{
string scanSummary;
switch (spectrumInfo)
{
case SpectrumInfoMzXML mzXmlSpectrum:
{
string filterLine;
// Only files created with ReAdW will have filter line text
if (string.IsNullOrWhiteSpace(mzXmlSpectrum.FilterLine))
{
filterLine = string.Empty;
}
else
{
filterLine = mzXmlSpectrum.FilterLine.Substring(0, 12) + "...";
}
scanSummary =
string.Format(
"{0,3} {1} {2,5} {3:F2} {4,3:0} {5,4:0} {6:0.0E+0} {7,8:F3} {8:0.0E+0} {9,8:F2} {10,-6} {11} {12,-5} {13} {14}",
spectrumInfo.ScanNumber, spectrumInfo.MSLevel,
spectrumInfo.PeaksCount, spectrumInfo.RetentionTimeMin,
spectrumInfo.MzRangeStart, spectrumInfo.MzRangeEnd,
spectrumInfo.TotalIonCurrent,
spectrumInfo.BasePeakMZ,
spectrumInfo.BasePeakIntensity,
spectrumInfo.ParentIonMZ,
mzXmlSpectrum.ActivationMethod,
spectrumInfo.Polarity,
spectrumInfo.Centroided,
mzXmlSpectrum.SpectrumType, filterLine);
break;
}
case SpectrumInfoMzData mzDataSpectrum:
var collisionEnergyUnits = mzDataSpectrum.CollisionEnergyUnits.Equals("Percent", StringComparison.OrdinalIgnoreCase)
? "%"
: " " + mzDataSpectrum.CollisionEnergyUnits;
scanSummary =
string.Format(
"{0,3} {1} {2,5} {3,5:F2} {4,3:0} {5,4:0} {6:0.0E+0} {7,8:F3} {8:0.0E+0} {9,8:F2} {10,-6} {11} {12,-6} {13,-10} {14} {15,4:F0}{16} {17,4}",
spectrumInfo.ScanNumber, spectrumInfo.MSLevel,
spectrumInfo.PeaksCount, spectrumInfo.RetentionTimeMin,
spectrumInfo.MzRangeStart, spectrumInfo.MzRangeEnd,
spectrumInfo.TotalIonCurrent, spectrumInfo.BasePeakMZ, spectrumInfo.BasePeakIntensity,
spectrumInfo.ParentIonMZ, mzDataSpectrum.CollisionMethod,
spectrumInfo.Polarity, spectrumInfo.Centroided,
mzDataSpectrum.SpectrumType, mzDataSpectrum.ScanMode,
mzDataSpectrum.CollisionEnergy,
collisionEnergyUnits,
mzDataSpectrum.ParentIonSpectrumID);
break;
case SpectrumInfoMsMsText msmsSpectrum:
scanSummary =
string.Format(
"{0,3} {1} {2,5} {3:F2} {4,3:0} {5,4:0} {6:0.0E+0} {7,8:F3} {8:0.0E+0} {9,8:F2} {10:F2}",
spectrumInfo.ScanNumber, spectrumInfo.MSLevel,
spectrumInfo.PeaksCount, spectrumInfo.RetentionTimeMin,
spectrumInfo.MzRangeStart, spectrumInfo.MzRangeEnd,
spectrumInfo.TotalIonCurrent, spectrumInfo.BasePeakMZ, spectrumInfo.BasePeakIntensity,
spectrumInfo.ParentIonMZ,
msmsSpectrum.ParentIonMH);
break;
default:
scanSummary = "Unrecognized spectrum type";
break;
}
Console.WriteLine(scanSummary);
if (expectedScanInfo.TryGetValue(spectrumInfo.ScanNumber, out var expectedScanSummary) && !string.IsNullOrWhiteSpace(expectedScanSummary))
{
Assert.AreEqual(string.Format("{0,3} {1}", spectrumInfo.ScanNumber, expectedScanSummary), scanSummary,
"Scan summary mismatch, scan " + spectrumInfo.ScanNumber);
}
}
public override void ParseObject(AssetsReader reader)
{
spectrumInfo = new SpectrumInfo(reader);
spectrumData = reader.ReadArrayOf((r) => new Spectrum(r));
}
public bool NextSpectrum()
{
if (_runningAsync)
{
_currentInfo = _pendingInfoList.Take();
if (_exception != null)
Helpers.WrapAndThrowException(_exception);
}
else
{
lock (_dataFileLock)
{
int i = _currentInfo != null ? _currentInfo.Index : -1;
_currentInfo = ReadSpectrum(ref i);
}
}
return !_currentInfo.IsLast;
}
private void BuildRefSpectra(SrmDocument document,
ISession session,
DbRefSpectra refSpectra,
SpectrumInfo[] spectra, // Yes, this could be IEnumerable, but then Resharper throws bogus warnings about possible multiple enumeration
IDictionary<string, long> dictFiles,
ICollection<SpectrumKeyTime> redundantSpectraKeys)
{
bool foundBestSpectrum = false;
foreach(SpectrumInfo spectrum in spectra)
{
if(spectrum.IsBest)
{
if(foundBestSpectrum)
{
throw new InvalidDataException(
string.Format(Resources.BlibDb_BuildRefSpectra_Multiple_reference_spectra_found_for_peptide__0__in_the_library__1__,
refSpectra.PeptideModSeq, FilePath));
}
foundBestSpectrum = true;
MakeRefSpectrum(spectrum, refSpectra);
}
// Determine if this spectrum is from a file that is in the document.
