private void DoValidate()
{
TransitionFullScan.ValidateRange(Start, TransitionFullScan.MIN_PRECURSOR_MULTI_FILTER, TransitionFullScan.MAX_PRECURSOR_MULTI_FILTER,
Resources.IsolationWindow_DoValidate_Isolation_window_Start_must_be_between__0__and__1__);
TransitionFullScan.ValidateRange(End, TransitionFullScan.MIN_PRECURSOR_MULTI_FILTER, TransitionFullScan.MAX_PRECURSOR_MULTI_FILTER,
Resources.IsolationWindow_DoValidate_Isolation_window_End_must_be_between__0__and__1__);
if (Start >= End)
{
throw new InvalidDataException(Resources.IsolationWindow_DoValidate_Isolation_window_Start_value_is_greater_than_the_End_value);
}
if (Target.HasValue && (Target.Value < Start || Target.Value >= End))
{
throw new InvalidDataException(Resources.IsolationWindow_DoValidate_Target_value_is_not_within_the_range_of_the_isolation_window);
}
if (StartMargin.HasValue)
{
if (StartMargin.Value < 0)
{
throw new InvalidDataException(Resources.IsolationWindow_DoValidate_Isolation_window_margin_must_be_non_negative);
}
if (EndMargin.HasValue)
{
if (EndMargin.Value < 0)
{
throw new InvalidDataException(Resources.IsolationWindow_DoValidate_Isolation_window_margin_must_be_non_negative);
}
}
if (IsolationStart >= IsolationEnd)
{
// If the margins are too large, clipping at the ends of the instrument range may result in no useable window area.
throw new InvalidDataException(Resources.IsolationWindow_DoValidate_Isolation_window_margins_cover_the_entire_isolation_window_at_the_extremes_of_the_instrument_range);
}
}
}
private void DoValidate()
{
SpecialHandlingType.Validate(SpecialHandling);
if (PrecursorFilter != null)
{
if (PrespecifiedIsolationWindows.Count > 0)
{
throw new InvalidDataException(Resources.IsolationScheme_DoValidate_Isolation_scheme_cannot_have_a_filter_and_a_prespecifed_isolation_window);
}
TransitionFullScan.ValidateRange(PrecursorFilter,
TransitionFullScan.MIN_PRECURSOR_MULTI_FILTER,
TransitionFullScan.MAX_PRECURSOR_MULTI_FILTER,
Resources.IsolationScheme_DoValidate_The_precursor_m_z_filter_must_be_between__0__and__1_);
if (PrecursorRightFilter.HasValue)
{
TransitionFullScan.ValidateRange(PrecursorRightFilter,
TransitionFullScan.MIN_PRECURSOR_MULTI_FILTER,
TransitionFullScan.MAX_PRECURSOR_MULTI_FILTER,
Resources.IsolationScheme_DoValidate_The_precursor_m_z_filter_must_be_between__0__and__1_);
}
if (WindowsPerScan.HasValue)
{
throw new InvalidDataException(Resources.IsolationScheme_DoValidate_Isolation_scheme_can_specify_multiplexed_windows_only_for_prespecified_isolation_windows);
}
}
else if (PrecursorRightFilter != null)
{
throw new InvalidDataException(Resources.IsolationScheme_DoValidate_Isolation_scheme_cannot_have_a_right_filter_without_a_left_filter);
}
else
{
if (PrespecifiedIsolationWindows.Count != 0 && IsAllIons)
{
throw new InvalidDataException(Resources.IsolationScheme_DoValidate_Isolation_scheme_for_all_ions_cannot_contain_isolation_windows);
}
if (Equals(SpecialHandling, SpecialHandlingType.MULTIPLEXED))
{
if (!WindowsPerScan.HasValue || WindowsPerScan.Value < 1)
{
throw new InvalidDataException(Resources.IsolationScheme_DoValidate_Multiplexed_windows_require_at_least_one_window_per_scan);
}
if (PrespecifiedIsolationWindows.Count % WindowsPerScan.Value != 0)
{
throw new InvalidDataException(Resources.IsolationScheme_DoValidate_The_number_of_prespecified_isolation_windows_must_be_a_multiple_of_the_windows_per_scan_in_multiplexed_sampling);
}
}
else
{
if (WindowsPerScan.HasValue)
{
throw new InvalidDataException(Resources.IsolationScheme_DoValidate_Windows_per_scan_requires_multiplexed_isolation_windows);
}
}
}
}
