// This function looks for spectra in the specified range. The original
// version of this function returned IEnumerable<TandemMassSpectrum>,
// and this is still conceptually what we are trying to do. However,
// the above appears to generate a lot of garbage, because this
// function occurs inside an inner loop of DatabaseSearcher.DoSearch.
//
// Thus, instead, we require the caller to pass in a buffer of indices,
// out_indices, which we clear and re-fill with an array of spectrum
// indices.
//
// If precursorMonoisotopicPeakCorrection is false, then you should
// pass
// minimumMonoisotopicPeakOffset = 0 and
// maximumMonoisotopicPeakOffset = 0.
public void GetTandemMassSpectraInMassRange(double precursorMass, MassTolerance precursorMassTolerance,
int minimumMonoisotopicPeakOffset, int maximumMonoisotopicPeakOffset,
List<int> out_indices)
{
out_indices.Clear();
for(int i = minimumMonoisotopicPeakOffset; i <= maximumMonoisotopicPeakOffset; i++)
{
double precursor_mass = precursorMass + i * Constants.C12_C13_MASS_DIFFERENCE;
double minimum_precursor_mass = precursor_mass - precursorMassTolerance;
double maximum_precursor_mass = precursor_mass + precursorMassTolerance;
int index = BinarySearch(NextHigherDouble(maximum_precursor_mass));
if(index == Count)
{
index--;
}
while(index >= 0 && this[index].PrecursorMass >= minimum_precursor_mass)
{
if(this[index].PrecursorMass <= maximum_precursor_mass)
{
out_indices.Add(index);
}
index--;
}
}
}
public void Load(string rawFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, MassTolerance isotopicMZTolerance, int maximumThreads)
{
Load(rawFilepath, minimumAssumedPrecursorChargeState, maximumAssumedPrecursorChargeState,
absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks,
assignChargeStates, maximumThreads);
}
public void Load(string rawFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, MassTolerance isotopicMZTolerance, int maximumThreads)
{
Load(rawFilepath, minimumAssumedPrecursorChargeState, maximumAssumedPrecursorChargeState,
absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks,
assignChargeStates, maximumThreads);
}
public PeptideSpectrumMatch(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance)
{
Spectrum = spectrum;
Peptide = peptide;
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance);
}
public PeptideSpectrumMatch(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance)
{
Spectrum = spectrum;
Peptide = peptide;
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance);
}
private static List<MSPeak> Deisotope(IEnumerable<MSPeak> peaks, int maxAbsoluteCharge, int polarity, MassTolerance isotopicMZTolerance)
{
List<MSPeak> new_peaks = new List<MSPeak>(peaks);
int p = new_peaks.Count - 1;
while(p >= 1)
{
int q = p - 1;
bool removed = false;
while(q >= 0)
{
if(new_peaks[p].MZ > (new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE) + isotopicMZTolerance)
{
break;
}
if(new_peaks[p].Intensity < new_peaks[q].Intensity)
{
if(polarity == 0)
{
if(Math.Abs(MassTolerance.CalculateMassError(new_peaks[p].MZ, new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE, isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.RemoveAt(p);
removed = true;
break;
}
}
else
{
for(int c = polarity; polarity > 0 ? c <= maxAbsoluteCharge : c >= -maxAbsoluteCharge; c += polarity)
{
if(Math.Abs(MassTolerance.CalculateMassError(new_peaks[p].MZ, new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE / Math.Abs(c), isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.RemoveAt(p);
removed = true;
break;
}
}
}
if(removed)
{
break;
}
}
q--;
}
p--;
}
return new_peaks;
}
private static List<MSPeak> AssignChargeStates(IList<MSPeak> peaks, int maxAbsoluteCharge, int polarity, MassTolerance isotopicMZTolerance)
{
List<MSPeak> new_peaks = new List<MSPeak>();
for(int i = 0; i < peaks.Count; i++)
{
int j = i + 1;
List<int> charges = new List<int>();
while(j < peaks.Count)
{
if(peaks[j].MZ > (peaks[i].MZ + Constants.C12_C13_MASS_DIFFERENCE) + isotopicMZTolerance)
{
break;
}
for(int c = polarity * maxAbsoluteCharge; polarity > 0 ? c >= 1 : c <= -1; c -= polarity)
{
// remove harmonic charges, e.g. don't consider peak as a +2 (0.5 Th spacing) if it could be a +4 (0.25 Th spacing)
if(HARMONIC_CHARGE_DETECTION)
{
bool harmonic = false;
foreach(int c2 in charges)
{
if(c2 % c == 0)
{
harmonic = true;
break;
}
}
if(harmonic)
{
continue;
}
}
if(Math.Abs(MassTolerance.CalculateMassError(peaks[j].MZ, peaks[i].MZ + Constants.C12_C13_MASS_DIFFERENCE / c, isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.Add(new MSPeak(peaks[i].MZ, peaks[i].Intensity, c, polarity));
charges.Add(c);
}
}
j++;
}
if(charges.Count == 0)
{
new_peaks.Add(new MSPeak(peaks[i].MZ, peaks[i].Intensity, 0, polarity));
}
}
return new_peaks;
}
public DatabaseSearcher(IList<string> dataFilepaths,
int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope,
string proteinFastaDatabaseFilepath, bool onTheFlyDecoys,
Protease protease, int maximumMissedCleavages, InitiatorMethionineBehavior initiatorMethionineBehavior,
IEnumerable<Modification> fixedModifications, IEnumerable<Modification> variableModifications, int maximumVariableModificationIsoforms,
MassTolerance precursorMassTolerance, MassType precursorMassType,
bool precursorMonoisotopicPeakCorrection, int minimumPrecursorMonoisotopicPeakOffset, int maximumPrecursorMonoisotopicPeakOffset,
MassTolerance productMassTolerance, MassType productMassType,
double maximumFalseDiscoveryRate, bool considerModifiedFormsAsUniquePeptides,
int maximumThreads, bool minimizeMemoryUsage,
string outputFolder)
{
this.dataFilepaths = dataFilepaths;
this.assignChargeStates = assignChargeStates;
this.deisotope = deisotope;
this.proteinFastaDatabaseFilepath = proteinFastaDatabaseFilepath;
this.onTheFlyDecoys = onTheFlyDecoys;
this.protease = protease;
this.maximumMissedCleavages = maximumMissedCleavages;
this.initiatorMethionineBehavior = initiatorMethionineBehavior;
this.fixedModifications = fixedModifications;
this.variableModifications = variableModifications;
this.maximumVariableModificationIsoforms = maximumVariableModificationIsoforms;
this.minimumAssumedPrecursorChargeState = minimumAssumedPrecursorChargeState;
this.maximumAssumedPrecursorChargeState = maximumAssumedPrecursorChargeState;
this.absoluteThreshold = absoluteThreshold;
this.relativeThresholdPercent = relativeThresholdPercent;
this.maximumNumberOfPeaks = maximumNumberOfPeaks;
this.precursorMassTolerance = precursorMassTolerance;
this.precursorMassType = precursorMassType;
this.precursorMonoisotopicPeakCorrection = precursorMonoisotopicPeakCorrection;
this.minimumPrecursorMonoisotopicPeakOffset = minimumPrecursorMonoisotopicPeakOffset;
this.maximumPrecursorMonoisotopicPeakOffset = maximumPrecursorMonoisotopicPeakOffset;
this.productMassTolerance = productMassTolerance;
this.productMassType = productMassType;
this.maximumFalseDiscoveryRate = maximumFalseDiscoveryRate;
this.considerModifiedFormsAsUniquePeptides = considerModifiedFormsAsUniquePeptides;
this.maximumThreads = maximumThreads;
this.minimizeMemoryUsage = minimizeMemoryUsage;
this.outputFolder = outputFolder;
}
public IEnumerable <TandemMassSpectrum> GetTandemMassSpectraInMassRange(double precursorMass, MassTolerance precursorMassTolerance)
{
double minimum_precursor_mass = precursorMass - precursorMassTolerance;
double maximum_precursor_mass = precursorMass + precursorMassTolerance;
int index = BinarySearch(NextHigherDouble(maximum_precursor_mass));
