private void WriteFile(string filepath)
{
onStartingFile(new FilepathEventArgs(filepath));
txt_outputs = new Dictionary<string, StreamWriter>();
mgf_outputs = new Dictionary<string, StreamWriter>();
SortedDictionary<string, int> spectrum_counts = new SortedDictionary<string, int>();
SortedDictionary<string, int> dta_counts = new SortedDictionary<string, int>();
SortedDictionary<int, double> retention_times = new SortedDictionary<int, double>();
SortedDictionary<int, double> scan_filter_mzs = new SortedDictionary<int, double>();
SortedDictionary<int, double> precursor_mzs = new SortedDictionary<int, double>();
SortedDictionary<int, double> precursor_intensities = new SortedDictionary<int, double>();
SortedDictionary<int, double> precursor_denormalized_intensities = new SortedDictionary<int, double>();
SortedDictionary<int, int> precursor_charge_states = new SortedDictionary<int, int>();
SortedDictionary<int, string> precursor_fragmentation_methods = new SortedDictionary<int, string>();
SortedDictionary<int, double> elapsed_scan_times = new SortedDictionary<int, double>();
SortedDictionary<int, double> ion_injection_times = new SortedDictionary<int, double>();
SortedDictionary<int, double?> precursor_sns = new SortedDictionary<int, double?>();
SortedDictionary<int, int> precursor_peak_depths = new SortedDictionary<int, int>();
using (RawFile raw = new RawFile(filepath))
{
// Open connection to the raw file
raw.Open();
// Can generate massive background spectrum here... to remove from all the other spectra
using (StreamWriter writer = new StreamWriter(Path.Combine(outputFolder, Path.GetFileNameWithoutExtension(filepath) + ".txt")))
{
int count = 0;
foreach (Spectrum msms in raw.GetNextMSMS())
{
// Clean the spectrum
CleanSpectrum(msms);
// Write the spectrum out
WriteSpectrumToFile(writer, msms);
// Change Progress
if (count > 100)
{
count = 0;
double progress = (double)(msms.ScanNumber - raw.FirstScanNumber + 1) / (raw.LastScanNumber - raw.FirstScanNumber + 1);
onUpdateProgress(new ProgressEventArgs((int)(progress * 100)));
}
count++;
}
}
}
// for (int scan_number = first_scan_number; scan_number <= last_scan_number; scan_number++)
// {
// string scan_filter = null;
// raw.GetFilterForScanNum(scan_number, ref scan_filter);
// if (scan_filter != null && scan_filter.Contains("@"))
// {
//* retention_times.Add(scan_number, time);
//* scan_filter_mzs.Add(scan_number, precursor_mz);
// if (!no_precursor_scan)
// {
// /
// int? precursor_index = null;
// int precusor_data_index = (int)RawLabelDataColumn.MZ;
// int min = precursor_data.GetLowerBound(1);
// int max = precursor_data.GetUpperBound(1);
// for (int i = min; i <= max; i++)
// {
// if (Math.Abs(precursor_data[precusor_data_index, i] - precursor_mz) <= PEAK_IDENTIFICATION_MASS_TOLERANCE)
// {
// if (!precursor_index.HasValue || precursor_data[(int)RawLabelDataColumn.Intensity, i] > precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value])
// {
// precursor_index = i;
// }
// }
// }
// if (!precursor_index.HasValue)
// {
// for (int i = precursor_data.GetLowerBound(1); i <= precursor_data.GetUpperBound(1); i++)
// {
// if (!precursor_index.HasValue || Math.Abs(precursor_data[(int)RawLabelDataColumn.MZ, i] - precursor_mz) < Math.Abs(precursor_data[(int)RawLabelDataColumn.MZ, precursor_index.Value] - precursor_mz))
// {
// precursor_index = i;
// }
// }
// }
// if (precursor_index.HasValue)