private void comboPrecursorIsotopes_SelectedIndexChanged(object sender, EventArgs e)
{
var precursorIsotopes = PrecursorIsotopesCurrent;
bool percentType = (precursorIsotopes == FullScanPrecursorIsotopes.Percent);
labelPrecursorIsotopeFilter.Text = percentType
? Resources.TransitionSettingsUI_comboPrecursorIsotopes_SelectedIndexChanged_Min_percent_of_base_peak
: Resources.TransitionSettingsUI_comboPrecursorIsotopes_SelectedIndexChanged_Peaks;
labelPrecursorIsotopeFilterPercent.Visible = percentType;
if (precursorIsotopes == FullScanPrecursorIsotopes.None)
{
textPrecursorIsotopeFilter.Text = string.Empty;
textPrecursorIsotopeFilter.Enabled = false;
comboEnrichments.SelectedIndex = -1;
comboEnrichments.Enabled = false;
// Selection change should set filter m/z textbox correctly
comboPrecursorAnalyzerType.SelectedIndex = -1;
comboPrecursorAnalyzerType.Enabled = false;
}
else
{
// If the combo is being set to the type it started with, use the starting values
if (precursorIsotopes == FullScan.PrecursorIsotopes)
{
textPrecursorIsotopeFilter.Text = FullScan.PrecursorIsotopeFilter.HasValue
? FullScan.PrecursorIsotopeFilter.Value.ToString(LocalizationHelper.CurrentCulture)
: string.Empty;
if (FullScan.IsotopeEnrichments != null)
{
comboEnrichments.SelectedItem = FullScan.IsotopeEnrichments.Name;
}
if (!comboPrecursorAnalyzerType.Enabled)
{
comboPrecursorAnalyzerType.SelectedItem = TransitionFullScan.MassAnalyzerToString(FullScan.PrecursorMassAnalyzer);
}
}
else
{
textPrecursorIsotopeFilter.Text = (percentType
? TransitionFullScan.DEFAULT_ISOTOPE_PERCENT
: TransitionFullScan.DEFAULT_ISOTOPE_COUNT).ToString(LocalizationHelper.CurrentCulture);
var precursorMassAnalyzer = PrecursorMassAnalyzer;
if (!comboPrecursorAnalyzerType.Enabled || (percentType && precursorMassAnalyzer == FullScanMassAnalyzerType.qit))
{
comboPrecursorAnalyzerType.SelectedItem = TransitionFullScan.MassAnalyzerToString(FullScanMassAnalyzerType.tof);
comboEnrichments.SelectedItem = IsotopeEnrichmentsList.GetDefault().Name;
}
}
comboEnrichments.Enabled = (comboEnrichments.SelectedIndex != -1);
textPrecursorIsotopeFilter.Enabled = true;
comboPrecursorAnalyzerType.Enabled = true;
}
UpdateRetentionTimeFilterUi();
}
private bool IsProfileMode(ComboBox comboAnalyzerType)
{
if (comboAnalyzerType.Visible && comboAnalyzerType.Enabled)
{
var analyzerType = TransitionFullScan.ParseMassAnalyzer((string)comboAnalyzerType.SelectedItem);
return(analyzerType != FullScanMassAnalyzerType.centroided && analyzerType != FullScanMassAnalyzerType.none);
}
return(false);
}
public ImportPeptideSearchSettings(
ImportResultsSettings importResultsSettings,
MatchModificationsControl.MatchModificationsSettings modificationsSettings,
TransitionSettingsControl.TransitionFilterAndLibrariesSettings filterAndLibSettings,
TransitionFullScan fullScanSettings, ImportFastaControl.ImportFastaSettings importFastaSettings)
{
ImportResultsSettings = importResultsSettings;
ModificationsSettings = modificationsSettings;
FilterAndLibrariesSettings = filterAndLibSettings;
FullScanSettings = fullScanSettings;
ImportFastaSettings = importFastaSettings;
}
public ImportPeptideSearchSettings(
ImportResultsSettings importResultsSettings,
MatchModificationsControl.MatchModificationsSettings modificationsSettings,
TransitionSettingsControl.TransitionFilterAndLibrariesSettings filterAndLibSettings,
TransitionFullScan fullScanSettings, ImportFastaControl.ImportFastaSettings importFastaSettings,
SrmDocument.DOCUMENT_TYPE docType)
{
ImportResultsSettings = importResultsSettings;
ModificationsSettings = modificationsSettings;
FilterAndLibrariesSettings = filterAndLibSettings;