if (index == Count)
{
index--;
}
while (index >= 0 && this[index].PrecursorMass >= minimum_precursor_mass)
{
if (this[index].PrecursorMass <= maximum_precursor_mass)
{
yield return(this[index]);
}
index--;
}
}
public IEnumerable <TandemMassSpectrum> GetTandemMassSpectraInMassRanges(double precursorMass, IEnumerable <double> acceptedPrecursorMassErrors, MassTolerance precursorMassTolerance)
{
foreach (double accepted_precursor_mass_error in acceptedPrecursorMassErrors)
{
foreach (TandemMassSpectrum spectrum in GetTandemMassSpectraInMassRange(precursorMass + accepted_precursor_mass_error, precursorMassTolerance))
{
yield return(spectrum);
}
}
}
static void Main(string[] args)
{
if(args.Length > 0)
{
Arguments arguments = new Arguments(args);
List<string> data = new List<string>(arguments["d"].Split(','));
int min_assumed_precursor_charge_state = 2;
if(arguments["minprecz"] != null)
{
min_assumed_precursor_charge_state = int.Parse(arguments["minprecz"]);
}
int max_assumed_precursor_charge_state = 4;
if(arguments["maxprecz"] != null)
{
max_assumed_precursor_charge_state = int.Parse(arguments["maxprecz"]);
}
double abs_threshold = -1.0;
if(arguments["at"] != null)
{
abs_threshold = double.Parse(arguments["at"], CultureInfo.InvariantCulture);
}
double rel_threshold_percent = -1.0;
if(arguments["rt"] != null)
{
rel_threshold_percent = double.Parse(arguments["rt"], CultureInfo.InvariantCulture);
}
int max_peaks = 400;
if(arguments["mp"] != null)
{
max_peaks = int.Parse(arguments["mp"]);
}
bool assign_charge_states = true;
if(arguments["acs"] != null)
{
assign_charge_states = bool.Parse(arguments["acs"]);
}
bool deisotope = true;
if(arguments["di"] != null)
{
deisotope = bool.Parse(arguments["di"]);
}
string database = arguments["db"];
bool append_decoys;
if(arguments["ad"] != null)
{
append_decoys = bool.Parse(arguments["ad"]);
}
else
{
append_decoys = !ProteinFastaReader.HasDecoyProteins(database);
}
ProteaseDictionary proteases = ProteaseDictionary.Instance;
Protease protease = proteases["trypsin (no proline rule)"];
if(arguments["p"] != null)
{
protease = proteases[arguments["p"]];
}
int max_missed_cleavages = 2;
if(arguments["mmc"] != null)
{
max_missed_cleavages = int.Parse(arguments["mmc"]);
}
InitiatorMethionineBehavior initiator_methionine_behavior = InitiatorMethionineBehavior.Variable;
if(arguments["imb"] != null)
{
initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), arguments["imb"], true);
}
ModificationDictionary mods = ModificationDictionary.Instance;
List<Modification> fixed_mods = new List<Modification>();
if(arguments["fm"] != null)
{
foreach(string fixed_mod in arguments["fm"].Split(','))
{
fixed_mods.Add(mods[fixed_mod]);
}
}
List<Modification> variable_mods = new List<Modification>();
if(arguments["vm"] != null)
{
foreach(string variable_mod in arguments["vm"].Split(','))
{
variable_mods.Add(mods[variable_mod]);
}
}
int max_variable_mod_isoforms_per_peptide = 1024;
if(arguments["mvmi"] != null)
{
max_variable_mod_isoforms_per_peptide = int.Parse(arguments["mvmi"]);
}
double precursor_mass_tolerance_value = 2.1;
if(arguments["precmtv"] != null)
{
precursor_mass_tolerance_value = double.Parse(arguments["precmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits precursor_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["precmtu"] != null)
{
precursor_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["precmtu"], true);
}
MassTolerance precursor_mass_tolerance = new MassTolerance(precursor_mass_tolerance_value, precursor_mass_tolerance_units);
MassType precursor_mass_type = MassType.Monoisotopic;
if(arguments["precmt"] != null)
{
precursor_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["precmt"], true);
}
bool prec_mono_correction = false;
if(arguments["pmc"] != null)
{
prec_mono_correction = bool.Parse(arguments["pmc"]);
}
int min_prec_mono_offset = -3;
if(arguments["minpmo"] != null)
{
min_prec_mono_offset = int.Parse(arguments["minpmo"]);
}
int max_prec_mono_offset = 1;
if(arguments["maxpmo"] != null)
{
max_prec_mono_offset = int.Parse(arguments["maxpmo"]);
}
double product_mass_tolerance_value = 0.025;
if(arguments["prodmtv"] != null)
{
product_mass_tolerance_value = double.Parse(arguments["prodmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits product_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["prodmtu"] != null)
{
product_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["prodmtu"], true);
}
MassTolerance product_mass_tolerance = new MassTolerance(product_mass_tolerance_value, product_mass_tolerance_units);
MassType product_mass_type = MassType.Monoisotopic;
if(arguments["prodmt"] != null)
{
product_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["prodmt"], true);
}
double max_fdr = 0.01;
if(arguments["fdr"] != null)
{
max_fdr = double.Parse(arguments["fdr"], CultureInfo.InvariantCulture) / 100.0;
}
bool consider_mods_unique = false;
if(arguments["cmu"] != null)
{
consider_mods_unique = bool.Parse(arguments["cmu"]);
}
int max_threads = Environment.ProcessorCount;
if(arguments["mt"] != null)
{
max_threads = int.Parse(arguments["mt"]);
}
bool minimize_memory_usage = false;
if(arguments["mmu"] != null)
{
minimize_memory_usage = bool.Parse(arguments["mmu"]);
}
string output_folder = Environment.CurrentDirectory;
if(arguments["o"] != null)
{
output_folder = arguments["o"];
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
abs_threshold, rel_threshold_percent, max_peaks,
assign_charge_states, deisotope,
database, append_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_mods, variable_mods, max_variable_mod_isoforms_per_peptide,
precursor_mass_tolerance, precursor_mass_type,
prec_mono_correction, min_prec_mono_offset, max_prec_mono_offset,
product_mass_tolerance, product_mass_type,
max_fdr, consider_mods_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
database_searcher.Search();
}
else
{
Console.WriteLine("USAGE");
}
}
private static List<MSPeak> Deisotope(IEnumerable<MSPeak> peaks, int maxAbsoluteCharge, int polarity, MassTolerance isotopicMZTolerance)
{
List<MSPeak> new_peaks = new List<MSPeak>(peaks);
int p = new_peaks.Count - 1;
while(p >= 1)
{
int q = p - 1;
bool removed = false;
while(q >= 0)
{
if(new_peaks[p].MZ > (new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE) + isotopicMZTolerance)
{
break;
}
if(new_peaks[p].Intensity < new_peaks[q].Intensity)
{
if(polarity == 0)
{
if(Math.Abs(MassTolerance.CalculateMassError(new_peaks[p].MZ, new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE, isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.RemoveAt(p);
removed = true;
break;
}
}
else
{
for(int c = polarity; polarity > 0 ? c <= maxAbsoluteCharge : c >= -maxAbsoluteCharge; c += polarity)
{
if(Math.Abs(MassTolerance.CalculateMassError(new_peaks[p].MZ, new_peaks[q].MZ + Constants.C12_C13_MASS_DIFFERENCE / Math.Abs(c), isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.RemoveAt(p);
removed = true;
break;
}
}
}
if(removed)
{
break;
}
}
q--;
}
p--;
}
return new_peaks;
}
// Calculates the score for this match. Both product_masses_buf and
// fast_q_sorter are modified by this method; see Init's documentation
// for details.
private void ScoreMatch(MassTolerance productMassTolerance, ref double[] product_masses_buf, FastQSorter fast_q_sorter)
{
// Calculate the theoretical product masses and store them in
// product_masses_buf, which is aliased under the more informative
// name theoretical_product_masses for the code below.