// {
// precursor_mz = precursor_data[(int)RawLabelDataColumn.MZ, precursor_index.Value];
// precursor_mzs.Add(scan_number, precursor_mz);
// precursor_intensities.Add(scan_number, precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value]);
// object precursor_header_labels = null;
// object precursor_header_values = null;
// int precursor_array_size = -1;
// raw.GetTrailerExtraForScanNum(precursor_scan_number, ref precursor_header_labels, ref precursor_header_values, ref precursor_array_size);
// string[] precursor_header_label_strings = (string[])precursor_header_labels;
// string[] precursor_header_value_strings = (string[])precursor_header_values;
// if (precursor_header_label_strings != null && precursor_header_value_strings != null)
// {
// for (int header_i = precursor_header_label_strings.GetLowerBound(0); header_i <= precursor_header_label_strings.GetUpperBound(0); header_i++)
// {
// if (precursor_header_label_strings[header_i].StartsWith("Ion Injection Time (ms)"))
// {
// precursor_denormalized_intensities.Add(scan_number, precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value] * double.Parse(precursor_header_value_strings[header_i]) / 1000.0);
// }
// }
// }
// if (precursor_data.GetLength(0) > 2)
// {
// precursor_sns.Add(scan_number, (precursor_data[(int)RawLabelDataColumn.Intensity, precursor_index.Value] - precursor_data[(int)RawLabelDataColumn.NoiseBaseline, precursor_index.Value]) / precursor_data[(int)RawLabelDataColumn.NoiseLevel, precursor_index.Value]);
// }
// else
// {
// precursor_sns.Add(scan_number, null);
// }
// int peak_depth = 1;
// int precursor_data_index = (int)RawLabelDataColumn.Intensity;
// double prec_value = precursor_data[precursor_data_index, precursor_index.Value];
// min = precursor_data.GetLowerBound(1);
// max = precursor_data.GetUpperBound(1);
// for (int i = min; i <= max; i++)
// {
// if (precursor_data[precursor_data_index, i] > prec_value && i != precursor_index.Value)
// {
// peak_depth++;
// }
// }
// precursor_peak_depths.Add(scan_number, peak_depth);
// }
// }
// object header_labels = null;
// object header_values = null;
// int array_size = -1;
// raw.GetTrailerExtraForScanNum(scan_number, ref header_labels, ref header_values, ref array_size);
// string[] header_label_strings = (string[])header_labels;
// string[] header_value_strings = (string[])header_values;
// int charge = 0;
// if (header_label_strings != null && header_value_strings != null)
// {
// for (int header_i = header_label_strings.GetLowerBound(0); header_i <= header_label_strings.GetUpperBound(0); header_i++)
// {
// if (header_label_strings[header_i].StartsWith("Charge"))
// {
// charge = int.Parse(header_value_strings[header_i]);
// if (scan_filter.Contains(" - "))
// {
// charge = -charge;
// }
// precursor_charge_states.Add(scan_number, charge);
// }
// else if (header_label_strings[header_i].StartsWith("Elapsed Scan Time (sec)"))
// {
// elapsed_scan_times.Add(scan_number, double.Parse(header_value_strings[header_i]));
// }
// else if (header_label_strings[header_i].StartsWith("Ion Injection Time (ms)"))
// {
// ion_injection_times.Add(scan_number, double.Parse(header_value_strings[header_i]));
// }
// }
// }
// object labels = null;
// object flags = null;
// raw.GetLabelData(ref labels, ref flags, ref scan_number);
// double[,] data = (double[,])labels;
// if (data.Length == 0)
// {
// double centroid_peak_width = -1.0;