FullScanSettings = fullScanSettings;
ImportFastaSettings = importFastaSettings;
_docType = docType;
}
private void comboAcquisitionMethod_SelectedIndexChanged(object sender, EventArgs e)
{
var acquisitionMethod = AcquisitionMethod;
if (acquisitionMethod == FullScanAcquisitionMethod.None)
{
EnableIsolationScheme(false);
// Selection change should set filter m/z textbox correctly
comboProductAnalyzerType.SelectedIndex = -1;
comboProductAnalyzerType.Enabled = false;
comboIsolationScheme.SelectedIndex = -1;
comboIsolationScheme.Enabled = false;
}
else
{
EnableIsolationScheme(acquisitionMethod == FullScanAcquisitionMethod.DIA);
// If the combo is being set to the type it started with, use the starting values
if (acquisitionMethod == FullScan.AcquisitionMethod)
{
if (!comboProductAnalyzerType.Enabled)
{
comboProductAnalyzerType.SelectedItem = TransitionFullScan.MassAnalyzerToString(FullScan.ProductMassAnalyzer);
}
}
else
{
if (!comboProductAnalyzerType.Enabled)
{
string tofAnalyzer = TransitionFullScan.MassAnalyzerToString(FullScanMassAnalyzerType.tof);
comboProductAnalyzerType.SelectedItem =
comboPrecursorAnalyzerType.SelectedItem != null &&
Equals(comboPrecursorAnalyzerType.SelectedItem.ToString(), tofAnalyzer)
? tofAnalyzer
: TransitionFullScan.MassAnalyzerToString(FullScanMassAnalyzerType.qit);
}
}
comboProductAnalyzerType.Enabled = true;
}
UpdateRetentionTimeFilterUi();
}
private void comboAcquisitionMethod_SelectedIndexChanged(object sender, EventArgs e)
{
var acquisitionMethod = AcquisitionMethod;
if (acquisitionMethod == FullScanAcquisitionMethod.None)
{
EnableIsolationScheme(false);
// Selection change should set filter m/z textbox correctly
comboProductAnalyzerType.SelectedIndex = -1;
comboProductAnalyzerType.Enabled = false;
comboIsolationScheme.SelectedIndex = -1;
comboIsolationScheme.Enabled = false;
}
else
{
EnableIsolationScheme(acquisitionMethod == FullScanAcquisitionMethod.DIA);
// If the combo is being set to the type it started with, use the starting values
if (acquisitionMethod == FullScan.AcquisitionMethod)
{
if (!comboProductAnalyzerType.Enabled)
{
comboProductAnalyzerType.SelectedItem = TransitionFullScan.MassAnalyzerToString(FullScan.ProductMassAnalyzer);
}
}
else
{
if (!comboProductAnalyzerType.Enabled)
{
comboProductAnalyzerType.SelectedItem =
comboPrecursorAnalyzerType.SelectedItem != null
? comboPrecursorAnalyzerType.SelectedItem.ToString()
: TransitionFullScan.MassAnalyzerToString(FullScanMassAnalyzerType.centroided);
}
}
comboProductAnalyzerType.Enabled = true;
}
FullScanEnabledChanged?.Invoke(new FullScanEnabledChangeEventArgs(null, comboProductAnalyzerType.Enabled));// Fire event so Filter iontypes settings can update as needed
UpdateRetentionTimeFilterUi();
}
private SrmDocument ChangeFullScanSettings(SrmDocument document, TransitionFullScan transitionFullScan)
{
return(document.ChangeSettings(
document.Settings.ChangeTransitionSettings(
document.Settings.TransitionSettings.ChangeFullScan(transitionFullScan))));
}
public bool ValidateFullScanSettings(MessageBoxHelper helper, out TransitionFullScan fullScanSettings, TabControl tabControl = null, int tabIndex = -1)
{
fullScanSettings = null;
double?precursorIsotopeFilter;
if (!ValidatePrecursorIsotopeFilter(helper, out precursorIsotopeFilter, tabControl, tabIndex))
{
return(false);
}
double?precursorRes;
if (!ValidatePrecursorRes(helper, precursorIsotopeFilter, out precursorRes, tabControl, tabIndex))
{
return(false);
}
double?precursorResMz;
if (!ValidatePrecursorResMz(helper, out precursorResMz, tabControl, tabIndex))
{
return(false);
}
double?productRes;
if (!ValidateProductRes(helper, out productRes, tabControl, tabIndex))