TotalProducts = Peptide.CalculateProductMasses(PRODUCT_TYPES[Spectrum.FragmentationMethod],
ref product_masses_buf, fast_q_sorter);
double[] theoretical_product_masses = product_masses_buf;
// speed optimizations
int num_theoretical_products = TotalProducts;
double[] experimental_masses = Spectrum.Masses;
double[] experimental_intensities = Spectrum.Intensities;
int num_experimental_peaks = experimental_masses.Length;
double product_mass_tolerance_value = productMassTolerance.Value;
MassToleranceUnits product_mass_tolerance_units = productMassTolerance.Units;
MatchingProducts = 0;
int t = 0;
int e = 0;
while(t < num_theoretical_products && e < num_experimental_peaks)
{
double mass_difference = experimental_masses[e] - theoretical_product_masses[t];
if(product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t] * 1e6;
}
if(Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingProducts++;
t++;
}
else if(mass_difference < 0)
{
e++;
}
else if(mass_difference > 0)
{
t++;
}
}
MatchingProductsFraction = (double)MatchingProducts / TotalProducts;
MatchingIntensity = 0.0;
int e2 = 0;
int t2 = 0;
while(e2 < num_experimental_peaks && t2 < num_theoretical_products)
{
double mass_difference = experimental_masses[e2] - theoretical_product_masses[t2];
if(product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t2] * 1e6;
}
if(Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingIntensity += experimental_intensities[e2];
e2++;
}
else if(mass_difference < 0)
{
e2++;
}
else if(mass_difference > 0)
{
t2++;
}
}
MatchingIntensityFraction = MatchingIntensity / Spectrum.TotalIntensity;
MorpheusScore = MatchingProducts + MatchingIntensityFraction;
}
private void btnSearch_Click(object sender, EventArgs e)
{
if (lstData.Items.Count == 0)
{
MessageBox.Show("No data files selected");
btnAdd.Focus();
return;
}
List <string> data_filepaths = new List <string>(lstData.Items.Count);
foreach (string data_filepath in lstData.Items)
{
data_filepaths.Add(data_filepath);
}
bool assign_charge_states = chkAssignChargeStates.Checked;
bool deisotope = chkDeisotope.Checked;
string fasta_filepath = txtFastaFile.Text;
if (!File.Exists(fasta_filepath))
{
if (fasta_filepath.Length > 0)
{
MessageBox.Show("Invalid protein database file: " + fasta_filepath);
}
else
{
MessageBox.Show("Invalid protein database file");
}
txtFastaFile.Focus();
return;
}
bool on_the_fly_decoys = chkOnTheFlyDecoys.Checked;
Protease protease = (Protease)cboProtease.SelectedItem;
int max_missed_cleavages = (int)numMaxMissedCleavages.Value;
InitiatorMethionineBehavior initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), cboInitiatorMethionineBehavior.Text, true);
List <Modification> fixed_modifications = new List <Modification>(clbFixedModifications.CheckedItems.Count);
foreach (object fixed_modification in clbFixedModifications.CheckedItems)
{
fixed_modifications.Add((Modification)fixed_modification);
}
List <Modification> variable_modifications = new List <Modification>(clbVariableModifications.CheckedItems.Count);
foreach (object variable_modification in clbVariableModifications.CheckedItems)
{
variable_modifications.Add((Modification)variable_modification);
}
int max_variable_mod_isoforms = (int)numMaxVariableModIsoforms.Value;
int min_assumed_precursor_charge_state = (int)numMinimumAssumedPrecursorChargeState.Value;
int max_assumed_precursor_charge_state = (int)numMaximumAssumedPrecursorChargeState.Value;
double absolute_threshold = -1.0;
if (chkAbsoluteThreshold.Checked)
{
if (!double.TryParse(txtAbsoluteThreshold.Text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out absolute_threshold))
{
MessageBox.Show("Cannot parse absolute MS/MS peak threshold: " + txtAbsoluteThreshold.Text);
txtAbsoluteThreshold.Focus();
return;
}
}
double relative_threshold_percent = -1.0;
if (chkRelativeThreshold.Checked)
{
if (!double.TryParse(txtRelativeThresholdPercent.Text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out relative_threshold_percent))
{
MessageBox.Show("Cannot parse relative MS/MS peak threshold: " + txtRelativeThresholdPercent.Text);
txtRelativeThresholdPercent.Focus();
return;
}
}
int max_peaks = -1;
if (chkMaxNumPeaks.Checked)
{
max_peaks = (int)numMaxPeaks.Value;
}
MassTolerance precursor_mass_tolerance = new MassTolerance((double)numPrecursorMassTolerance.Value, (MassToleranceUnits)cboPrecursorMassToleranceUnits.SelectedIndex);
MassType precursor_mass_type = (MassType)cboPrecursorMassType.SelectedIndex;
List <double> accepted_precursor_mass_errors = new List <double>();
if (txtAcceptedPrecursorMassErrors.Text.Length > 0)
{
foreach (string accepted_precursor_mass_error_text in txtAcceptedPrecursorMassErrors.Text.Split(';'))
{
double accepted_precursor_mass_error;
if (!double.TryParse(accepted_precursor_mass_error_text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out accepted_precursor_mass_error))
{
MessageBox.Show("Cannot parse accepted precursor mass errors: " + txtRelativeThresholdPercent.Text);
txtAcceptedPrecursorMassErrors.Focus();
return;
}
accepted_precursor_mass_errors.Add(accepted_precursor_mass_error);
}
}
else
{
accepted_precursor_mass_errors.Add(0.0);
}
MassTolerance product_mass_tolerance = new MassTolerance((double)numProductMassTolerance.Value, (MassToleranceUnits)cboProductMassToleranceUnits.SelectedIndex);
MassType product_mass_type = (MassType)cboProductMassType.SelectedIndex;
double max_false_discovery_rate = (double)numMaximumFalseDiscoveryRatePercent.Value / 100.0;
bool consider_modified_unique = chkConsiderModifiedUnique.Checked;
int max_threads = (int)numMaxThreads.Value;
bool minimize_memory_usage = chkMinimizeMemoryUsage.Checked;
string output_folder = txtOutputFolder.Text;
if (!Directory.Exists(output_folder))
{
try
{
Directory.CreateDirectory(output_folder);
}
catch
{
if (output_folder.Length > 0)
{
MessageBox.Show("Invalid output folder: " + output_folder);
}
else
{
MessageBox.Show("Invalid output folder");
}
txtOutputFolder.Focus();
return;
}
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data_filepaths,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
absolute_threshold, relative_threshold_percent, max_peaks,
assign_charge_states, deisotope,
fasta_filepath, on_the_fly_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_modifications, variable_modifications, max_variable_mod_isoforms,
precursor_mass_tolerance, precursor_mass_type,
accepted_precursor_mass_errors,
product_mass_tolerance, product_mass_type,
max_false_discovery_rate, consider_modified_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.ReportTaskWithoutProgress += HandleReportTaskWithoutProgress;
database_searcher.ReportTaskWithProgress += HandleReportTaskWithProgress;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
lstData.SelectedItem = null;
tspbProgress.Value = tspbProgress.Minimum;
Thread thread = new Thread(new ThreadStart(database_searcher.Search));
thread.IsBackground = true;
thread.Start();
}
static void Main(string[] args)
{
if(args.Length > 0)
{
Arguments arguments = new Arguments(args);
List<string> data = new List<string>(arguments["d"].Split(','));