// labels = null;
// flags = null;
// int mass_list_array_size = -1;
// raw.GetMassListFromScanNum(ref scan_number, null, 0, 0, 0, 1, ref centroid_peak_width, ref labels, ref flags, ref mass_list_array_size);
// data = (double[,])labels;
// }
// double total_ion_current = 0.0;
// double base_peak_mz = -1.0;
// double base_peak_intensity = -1.0;
// for (int data_i = data.GetLowerBound(1); data_i <= data.GetUpperBound(1); data_i++)
// {
// total_ion_current += data[(int)RawLabelDataColumn.Intensity, data_i];
// if (base_peak_mz < 0.0 ||
// data[(int)RawLabelDataColumn.Intensity, data_i] > base_peak_intensity)
// {
// base_peak_mz = data[(int)RawLabelDataColumn.MZ, data_i];
// base_peak_intensity = data[(int)RawLabelDataColumn.Intensity, data_i];
// }
// }
// List<int> charges = new List<int>();
// if (charge == 0 || no_precursor_scan)
// {
// for (int assumed_charge_state = minimumAssumedPrecursorChargeState; assumed_charge_state <= maximumAssumedPrecursorChargeState; assumed_charge_state++)
// {
// charges.Add(assumed_charge_state);
// }
// }
// else
// {
// charges.Add(charge);
// }
// string mass_analyzer = scan_filter.Substring(0, 4).ToUpper();
// if (!mass_analyzer.Contains("MS"))
// {
// mass_analyzer = "TQMS";
// }
// string fragmentation_method = null;
// if (groupByActivationEnergyTime)
// {
// foreach (int i in AllIndicesOf(scan_filter, '@'))
// {
// string temp_scan_filter = scan_filter.Substring(i + 1);
// temp_scan_filter = temp_scan_filter.Substring(0, temp_scan_filter.IndexOf(' '));
// fragmentation_method += temp_scan_filter.ToUpper() + '-';
// }
// }
// else
// {
// foreach (int i in AllIndicesOf(scan_filter, '@'))
// {
// fragmentation_method += scan_filter.Substring(i + 1, 3).ToUpper() + '-';
// }
// }
// fragmentation_method = fragmentation_method.Substring(0, fragmentation_method.Length - 1);
// string base_output_filename = Path.GetFileNameWithoutExtension(filepath) + '_' + mass_analyzer + '_' + fragmentation_method;
// precursor_fragmentation_methods.Add(scan_number, fragmentation_method);
// if (!spectrum_counts.ContainsKey(mass_analyzer))
// {
// spectrum_counts.Add(mass_analyzer, 0);
// }
// spectrum_counts[mass_analyzer]++;
// if (!dta_counts.ContainsKey(mass_analyzer))
// {
// dta_counts.Add(mass_analyzer, 0);
// }
// dta_counts[mass_analyzer] += charges.Count;
// if (!spectrum_counts.ContainsKey(fragmentation_method))
// {
// spectrum_counts.Add(fragmentation_method, 0);
// }
// spectrum_counts[fragmentation_method]++;
// if (!dta_counts.ContainsKey(fragmentation_method))
// {
// dta_counts.Add(fragmentation_method, 0);
// }
// dta_counts[fragmentation_method] += charges.Count;
// if (!spectrum_counts.ContainsKey(mass_analyzer + ' ' + fragmentation_method))
// {
// spectrum_counts.Add(mass_analyzer + ' ' + fragmentation_method, 0);
// }
// spectrum_counts[mass_analyzer + ' ' + fragmentation_method]++;
// if (!dta_counts.ContainsKey(mass_analyzer + ' ' + fragmentation_method))
// {
// dta_counts.Add(mass_analyzer + ' ' + fragmentation_method, 0);
// }
// dta_counts[mass_analyzer + ' ' + fragmentation_method] += charges.Count;
// if (sequestDtaOutput || omssaTxtOutput || mascotMgfOutput)
// {
// List<MSPeak> all_peaks = new List<MSPeak>();
// for (int data_i = data.GetLowerBound(1); data_i <= data.GetUpperBound(1); data_i++)
// {
// double mz = data[(int)RawLabelDataColumn.MZ, data_i];