{
return(false);
}
double?productResMz;
if (!ValidateProductResMz(helper, out productResMz, tabControl, tabIndex))
{
return(false);
}
RetentionTimeFilterType retentionTimeFilterType = RetentionTimeFilterType;
double retentionTimeFilterLength;
if (!ValidateRetentionTimeFilterLength(out retentionTimeFilterLength))
{
return(false);
}
fullScanSettings = new TransitionFullScan(AcquisitionMethod,
IsolationScheme,
ProductMassAnalyzer,
productRes,
productResMz,
PrecursorIsotopesCurrent,
precursorIsotopeFilter,
PrecursorMassAnalyzer,
precursorRes,
precursorResMz,
UseSelectiveExtraction,
Enrichments,
retentionTimeFilterType,
retentionTimeFilterLength);
return(true);
}
public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo,
IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false)
{
_fullScan = document.Settings.TransitionSettings.FullScan;
_instrument = document.Settings.TransitionSettings.Instrument;
_acquisitionMethod = _fullScan.AcquisitionMethod;
if (instrumentInfo != null)
{
_isWatersFile = instrumentInfo.IsWatersFile;
}
IsFirstPass = firstPass;
var comparer = PrecursorTextId.PrecursorTextIdComparerInstance;
var dictPrecursorMzToFilter = new SortedDictionary <PrecursorTextId, SpectrumFilterPair>(comparer);
if (EnabledMs || EnabledMsMs)
{
if (EnabledMs)
{
_isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (!firstPass)
{
var key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.summed); // TIC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
key = new PrecursorTextId(SignedMz.ZERO, null, ChromExtractor.base_peak); // BPC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
}
}
if (EnabledMsMs)
{
_isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA &&
_fullScan.IsolationScheme.IsAllIons)
{
if (instrumentInfo != null)
{
_isWatersMse = _isWatersFile;
_isAgilentMse = instrumentInfo.IsAgilentFile;
}
_mseLevel = 1;
}
}
Func <double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow;
Func <double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow;
_minTime = _instrument.MinTime;
_maxTime = _instrument.MaxTime;
bool canSchedule = CanSchedule(document, retentionTimePredictor);
// TODO: Figure out a way to turn off time sharing on first SIM scan so that
// times can be shared for MS1 without SIM scans
_isSharedTime = !canSchedule;
// If we're using bare measured drift times from spectral libraries, go get those now
var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes
? document.Settings.GetIonMobilities(msDataFileUri)
: null;
foreach (var nodePep in document.Molecules)
{
if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep))
{
continue;
}
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (nodeGroup.Children.Count == 0)
{
continue;
}
double? minTime = _minTime, maxTime = _maxTime;
double? startDriftTimeMsec = null, endDriftTimeMsec = null;
double windowDT;
double highEnergyDriftTimeOffsetMsec = 0;
DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT);
if (centerDriftTime.DriftTimeMsec(false).HasValue)
{
startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time
endDriftTimeMsec = startDriftTimeMsec + windowDT;
highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec;
}
if (canSchedule)
{
if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType)
{
double?centerTime = null;
double windowRT = 0;
if (retentionTimePredictor != null)
{
centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep);
}
else
{
var prediction = document.Settings.PeptideSettings.Prediction;
if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated)
{
centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport(