int min_assumed_precursor_charge_state = 2;
if(arguments["minprecz"] != null)
{
min_assumed_precursor_charge_state = int.Parse(arguments["minprecz"]);
}
int max_assumed_precursor_charge_state = 4;
if(arguments["maxprecz"] != null)
{
max_assumed_precursor_charge_state = int.Parse(arguments["maxprecz"]);
}
double abs_threshold = -1.0;
if(arguments["at"] != null)
{
abs_threshold = double.Parse(arguments["at"], CultureInfo.InvariantCulture);
}
double rel_threshold_percent = -1.0;
if(arguments["rt"] != null)
{
rel_threshold_percent = double.Parse(arguments["rt"], CultureInfo.InvariantCulture);
}
int max_peaks = 400;
if(arguments["mp"] != null)
{
max_peaks = int.Parse(arguments["mp"]);
}
bool assign_charge_states = true;
if(arguments["acs"] != null)
{
assign_charge_states = bool.Parse(arguments["acs"]);
}
bool deisotope = true;
if(arguments["di"] != null)
{
deisotope = bool.Parse(arguments["di"]);
}
string database = arguments["db"];
Dictionary<string, Modification> known_variable_modifications = null;
HashSet<Modification> variable_mods = new HashSet<Modification>();
if(Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase))
{
bool no_uniprot_mods = false;
if(arguments["noup"] != null)
{
no_uniprot_mods = bool.Parse(arguments["noup"]);
}
if (!no_uniprot_mods)
{
known_variable_modifications = ProteomeDatabaseReader.ReadUniProtXmlModifications(database);
variable_mods.UnionWith(known_variable_modifications.Values);
}
}
bool append_decoys = false;
if(arguments["ad"] != null)
{
append_decoys = bool.Parse(arguments["ad"]);
}
else
{
append_decoys = Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase) || !ProteomeDatabaseReader.HasDecoyProteins(database);
}
ProteaseDictionary proteases = ProteaseDictionary.Instance;
Protease protease = proteases["trypsin (no proline rule)"];
if(arguments["p"] != null)
{
protease = proteases[arguments["p"]];
}
int max_missed_cleavages = 2;
if(arguments["mmc"] != null)
{
max_missed_cleavages = int.Parse(arguments["mmc"]);
}
InitiatorMethionineBehavior initiator_methionine_behavior = InitiatorMethionineBehavior.Variable;
if(arguments["imb"] != null)
{
initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), arguments["imb"], true);
}
ModificationDictionary mods = ModificationDictionary.Instance;
List<Modification> fixed_mods = new List<Modification>();
if(arguments["fm"] != null)
{
foreach(string fixed_mod in arguments["fm"].Split(';'))
{
fixed_mods.Add(mods[fixed_mod]);
}
}
if(arguments["vm"] != null)
{
foreach(string variable_mod in arguments["vm"].Split(';'))
{
Modification mod;
if(!mods.TryGetValue(variable_mod, out mod))
{
known_variable_modifications.TryGetValue(variable_mod, out mod);
}
variable_mods.Add(mod);
}
}
int max_variable_mod_isoforms_per_peptide = 1024;
if(arguments["mvmi"] != null)
{
max_variable_mod_isoforms_per_peptide = int.Parse(arguments["mvmi"]);
}
double precursor_mass_tolerance_value = 2.1;
if(arguments["precmtv"] != null)
{
precursor_mass_tolerance_value = double.Parse(arguments["precmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits precursor_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["precmtu"] != null)
{
precursor_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["precmtu"], true);
}
MassTolerance precursor_mass_tolerance = new MassTolerance(precursor_mass_tolerance_value, precursor_mass_tolerance_units);
MassType precursor_mass_type = MassType.Monoisotopic;
if(arguments["precmt"] != null)
{
precursor_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["precmt"], true);
}
List<double> accepted_precursor_mass_errors = new List<double>();
if(arguments["apme"] != null && arguments["apme"].Length > 0)
{
foreach(string accepted_precursor_mass_error in arguments["apme"].Split(';'))
{
accepted_precursor_mass_errors.Add(double.Parse(accepted_precursor_mass_error, CultureInfo.InvariantCulture));
}
}
else
{
accepted_precursor_mass_errors.Add(0.0);
}
double product_mass_tolerance_value = 0.015;
if(arguments["prodmtv"] != null)
{
product_mass_tolerance_value = double.Parse(arguments["prodmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits product_mass_tolerance_units = MassToleranceUnits.Da;
if(arguments["prodmtu"] != null)
{
product_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["prodmtu"], true);
}
MassTolerance product_mass_tolerance = new MassTolerance(product_mass_tolerance_value, product_mass_tolerance_units);
MassType product_mass_type = MassType.Monoisotopic;
if(arguments["prodmt"] != null)
{
product_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["prodmt"], true);
}
double max_fdr = 0.01;
if(arguments["fdr"] != null)
{
max_fdr = double.Parse(arguments["fdr"], CultureInfo.InvariantCulture) / 100.0;
}
bool consider_mods_unique = false;
if(arguments["cmu"] != null)
{
consider_mods_unique = bool.Parse(arguments["cmu"]);
}
int max_threads = Environment.ProcessorCount;
if(arguments["mt"] != null)
{
max_threads = int.Parse(arguments["mt"]);
}
bool minimize_memory_usage = false;
if(arguments["mmu"] != null)
{
minimize_memory_usage = bool.Parse(arguments["mmu"]);
}
string output_folder = Environment.CurrentDirectory;
if(arguments["o"] != null)
{
output_folder = arguments["o"];
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
abs_threshold, rel_threshold_percent, max_peaks,
assign_charge_states, deisotope,
database, append_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_mods, variable_mods, max_variable_mod_isoforms_per_peptide,
precursor_mass_tolerance, precursor_mass_type,
accepted_precursor_mass_errors,
product_mass_tolerance, product_mass_type,
max_fdr, consider_mods_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
database_searcher.Search();
}
else
{
Console.WriteLine(Program.GetProductNameAndVersion() + " USAGE");
}
}
public void Load(string mzmlFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, MassTolerance isotopicMZTolerance, int maximumThreads)
{
OnReportTaskWithoutProgress(EventArgs.Empty);
XmlDocument mzML_temp = new XmlDocument();
mzML_temp.Load(mzmlFilepath);
XPathNavigator mzML = mzML_temp.CreateNavigator();
XmlNamespaceManager xnm = new XmlNamespaceManager(mzML.NameTable);
xnm.AddNamespace("mzML", mzML_temp.DocumentElement.NamespaceURI);
Dictionary<string, XPathNodeIterator> referenceable_param_groups = new Dictionary<string, XPathNodeIterator>();
foreach(XPathNavigator referenceable_param_group in mzML.Select("//mzML:mzML/mzML:referenceableParamGroupList/mzML:referenceableParamGroup", xnm))
{
referenceable_param_groups.Add(referenceable_param_group.GetAttribute("id", string.Empty), referenceable_param_group.SelectChildren(XPathNodeType.All));
}
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Dictionary<string, SpectrumNavigator> ms1s = null;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<string, SpectrumNavigator>();
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
string scan_id = spectrum_navigator.GetAttribute("id", string.Empty);
int ms_level = -1;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
break;
}
}
}
}
}
if(ms_level == 1)