// If it is not, do not save the retention time for this spectrum, and do not
// add it to the redundant library. However, if this is the reference (best) spectrum
// we must save its retention time.
// NOTE: Spectra not used in the results get used for too much now for this to be useful
// var matchingFile = document.Settings.HasResults
// ? document.Settings.MeasuredResults.FindMatchingMSDataFile(MsDataFileUri.Parse(spectrum.FilePath))
// : null;
// if (!spectrum.IsBest && matchingFile == null)
// continue;
// If this source file has already been saved, get its database Id.
// Otherwise, save it.
long spectrumSourceId = GetSpecturmSourceId(session, spectrum.FilePath, dictFiles);
// spectrumKey in the SpectrumInfo is an integer for reference(best) spectra,
// or object of type SpectrumLiteKey for redundant spectra
object key = spectrum.SpectrumKey;
var specLiteKey = key as SpectrumLiteKey;
var dbRetentionTimes = new DbRetentionTimes
{
RedundantRefSpectraId = specLiteKey != null ? specLiteKey.RedundantId : 0,
RetentionTime = spectrum.RetentionTime,
SpectrumSourceId = spectrumSourceId,
BestSpectrum = spectrum.IsBest ? 1 : 0,
IonMobilityType = 0,
IonMobilityValue = 0,
};
if (null != spectrum.IonMobilityInfo)
{
if (spectrum.IonMobilityInfo.IsCollisionalCrossSection)
{
dbRetentionTimes.IonMobilityType =
(int) BiblioSpecLiteLibrary.IonMobilityType.collisionalCrossSection;
}
else
{
dbRetentionTimes.IonMobilityType = (int) BiblioSpecLiteLibrary.IonMobilityType.driftTime;
}
dbRetentionTimes.IonMobilityValue = spectrum.IonMobilityInfo.Value;
dbRetentionTimes.IonMobilityHighEnergyDriftTimeOffsetMsec = spectrum.IonMobilityInfo.HighEnergyDriftTimeOffsetMsec;
}
if (refSpectra.RetentionTimes == null)
refSpectra.RetentionTimes = new List<DbRetentionTimes>();
refSpectra.RetentionTimes.Add(dbRetentionTimes);
if (specLiteKey != null)
{
redundantSpectraKeys.Add(new SpectrumKeyTime(specLiteKey, dbRetentionTimes, spectrum.FilePath));
}
}
}
private static void MakeRefSpectrum(SpectrumInfo spectrum, DbRefSpectra refSpectra)
{
short copies = (short)spectrum.SpectrumHeaderInfo.GetRankValue(LibrarySpec.PEP_RANK_COPIES);
var peaksInfo = spectrum.SpectrumPeaksInfo;
refSpectra.Copies = copies;
refSpectra.NumPeaks = (ushort) peaksInfo.Peaks.Length;
refSpectra.Peaks = new DbRefSpectraPeaks
{
RefSpectra = refSpectra,
PeakIntensity = IntensitiesToBytes(peaksInfo.Peaks),
PeakMZ = MZsToBytes(peaksInfo.Peaks)
};
ModsFromModifiedSequence(refSpectra);
}
private static DbRefSpectra MakeRefSpectrum(SpectrumInfo spectrum, string peptideSeq, string modifiedPeptideSeq, double precMz, int precChg)
{
var refSpectra = new DbRefSpectra
{
PeptideSeq = peptideSeq,
PrecursorMZ = precMz,
PrecursorCharge = precChg,
PeptideModSeq = modifiedPeptideSeq
};
MakeRefSpectrum(spectrum, refSpectra);
return refSpectra;
}