document, nodePep, nodeGroup, out windowRT);
}
}
// Force the center time to be at least zero
if (centerTime.HasValue && centerTime.Value < 0)
{
centerTime = 0;
}
if (_fullScan.RetentionTimeFilterLength != 0)
{
windowRT = _fullScan.RetentionTimeFilterLength * 2;
}
if (centerTime != null)
{
double startTime = centerTime.Value - windowRT / 2;
double endTime = startTime + windowRT;
minTime = Math.Max(minTime ?? 0, startTime);
maxTime = Math.Min(maxTime ?? double.MaxValue, endTime);
}
}
else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType)
{
var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri);
if (times.Length > 0)
{
minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength);
maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength);
}
}
}
SpectrumFilterPair filter;
string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions
var mz = new SignedMz(nodeGroup.PrecursorMz, nodeGroup.PrecursorCharge < 0);
var key = new PrecursorTextId(mz, textId, ChromExtractor.summed);
if (!dictPrecursorMzToFilter.TryGetValue(key, out filter))
{
filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime,
startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec,
_isHighAccMsFilter, _isHighAccProductFilter);
dictPrecursorMzToFilter.Add(key, filter);
}
if (!EnabledMs)
{
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
select nodeTran.Mz, calcWindowsQ3);
}
else if (!EnabledMsMs)
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
}
else
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
where !nodeTran.IsMs1
select nodeTran.Mz, calcWindowsQ3);
}
}
}
_filterMzValues = dictPrecursorMzToFilter.Values.ToArray();
var listChromKeyFilterIds = new List <ChromKey>();
foreach (var spectrumFilterPair in _filterMzValues)
{
spectrumFilterPair.AddChromKeys(listChromKeyFilterIds);
}
_productChromKeys = listChromKeyFilterIds.ToArray();
// Sort a copy of the filter pairs by maximum retention time so that we can detect when
// filters are no longer active.
_filterRTValues = new SpectrumFilterPair[_filterMzValues.Length];
Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length);
Array.Sort(_filterRTValues, CompareByRT);
}
InitRTLimits();
}
private SrmDocument ChangeFullScanSettings(SrmDocument document, TransitionFullScan transitionFullScan)
{
return document.ChangeSettings(
document.Settings.ChangeTransitionSettings(
document.Settings.TransitionSettings.ChangeFullScan(transitionFullScan)));
}
private static bool IsOnlyMsEnabled(TransitionFullScan fullScan)
{
return fullScan.IsEnabledMs && !fullScan.IsEnabledMsMs;
}
public static bool IsMultipleIonSources(TransitionFullScan fullScan, TransitionGroupDocNode nodeGroup)
{
return fullScan.IsEnabledMs &&
(fullScan.IsEnabledMsMs ||
(nodeGroup != null && nodeGroup.Transitions.Contains(nodeTran => !nodeTran.IsMs1)));
}
/// <summary>
/// Constructor for an IsotopeDistInfo using TransitionFullScanSettings
/// </summary>
public static IsotopeDistInfo MakeIsotopeDistInfo(MassDistribution mzDistribution, TypedMass monoisotopicMass, Adduct adduct, TransitionFullScan fullScan)
{
// Centering resolution must be inversely proportional to charge state
// High charge states can bring major peaks close enough together to
// cause them to be combined and centered in isotope distribution valleys
double massResolution = TransitionFullScan.ISOTOPE_PEAK_CENTERING_RES /
(1 + Math.Abs(adduct.AdductCharge / 15.0));
return(new IsotopeDistInfo(mzDistribution, monoisotopicMass, adduct,
fullScan.GetPrecursorFilterWindow,
massResolution,
TransitionFullScan.MIN_ISOTOPE_PEAK_ABUNDANCE));
}