{
lock(ms1s)
{
ms1s.Add(scan_id, new SpectrumNavigator(spectrum_navigator, xnm));
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
int num_spectra = int.Parse(mzML.SelectSingleNode("//mzML:mzML/mzML:run/mzML:spectrumList", xnm).GetAttribute("count", string.Empty));
OnReportTaskWithProgress(EventArgs.Empty);
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
int spectrum_index = int.Parse(spectrum_navigator.GetAttribute("index", string.Empty));
int spectrum_number = spectrum_index + 1;
string spectrum_id = spectrum_navigator.GetAttribute("id", string.Empty);
string spectrum_title = null;
int ms_level = -1;
int polarity = 0;
double retention_time_minutes = double.NaN;
string precursor_scan_id = null;
double precursor_mz = double.NaN;
int charge = 0;
double precursor_intensity = double.NaN;
string fragmentation_method = "collision-induced dissociation";
double[] mz = null;
double[] intensity = null;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("spectrum title", StringComparison.OrdinalIgnoreCase))
{
spectrum_title = spectrum_child_navigator.GetAttribute("value", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
}
else if(navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("scanList", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in spectrum_child_navigator.Select("mzML:scan/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("scan start time", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
if(navigator.GetAttribute("unitName", string.Empty).StartsWith("s", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = TimeSpan.FromSeconds(retention_time_minutes).TotalMinutes;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("precursorList", StringComparison.OrdinalIgnoreCase))
{
XPathNavigator precursor_node = spectrum_child_navigator.SelectSingleNode("mzML:precursor", xnm);
precursor_scan_id = precursor_node.GetAttribute("spectrumRef", string.Empty);
foreach(XPathNavigator navigator in precursor_node.Select("mzML:selectedIonList/mzML:selectedIon/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("selected ion m/z", StringComparison.OrdinalIgnoreCase))
{
precursor_mz = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
else if(navigator.GetAttribute("name", string.Empty).Equals("charge state", StringComparison.OrdinalIgnoreCase))
{
charge = int.Parse(navigator.GetAttribute("value", string.Empty));
if(polarity < 0)
{
charge = -charge;
}
}
else if(navigator.GetAttribute("name", string.Empty).Equals("peak intensity", StringComparison.OrdinalIgnoreCase))
{
precursor_intensity = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
}
XPathNavigator navigator2 = spectrum_child_navigator.SelectSingleNode("mzML:precursor/mzML:activation/mzML:cvParam", xnm);
if(navigator2 != null)
{
fragmentation_method = navigator2.GetAttribute("name", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("binaryDataArrayList", StringComparison.OrdinalIgnoreCase))
{
ReadDataFromSpectrumNavigator(spectrum_child_navigator.Select("mzML:binaryDataArray/*", xnm), out mz, out intensity);
}
if(ms_level == 1)
{
break;
}
}
if(ms_level >= 2)
{
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1 && precursor_scan_id != null)
{
SpectrumNavigator ms1;
if(ms1s.TryGetValue(precursor_scan_id, out ms1))
{
double[] ms1_mz;
double[] ms1_intensity;
ms1.GetSpectrum(out ms1_mz, out ms1_intensity);
int index = -1;
for(int i = ms1_mz.GetLowerBound(0); i <= ms1_mz.GetUpperBound(0); i++)
{
if(index < 0 || Math.Abs(ms1_mz[i] - precursor_mz) < Math.Abs(ms1_mz[index] - precursor_mz))
{
index = i;
}
}
precursor_mz = ms1_mz[index];
precursor_intensity = ms1_intensity[index];
}
}
if(mz != null && intensity != null && mz.Length > 0 && intensity.Length > 0)
{
List<MSPeak> peaks = new List<MSPeak>(mz.Length);
for(int i = 0; i < mz.Length; i++)
{
peaks.Add(new MSPeak(mz[i], intensity[i], 0, polarity));
}
peaks = FilterPeaks(peaks, absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks);
if(peaks.Count > 0)
{
peaks.Sort(MSPeak.AscendingMZComparison);
for(int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
List<MSPeak> new_peaks = peaks;
if(assignChargeStates)
{
new_peaks = AssignChargeStates(new_peaks, c, polarity, isotopicMZTolerance);
if(deisotope)
{
new_peaks = Deisotope(new_peaks, c, polarity, isotopicMZTolerance);
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(mzmlFilepath, spectrum_number, spectrum_id, spectrum_title, retention_time_minutes, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, new_peaks);
lock(this)
{
Add(spectrum);
}
}
}
}
}
lock(progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / num_spectra * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
private void ScoreMatch(MassTolerance productMassTolerance)
{
double[] theoretical_product_masses = Peptide.CalculateProductMasses(PRODUCT_TYPES[Spectrum.FragmentationMethod]).ToArray();
TotalProducts = theoretical_product_masses.Length;
// speed optimizations
int num_theoretical_products = theoretical_product_masses.Length;
double[] experimental_masses = Spectrum.Masses;
double[] experimental_intensities = Spectrum.Intensities;
int num_experimental_peaks = experimental_masses.Length;
double product_mass_tolerance_value = productMassTolerance.Value;
MassToleranceUnits product_mass_tolerance_units = productMassTolerance.Units;
MatchingProducts = 0;
int t = 0;
int e = 0;
while (t < num_theoretical_products && e < num_experimental_peaks)
{
double mass_difference = experimental_masses[e] - theoretical_product_masses[t];
if (product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t] * 1e6;
}
if (Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingProducts++;
t++;
}
else if (mass_difference < 0)
{
e++;
}
else if (mass_difference > 0)
{
t++;
}
}
MatchingProductsFraction = (double)MatchingProducts / TotalProducts;
MatchingIntensity = 0.0;
int e2 = 0;
int t2 = 0;
while (e2 < num_experimental_peaks && t2 < num_theoretical_products)
{
double mass_difference = experimental_masses[e2] - theoretical_product_masses[t2];
if (product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t2] * 1e6;
}
if (Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingIntensity += experimental_intensities[e2];
e2++;
}
else if (mass_difference < 0)
{
e2++;
}
else if (mass_difference > 0)
{
t2++;
}
}
MatchingIntensityFraction = MatchingIntensity / Spectrum.TotalIntensity;
MorpheusScore = MatchingProducts + MatchingIntensityFraction;
}
// This Init method needs to be called before this object can be used.
// For more info, see how we use these objects in DatabaseSearcher.
//
// We copy the peptide parameter deeply (because these sometimes come
// from reusable buffers) but not the spectrum parameter (because these
// are not reused).
//
// The array product_masses_buf is used for temporary internal storage
// and may be resized. It needs to be local to the current thread; no
// locking is performed. Its contents are not of interest to the
// caller.
//
// The fast_q_sorter object also need to be local to the current
// thread, as its internal state will be modified.
public void Init(TandemMassSpectrum spectrum, Peptide peptide, MassTolerance productMassTolerance,
ref double[] product_masses_buf, FastQSorter fast_q_sorter)
{
Spectrum = spectrum;
if(Peptide == null)
Peptide = new Peptide();
Peptide.CopyFrom(peptide);
PrecursorMassErrorDa = spectrum.PrecursorMass - (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass);
PrecursorMassErrorPpm = PrecursorMassErrorDa / (precursorMassType == MassType.Average ? peptide.AverageMass : peptide.MonoisotopicMass) * 1e6;
ScoreMatch(productMassTolerance, ref product_masses_buf, fast_q_sorter);
}
private void btnSearch_Click(object sender, EventArgs e)
{
if(lstData.Items.Count == 0)
{
MessageBox.Show("No data files selected");
btnAdd.Focus();
return;
}
List<string> data_filepaths = new List<string>(lstData.Items.Count);
foreach(string data_filepath in lstData.Items)
{
data_filepaths.Add(data_filepath);
}
bool assign_charge_states = chkAssignChargeStates.Checked;
bool deisotope = chkDeisotope.Checked;
string fasta_filepath = txtFastaFile.Text;
if(!File.Exists(fasta_filepath))
{
if(fasta_filepath.Length > 0)
{
MessageBox.Show("Invalid protein database file: " + fasta_filepath);
}
else
{
MessageBox.Show("Invalid protein database file");
}
txtFastaFile.Focus();
return;
}
bool on_the_fly_decoys = chkOnTheFlyDecoys.Checked;
Protease protease = (Protease)cboProtease.SelectedItem;
int max_missed_cleavages = (int)numMaxMissedCleavages.Value;
InitiatorMethionineBehavior initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), cboInitiatorMethionineBehavior.Text, true);
List<Modification> fixed_modifications = new List<Modification>(clbFixedModifications.CheckedItems.Count);
foreach(object fixed_modification in clbFixedModifications.CheckedItems)
{
fixed_modifications.Add((Modification)fixed_modification);
}
List<Modification> variable_modifications = new List<Modification>(clbVariableModifications.CheckedItems.Count);
foreach(object variable_modification in clbVariableModifications.CheckedItems)
{
variable_modifications.Add((Modification)variable_modification);
}
int max_variable_mod_isoforms = (int)numMaxVariableModIsoforms.Value;
int min_assumed_precursor_charge_state = (int)numMinimumAssumedPrecursorChargeState.Value;
int max_assumed_precursor_charge_state = (int)numMaximumAssumedPrecursorChargeState.Value;
double absolute_threshold = -1.0;
if(chkAbsoluteThreshold.Checked)
{
if(!double.TryParse(txtAbsoluteThreshold.Text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out absolute_threshold))
{
MessageBox.Show("Cannot parse absolute MS/MS peak threshold: " + txtAbsoluteThreshold.Text);
txtAbsoluteThreshold.Focus();
return;
}
}
double relative_threshold_percent = -1.0;
if(chkRelativeThreshold.Checked)
{
if(!double.TryParse(txtRelativeThresholdPercent.Text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out relative_threshold_percent))
{
MessageBox.Show("Cannot parse relative MS/MS peak threshold: " + txtRelativeThresholdPercent.Text);
txtRelativeThresholdPercent.Focus();
return;
}
}
int max_peaks = -1;
if(chkMaxNumPeaks.Checked)
{
max_peaks = (int)numMaxPeaks.Value;
}
MassTolerance precursor_mass_tolerance = new MassTolerance((double)numPrecursorMassTolerance.Value, (MassToleranceUnits)cboPrecursorMassToleranceUnits.SelectedIndex);
MassType precursor_mass_type = (MassType)cboPrecursorMassType.SelectedIndex;
List<double> accepted_precursor_mass_errors = new List<double>();
if(txtAcceptedPrecursorMassErrors.Text.Length > 0)
{
foreach(string accepted_precursor_mass_error_text in txtAcceptedPrecursorMassErrors.Text.Split(';'))
{
double accepted_precursor_mass_error;
if(!double.TryParse(accepted_precursor_mass_error_text, NumberStyles.Float | NumberStyles.AllowThousands, CultureInfo.InvariantCulture, out accepted_precursor_mass_error))
{
MessageBox.Show("Cannot parse accepted precursor mass errors: " + txtRelativeThresholdPercent.Text);
txtAcceptedPrecursorMassErrors.Focus();
return;
}
accepted_precursor_mass_errors.Add(accepted_precursor_mass_error);
}
}
else
{
accepted_precursor_mass_errors.Add(0.0);
}
MassTolerance product_mass_tolerance = new MassTolerance((double)numProductMassTolerance.Value, (MassToleranceUnits)cboProductMassToleranceUnits.SelectedIndex);
MassType product_mass_type = (MassType)cboProductMassType.SelectedIndex;
double max_false_discovery_rate = (double)numMaximumFalseDiscoveryRatePercent.Value / 100.0;
bool consider_modified_unique = chkConsiderModifiedUnique.Checked;
int max_threads = (int)numMaxThreads.Value;
bool minimize_memory_usage = chkMinimizeMemoryUsage.Checked;
string output_folder = txtOutputFolder.Text;
if(!Directory.Exists(output_folder))
{
try
{
Directory.CreateDirectory(output_folder);
}
catch
{
if(output_folder.Length > 0)
{
MessageBox.Show("Invalid output folder: " + output_folder);
}
else
{
MessageBox.Show("Invalid output folder");
}
txtOutputFolder.Focus();
return;
}
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data_filepaths,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
absolute_threshold, relative_threshold_percent, max_peaks,
assign_charge_states, deisotope,
fasta_filepath, on_the_fly_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_modifications, variable_modifications, max_variable_mod_isoforms,
precursor_mass_tolerance, precursor_mass_type,
accepted_precursor_mass_errors,
product_mass_tolerance, product_mass_type,
max_false_discovery_rate, consider_modified_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.ReportTaskWithoutProgress += HandleReportTaskWithoutProgress;
database_searcher.ReportTaskWithProgress += HandleReportTaskWithProgress;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
lstData.SelectedItem = null;
tspbProgress.Value = tspbProgress.Minimum;
Thread thread = new Thread(new ThreadStart(database_searcher.Search));
thread.IsBackground = true;
thread.Start();
}
private static List<MSPeak> AssignChargeStates(IList<MSPeak> peaks, int maxAbsoluteCharge, int polarity, MassTolerance isotopicMZTolerance)
{
List<MSPeak> new_peaks = new List<MSPeak>();
for(int i = 0; i < peaks.Count; i++)
{
int j = i + 1;
List<int> charges = new List<int>();
while(j < peaks.Count)
{
if(peaks[j].MZ > (peaks[i].MZ + Constants.C12_C13_MASS_DIFFERENCE) + isotopicMZTolerance)
{
break;
}
for(int c = polarity * maxAbsoluteCharge; polarity > 0 ? c >= 1 : c <= -1; c -= polarity)
{
// remove harmonic charges, e.g. don't consider peak as a +2 (0.5 Th spacing) if it could be a +4 (0.25 Th spacing)
if(HARMONIC_CHARGE_DETECTION)
{
bool harmonic = false;
foreach(int c2 in charges)
{
if(c2 % c == 0)
{
harmonic = true;
break;
}
}
if(harmonic)
{
continue;
}
}
if(Math.Abs(MassTolerance.CalculateMassError(peaks[j].MZ, peaks[i].MZ + Constants.C12_C13_MASS_DIFFERENCE / c, isotopicMZTolerance.Units)) <= isotopicMZTolerance.Value)
{
new_peaks.Add(new MSPeak(peaks[i].MZ, peaks[i].Intensity, c, polarity));
charges.Add(c);
}
}
j++;
}
if(charges.Count == 0)
{
new_peaks.Add(new MSPeak(peaks[i].MZ, peaks[i].Intensity, 0, polarity));
}
}
return new_peaks;
}
private void ScoreMatch(MassTolerance productMassTolerance)
{
double[] theoretical_product_masses = Peptide.CalculateProductMasses(PRODUCT_TYPES[Spectrum.FragmentationMethod]).ToArray();
TotalProducts = theoretical_product_masses.Length;
// speed optimizations
int num_theoretical_products = theoretical_product_masses.Length;
double[] experimental_masses = Spectrum.Masses;
double[] experimental_intensities = Spectrum.Intensities;
int num_experimental_peaks = experimental_masses.Length;
double product_mass_tolerance_value = productMassTolerance.Value;