public SpectrumFilter(SrmDocument document, MsDataFileUri msDataFileUri, IFilterInstrumentInfo instrumentInfo,
IRetentionTimePredictor retentionTimePredictor = null, bool firstPass = false)
{
_fullScan = document.Settings.TransitionSettings.FullScan;
_instrument = document.Settings.TransitionSettings.Instrument;
_acquisitionMethod = _fullScan.AcquisitionMethod;
if (instrumentInfo != null)
_isWatersFile = instrumentInfo.IsWatersFile;
IsFirstPass = firstPass;
var comparer = PrecursorTextId.PrecursorTextIdComparerInstance;
var dictPrecursorMzToFilter = new SortedDictionary<PrecursorTextId, SpectrumFilterPair>(comparer);
if (EnabledMs || EnabledMsMs)
{
if (EnabledMs)
{
_isHighAccMsFilter = !Equals(_fullScan.PrecursorMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (!firstPass)
{
var key = new PrecursorTextId(0, null, ChromExtractor.summed); // TIC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
key = new PrecursorTextId(0, null, ChromExtractor.base_peak); // BPC
dictPrecursorMzToFilter.Add(key, new SpectrumFilterPair(key, PeptideDocNode.UNKNOWN_COLOR, dictPrecursorMzToFilter.Count,
_instrument.MinTime, _instrument.MaxTime, null, null, 0, _isHighAccMsFilter, _isHighAccProductFilter));
}
}
if (EnabledMsMs)
{
_isHighAccProductFilter = !Equals(_fullScan.ProductMassAnalyzer,
FullScanMassAnalyzerType.qit);
if (_fullScan.AcquisitionMethod == FullScanAcquisitionMethod.DIA &&
_fullScan.IsolationScheme.IsAllIons)
{
if (instrumentInfo != null)
{
_isWatersMse = _isWatersFile;
_isAgilentMse = instrumentInfo.IsAgilentFile;
}
_mseLevel = 1;
}
}
Func<double, double> calcWindowsQ1 = _fullScan.GetPrecursorFilterWindow;
Func<double, double> calcWindowsQ3 = _fullScan.GetProductFilterWindow;
_minTime = _instrument.MinTime;
_maxTime = _instrument.MaxTime;
bool canSchedule = CanSchedule(document, retentionTimePredictor);
// TODO: Figure out a way to turn off time sharing on first SIM scan so that
// times can be shared for MS1 without SIM scans
_isSharedTime = !canSchedule;
// If we're using bare measured drift times from spectral libraries, go get those now
var libraryIonMobilityInfo = document.Settings.PeptideSettings.Prediction.UseLibraryDriftTimes
? document.Settings.GetIonMobilities(msDataFileUri)
: null;
foreach (var nodePep in document.Molecules)
{
if (firstPass && !retentionTimePredictor.IsFirstPassPeptide(nodePep))
continue;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
if (nodeGroup.Children.Count == 0)
continue;
double? minTime = _minTime, maxTime = _maxTime;
double? startDriftTimeMsec = null, endDriftTimeMsec = null;
double windowDT;
double highEnergyDriftTimeOffsetMsec = 0;
DriftTimeInfo centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
nodePep, nodeGroup, libraryIonMobilityInfo, out windowDT);
if (centerDriftTime.DriftTimeMsec(false).HasValue)
{
startDriftTimeMsec = centerDriftTime.DriftTimeMsec(false) - windowDT / 2; // Get the low energy drift time
endDriftTimeMsec = startDriftTimeMsec + windowDT;
highEnergyDriftTimeOffsetMsec = centerDriftTime.HighEnergyDriftTimeOffsetMsec;
}
if (canSchedule)
{
if (RetentionTimeFilterType.scheduling_windows == _fullScan.RetentionTimeFilterType)
{
double? centerTime = null;
double windowRT = 0;
if (retentionTimePredictor != null)
{
centerTime = retentionTimePredictor.GetPredictedRetentionTime(nodePep);
}
else
{
var prediction = document.Settings.PeptideSettings.Prediction;
if (prediction.RetentionTime == null || !prediction.RetentionTime.IsAutoCalculated)
{
centerTime = document.Settings.PeptideSettings.Prediction.PredictRetentionTimeForChromImport(
document, nodePep, nodeGroup, out windowRT);
}
}
// Force the center time to be at least zero
if (centerTime.HasValue && centerTime.Value < 0)
centerTime = 0;
if (_fullScan.RetentionTimeFilterLength != 0)
{
windowRT = _fullScan.RetentionTimeFilterLength * 2;
}
if (centerTime != null)
{
double startTime = centerTime.Value - windowRT / 2;
double endTime = startTime + windowRT;
minTime = Math.Max(minTime ?? 0, startTime);
maxTime = Math.Min(maxTime ?? double.MaxValue, endTime);
}
}
else if (RetentionTimeFilterType.ms2_ids == _fullScan.RetentionTimeFilterType)
{
var times = document.Settings.GetBestRetentionTimes(nodePep, msDataFileUri);
if (times.Length > 0)
{
minTime = Math.Max(minTime ?? 0, times.Min() - _fullScan.RetentionTimeFilterLength);
maxTime = Math.Min(maxTime ?? double.MaxValue, times.Max() + _fullScan.RetentionTimeFilterLength);
}
}
}
SpectrumFilterPair filter;
string textId = nodePep.RawTextId; // Modified Sequence for peptides, or some other string for custom ions
double mz = nodeGroup.PrecursorMz;
var key = new PrecursorTextId(mz, textId, ChromExtractor.summed);
if (!dictPrecursorMzToFilter.TryGetValue(key, out filter))
{
filter = new SpectrumFilterPair(key, nodePep.Color, dictPrecursorMzToFilter.Count, minTime, maxTime,
startDriftTimeMsec, endDriftTimeMsec, highEnergyDriftTimeOffsetMsec,
_isHighAccMsFilter, _isHighAccProductFilter);
dictPrecursorMzToFilter.Add(key, filter);
}
if (!EnabledMs)
{
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
select nodeTran.Mz, calcWindowsQ3);
}
else if (!EnabledMsMs)
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
}
else
{
filter.AddQ1FilterValues(GetMS1MzValues(nodeGroup), calcWindowsQ1);
filter.AddQ3FilterValues(from TransitionDocNode nodeTran in nodeGroup.Children
where !nodeTran.IsMs1
select nodeTran.Mz, calcWindowsQ3);
}
}
}
_filterMzValues = dictPrecursorMzToFilter.Values.ToArray();
var listChromKeyFilterIds = new List<ChromKey>();
foreach (var spectrumFilterPair in _filterMzValues)
{
spectrumFilterPair.AddChromKeys(listChromKeyFilterIds);
}
_productChromKeys = listChromKeyFilterIds.ToArray();
// Sort a copy of the filter pairs by maximum retention time so that we can detect when
// filters are no longer active.
_filterRTValues = new SpectrumFilterPair[_filterMzValues.Length];
Array.Copy(_filterMzValues, _filterRTValues, _filterMzValues.Length);
Array.Sort(_filterRTValues, CompareByRT);
}
InitRTLimits();
}
public bool ValidateFullScanSettings(MessageBoxHelper helper, out TransitionFullScan fullScanSettings, TabControl tabControl = null, int tabIndex = -1)
{
fullScanSettings = null;
double? precursorIsotopeFilter;
if (!ValidatePrecursorIsotopeFilter(helper, out precursorIsotopeFilter, tabControl, tabIndex))
return false;
double? precursorRes;
if (!ValidatePrecursorRes(helper, precursorIsotopeFilter, out precursorRes, tabControl, tabIndex))
return false;
double? precursorResMz;
if (!ValidatePrecursorResMz(helper, out precursorResMz, tabControl, tabIndex))
return false;
double? productRes;
if (!ValidateProductRes(helper, out productRes, tabControl, tabIndex))
return false;
double? productResMz;
if (!ValidateProductResMz(helper, out productResMz, tabControl, tabIndex))
return false;
RetentionTimeFilterType retentionTimeFilterType = RetentionTimeFilterType;
double retentionTimeFilterLength;
if (!ValidateRetentionTimeFilterLength(out retentionTimeFilterLength))
return false;
fullScanSettings = new TransitionFullScan(AcquisitionMethod,
IsolationScheme,
ProductMassAnalyzer,
productRes,
productResMz,
PrecursorIsotopesCurrent,
precursorIsotopeFilter,
PrecursorMassAnalyzer,
precursorRes,
precursorResMz,
Enrichments,
retentionTimeFilterType,
retentionTimeFilterLength);
return true;
}