MassToleranceUnits product_mass_tolerance_units = productMassTolerance.Units;
MatchingProducts = 0;
int t = 0;
int e = 0;
while(t < num_theoretical_products && e < num_experimental_peaks)
{
double mass_difference = experimental_masses[e] - theoretical_product_masses[t];
if(product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t] * 1e6;
}
if(Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingProducts++;
t++;
}
else if(mass_difference < 0)
{
e++;
}
else if(mass_difference > 0)
{
t++;
}
}
MatchingProductsFraction = (double)MatchingProducts / TotalProducts;
MatchingIntensity = 0.0;
int e2 = 0;
int t2 = 0;
while(e2 < num_experimental_peaks && t2 < num_theoretical_products)
{
double mass_difference = experimental_masses[e2] - theoretical_product_masses[t2];
if(product_mass_tolerance_units == MassToleranceUnits.ppm)
{
mass_difference = mass_difference / theoretical_product_masses[t2] * 1e6;
}
if(Math.Abs(mass_difference) <= product_mass_tolerance_value)
{
MatchingIntensity += experimental_intensities[e2];
e2++;
}
else if(mass_difference < 0)
{
e2++;
}
else if(mass_difference > 0)
{
t2++;
}
}
MatchingIntensityFraction = MatchingIntensity / Spectrum.TotalIntensity;
MorpheusScore = MatchingProducts + MatchingIntensityFraction;
}
static void Main(string[] args)
{
if (args.Length > 0)
{
Arguments arguments = new Arguments(args);
List <string> data = new List <string>(arguments["d"].Split(','));
int min_assumed_precursor_charge_state = 2;
if (arguments["minprecz"] != null)
{
min_assumed_precursor_charge_state = int.Parse(arguments["minprecz"]);
}
int max_assumed_precursor_charge_state = 4;
if (arguments["maxprecz"] != null)
{
max_assumed_precursor_charge_state = int.Parse(arguments["maxprecz"]);
}
double abs_threshold = -1.0;
if (arguments["at"] != null)
{
abs_threshold = double.Parse(arguments["at"], CultureInfo.InvariantCulture);
}
double rel_threshold_percent = -1.0;
if (arguments["rt"] != null)
{
rel_threshold_percent = double.Parse(arguments["rt"], CultureInfo.InvariantCulture);
}
int max_peaks = 400;
if (arguments["mp"] != null)
{
max_peaks = int.Parse(arguments["mp"]);
}
bool assign_charge_states = true;
if (arguments["acs"] != null)
{
assign_charge_states = bool.Parse(arguments["acs"]);
}
bool deisotope = true;
if (arguments["di"] != null)
{
deisotope = bool.Parse(arguments["di"]);
}
string database = arguments["db"];
Dictionary <string, Modification> known_variable_modifications = null;
HashSet <Modification> variable_mods = new HashSet <Modification>();
if (Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase))
{
bool no_uniprot_mods = false;
if (arguments["noup"] != null)
{
no_uniprot_mods = bool.Parse(arguments["noup"]);
}
if (!no_uniprot_mods)
{
known_variable_modifications = ProteomeDatabaseReader.ReadUniProtXmlModifications(database);
variable_mods.UnionWith(known_variable_modifications.Values);
}
}
bool append_decoys = false;
if (arguments["ad"] != null)
{
append_decoys = bool.Parse(arguments["ad"]);
}
else
{
append_decoys = Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase) || !ProteomeDatabaseReader.HasDecoyProteins(database);
}
ProteaseDictionary proteases = ProteaseDictionary.Instance;
Protease protease = proteases["trypsin (no proline rule)"];
if (arguments["p"] != null)
{
protease = proteases[arguments["p"]];
}
int max_missed_cleavages = 2;
if (arguments["mmc"] != null)
{
max_missed_cleavages = int.Parse(arguments["mmc"]);
}
InitiatorMethionineBehavior initiator_methionine_behavior = InitiatorMethionineBehavior.Variable;
if (arguments["imb"] != null)
{
initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), arguments["imb"], true);
}
ModificationDictionary mods = ModificationDictionary.Instance;
List <Modification> fixed_mods = new List <Modification>();
if (arguments["fm"] != null)
{
foreach (string fixed_mod in arguments["fm"].Split(';'))
{
fixed_mods.Add(mods[fixed_mod]);
}
}
if (arguments["vm"] != null)
{
foreach (string variable_mod in arguments["vm"].Split(';'))
{
Modification mod;
if (!mods.TryGetValue(variable_mod, out mod))
{
known_variable_modifications.TryGetValue(variable_mod, out mod);
}
variable_mods.Add(mod);
}
}
int max_variable_mod_isoforms_per_peptide = 1024;
if (arguments["mvmi"] != null)
{
max_variable_mod_isoforms_per_peptide = int.Parse(arguments["mvmi"]);
}
double precursor_mass_tolerance_value = 2.1;
if (arguments["precmtv"] != null)
{
precursor_mass_tolerance_value = double.Parse(arguments["precmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits precursor_mass_tolerance_units = MassToleranceUnits.Da;
if (arguments["precmtu"] != null)
{
precursor_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["precmtu"], true);
}
MassTolerance precursor_mass_tolerance = new MassTolerance(precursor_mass_tolerance_value, precursor_mass_tolerance_units);
MassType precursor_mass_type = MassType.Monoisotopic;
if (arguments["precmt"] != null)
{
precursor_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["precmt"], true);
}
List <double> accepted_precursor_mass_errors = new List <double>();
if (arguments["apme"] != null && arguments["apme"].Length > 0)
{
foreach (string accepted_precursor_mass_error in arguments["apme"].Split(';'))
{
accepted_precursor_mass_errors.Add(double.Parse(accepted_precursor_mass_error, CultureInfo.InvariantCulture));
}
}
else
{
accepted_precursor_mass_errors.Add(0.0);
}
double product_mass_tolerance_value = 0.015;
if (arguments["prodmtv"] != null)
{
product_mass_tolerance_value = double.Parse(arguments["prodmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits product_mass_tolerance_units = MassToleranceUnits.Da;
if (arguments["prodmtu"] != null)
{
product_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["prodmtu"], true);
}
MassTolerance product_mass_tolerance = new MassTolerance(product_mass_tolerance_value, product_mass_tolerance_units);
MassType product_mass_type = MassType.Monoisotopic;
if (arguments["prodmt"] != null)
{
product_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["prodmt"], true);
}
double max_fdr = 0.01;
if (arguments["fdr"] != null)
{
max_fdr = double.Parse(arguments["fdr"], CultureInfo.InvariantCulture) / 100.0;
}
bool consider_mods_unique = false;
if (arguments["cmu"] != null)
{
consider_mods_unique = bool.Parse(arguments["cmu"]);
}
int max_threads = Environment.ProcessorCount;
if (arguments["mt"] != null)
{
max_threads = int.Parse(arguments["mt"]);
}
bool minimize_memory_usage = false;
if (arguments["mmu"] != null)
{
minimize_memory_usage = bool.Parse(arguments["mmu"]);
}
string output_folder = Environment.CurrentDirectory;
if (arguments["o"] != null)
{
output_folder = arguments["o"];
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
abs_threshold, rel_threshold_percent, max_peaks,
assign_charge_states, deisotope,
database, append_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_mods, variable_mods, max_variable_mod_isoforms_per_peptide,
precursor_mass_tolerance, precursor_mass_type,
accepted_precursor_mass_errors,
product_mass_tolerance, product_mass_type,
max_fdr, consider_mods_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
database_searcher.Search();
}
else
{
Console.WriteLine(Program.GetProductNameAndVersion() + " USAGE");
}
}
public void Load(string mzmlFilepath, int minimumAssumedPrecursorChargeState, int maximumAssumedPrecursorChargeState,
double absoluteThreshold, double relativeThresholdPercent, int maximumNumberOfPeaks,
bool assignChargeStates, bool deisotope, MassTolerance isotopicMZTolerance, int maximumThreads)
{
OnReportTaskWithoutProgress(EventArgs.Empty);
XmlDocument mzML_temp = new XmlDocument();
mzML_temp.Load(mzmlFilepath);
XPathNavigator mzML = mzML_temp.CreateNavigator();
XmlNamespaceManager xnm = new XmlNamespaceManager(mzML.NameTable);
xnm.AddNamespace("mzML", mzML_temp.DocumentElement.NamespaceURI);
Dictionary<string, XPathNodeIterator> referenceable_param_groups = new Dictionary<string, XPathNodeIterator>();
foreach(XPathNavigator referenceable_param_group in mzML.Select("//mzML:mzML/mzML:referenceableParamGroupList/mzML:referenceableParamGroup", xnm))
{
referenceable_param_groups.Add(referenceable_param_group.GetAttribute("id", string.Empty), referenceable_param_group.SelectChildren(XPathNodeType.All));
}
ParallelOptions parallel_options = new ParallelOptions();
parallel_options.MaxDegreeOfParallelism = maximumThreads;
Dictionary<string, SpectrumNavigator> ms1s = null;
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1)
{
ms1s = new Dictionary<string, SpectrumNavigator>();
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
string scan_id = spectrum_navigator.GetAttribute("id", string.Empty);
int ms_level = -1;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
break;
}
}
}
}
}
if(ms_level == 1)
{
lock(ms1s)
{
ms1s.Add(scan_id, new SpectrumNavigator(spectrum_navigator, xnm));
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
int num_spectra = int.Parse(mzML.SelectSingleNode("//mzML:mzML/mzML:run/mzML:spectrumList", xnm).GetAttribute("count", string.Empty));
OnReportTaskWithProgress(EventArgs.Empty);
object progress_lock = new object();
int spectra_processed = 0;
int old_progress = 0;
#if NON_MULTITHREADED
foreach(XPathNavigator spectrum_navigator in mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>())
#else
Parallel.ForEach(mzML.Select("//mzML:mzML/mzML:run/mzML:spectrumList/mzML:spectrum", xnm).Cast<XPathNavigator>(), parallel_options, spectrum_navigator =>
#endif
{
int spectrum_index = int.Parse(spectrum_navigator.GetAttribute("index", string.Empty));
int spectrum_number = spectrum_index + 1;
string spectrum_id = spectrum_navigator.GetAttribute("id", string.Empty);
string spectrum_title = null;
int ms_level = -1;
int polarity = 0;
double retention_time_minutes = double.NaN;
string precursor_scan_id = null;
double precursor_mz = double.NaN;
int charge = 0;
double precursor_intensity = double.NaN;
string fragmentation_method = "collision-induced dissociation";
double[] mz = null;
double[] intensity = null;
foreach(XPathNavigator spectrum_child_navigator in spectrum_navigator.SelectChildren(XPathNodeType.All))
{
if(spectrum_child_navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(spectrum_child_navigator.GetAttribute("value", string.Empty));
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
else if(spectrum_child_navigator.GetAttribute("name", string.Empty).Equals("spectrum title", StringComparison.OrdinalIgnoreCase))
{
spectrum_title = spectrum_child_navigator.GetAttribute("value", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("referenceableParamGroupRef", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in referenceable_param_groups[spectrum_child_navigator.GetAttribute("ref", string.Empty)])
{
if(navigator.Name.Equals("cvParam", StringComparison.OrdinalIgnoreCase))
{
if(navigator.GetAttribute("name", string.Empty).Equals("ms level", StringComparison.OrdinalIgnoreCase))
{
ms_level = int.Parse(navigator.GetAttribute("value", string.Empty));
}
else if(navigator.GetAttribute("name", string.Empty).Equals("positive scan", StringComparison.OrdinalIgnoreCase))
{
polarity = 1;
}
else if(navigator.GetAttribute("name", string.Empty).Equals("negative scan", StringComparison.OrdinalIgnoreCase))
{
polarity = -1;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("scanList", StringComparison.OrdinalIgnoreCase))
{
foreach(XPathNavigator navigator in spectrum_child_navigator.Select("mzML:scan/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("scan start time", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
if(navigator.GetAttribute("unitName", string.Empty).StartsWith("s", StringComparison.OrdinalIgnoreCase))
{
retention_time_minutes = TimeSpan.FromSeconds(retention_time_minutes).TotalMinutes;
}
}
}
}
else if(spectrum_child_navigator.Name.Equals("precursorList", StringComparison.OrdinalIgnoreCase))
{
XPathNavigator precursor_node = spectrum_child_navigator.SelectSingleNode("mzML:precursor", xnm);
precursor_scan_id = precursor_node.GetAttribute("spectrumRef", string.Empty);
foreach(XPathNavigator navigator in precursor_node.Select("mzML:selectedIonList/mzML:selectedIon/mzML:cvParam", xnm))
{
if(navigator.GetAttribute("name", string.Empty).Equals("selected ion m/z", StringComparison.OrdinalIgnoreCase))
{
precursor_mz = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
else if(navigator.GetAttribute("name", string.Empty).Equals("charge state", StringComparison.OrdinalIgnoreCase))
{
charge = int.Parse(navigator.GetAttribute("value", string.Empty));
if(polarity < 0)
{
charge = -charge;
}
}
else if(navigator.GetAttribute("name", string.Empty).Equals("peak intensity", StringComparison.OrdinalIgnoreCase))
{
precursor_intensity = double.Parse(navigator.GetAttribute("value", string.Empty), CultureInfo.InvariantCulture);
}
}
XPathNavigator navigator2 = spectrum_child_navigator.SelectSingleNode("mzML:precursor/mzML:activation/mzML:cvParam", xnm);
if(navigator2 != null)
{
fragmentation_method = navigator2.GetAttribute("name", string.Empty);
}
}
else if(spectrum_child_navigator.Name.Equals("binaryDataArrayList", StringComparison.OrdinalIgnoreCase))
{
ReadDataFromSpectrumNavigator(spectrum_child_navigator.Select("mzML:binaryDataArray/*", xnm), out mz, out intensity);
}
if(ms_level == 1)
{
break;
}
}
if(ms_level >= 2)
{
if(GET_PRECURSOR_MZ_AND_INTENSITY_FROM_MS1 && precursor_scan_id != null)
{
SpectrumNavigator ms1;
if(ms1s.TryGetValue(precursor_scan_id, out ms1))
{
double[] ms1_mz;
double[] ms1_intensity;
ms1.GetSpectrum(out ms1_mz, out ms1_intensity);
int index = -1;
for(int i = ms1_mz.GetLowerBound(0); i <= ms1_mz.GetUpperBound(0); i++)
{
if(index < 0 || Math.Abs(ms1_mz[i] - precursor_mz) < Math.Abs(ms1_mz[index] - precursor_mz))
{
index = i;
}
}
precursor_mz = ms1_mz[index];
precursor_intensity = ms1_intensity[index];
}
}
if(mz != null && intensity != null && mz.Length > 0 && intensity.Length > 0)
{
List<MSPeak> peaks = new List<MSPeak>(mz.Length);
for(int i = 0; i < mz.Length; i++)
{
peaks.Add(new MSPeak(mz[i], intensity[i], 0, polarity));
}
peaks = FilterPeaks(peaks, absoluteThreshold, relativeThresholdPercent, maximumNumberOfPeaks);
if(peaks.Count > 0)
{
peaks.Sort(MSPeak.AscendingMZComparison);
for(int c = (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? minimumAssumedPrecursorChargeState : charge);
c <= (ALWAYS_USE_PRECURSOR_CHARGE_STATE_RANGE || charge == 0 ? maximumAssumedPrecursorChargeState : charge); c++)
{
List<MSPeak> new_peaks = peaks;
if(assignChargeStates)
{
new_peaks = AssignChargeStates(new_peaks, c, polarity, isotopicMZTolerance);
if(deisotope)
{
new_peaks = Deisotope(new_peaks, c, polarity, isotopicMZTolerance);
}
}
double precursor_mass = MSPeak.MassFromMZ(precursor_mz, c);
TandemMassSpectrum spectrum = new TandemMassSpectrum(mzmlFilepath, spectrum_number, spectrum_id, spectrum_title, retention_time_minutes, fragmentation_method, precursor_mz, precursor_intensity, c, precursor_mass, new_peaks);
lock(this)
{
Add(spectrum);
}
}
}
}
}
lock(progress_lock)
{
spectra_processed++;
int new_progress = (int)((double)spectra_processed / num_spectra * 100);
if(new_progress > old_progress)
{
OnUpdateProgress(new ProgressEventArgs(new_progress));
old_progress = new_progress;
}
}
}
#if !NON_MULTITHREADED
);
#endif
}