// all_peaks.Add(new MSPeak(mz, data[(int)RawLabelDataColumn.Intensity, data_i]));
// }
// foreach (int charge_i in charges)
// {
// double retention_time_min = double.NaN;
// raw.RTFromScanNum(scan_number, ref retention_time_min);
// double retention_time_s = retention_time_min * 60;
// string dta_filepath = Path.GetFileNameWithoutExtension(filepath) +
// '.' + mass_analyzer + '.' + fragmentation_method +
// '.' + scan_number.ToString() + '.' +
// scan_number.ToString() + '.' +
// charge_i.ToString() + '.' +
// "RT_" + retention_time_min.ToString("0.000") + "_min_" + retention_time_s.ToString("0.0") + "_s" +
// ".dta";
// double precursor_mass = MassFromMZ(precursor_mz, charge_i);
// StringBuilder dta_content_sb = new StringBuilder();
// StringBuilder mgf_content_sb = new StringBuilder();
// dta_content_sb.AppendLine((precursor_mass + PROTON_MASS).ToString("0.00000") + ' ' + charge_i.ToString());
// mgf_content_sb.AppendLine("BEGIN IONS");
// mgf_content_sb.AppendLine("Title=" + Path.GetFileNameWithoutExtension(dta_filepath));
// mgf_content_sb.AppendLine("SCANS=" + scan_number.ToString());
// mgf_content_sb.AppendLine("RTINSECONDS=" + retention_time_s.ToString());
// mgf_content_sb.AppendLine("PEPMASS=" + precursor_mz.ToString("0.00000"));
// mgf_content_sb.AppendLine("CHARGE=" + charge_i.ToString("0+;0-"));
// List<MSPeak> peaks = new List<MSPeak>(all_peaks);
// bool isHCD = fragmentation_method.StartsWith("HCD");
// bool isETD = fragmentation_method.StartsWith("ETD") || fragmentation_method.StartsWith("ECD");
// // FOR AARON
//#if Aaron_Experiment
// isETD = isETD || scan_filter.Contains("hcd0.5") || scan_filter.Contains("hcd1.5");
//#endif
// //
// if (neutralLossesIncluded)
// {
// List<KeyValuePair<double, double>> mzs = new List<KeyValuePair<double, double>>();
// foreach (double nl_mass in this.neutralLosses)
// {
// double mz = precursor_mz - MZFromMass(nl_mass, charge_i);
// double min = mz - LOW_PRECURSOR_CLEANING_WINDOW_MZ;
// double max = mz + HIGH_PRECURSOR_CLEANING_WINDOW_MZ;
// mzs.Add(new KeyValuePair<double, double>(min, max));
// }
// int p = 0;
// while (p < peaks.Count)
// {
// double mz = peaks[p].MZ;
// if (mz >= precursor_mz)
// {
// break;
// }
// bool removed = false;
// foreach (KeyValuePair<double, double> minmax in mzs)
// {
// if (mz >= minmax.Key && mz <= minmax.Value)
// {
// peaks.RemoveAt(p);
// removed = true;
// break;
// }
// }
// if (!removed)
// {
// p++;
// }
// }
// }
// // ETD pre-processing
// if (enableEtdPreProcessing && isETD)
// {
// // negative ETD
// if (scan_filter.Contains(" - "))
// {
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// bool clean = false;
// for (int reduced_precursor_charge = -2; reduced_precursor_charge >= charge_i + 1; reduced_precursor_charge--)
// {
// if (mz >= MZFromMass(precursor_mass - NETD_LOW_NEUTRAL_LOSS_CLEANING_WINDOW_DA, reduced_precursor_charge) &&
// mz <= MZFromMass(precursor_mass + NETD_HIGH_NEUTRAL_LOSS_CLEANING_WINDOW_DA, reduced_precursor_charge))
// {
// clean = true;
// break;
// }
// if (mz >= MZFromMass(precursor_mass + NETD_ADDUCT_CLEANING_WINDOW_DA, reduced_precursor_charge) - NETD_ADDUCT_LOW_CLEANING_WINDOW_MZ &&
// mz <= MZFromMass(precursor_mass + NETD_ADDUCT_CLEANING_WINDOW_DA, reduced_precursor_charge) + NETD_ADDUCT_LOW_CLEANING_WINDOW_MZ)
// {
// clean = true;
// break;
// }
// }
// if (!clean)
// {
// if (mz >= MZFromMass(precursor_mass, -1) - NETD_SINGLY_CHARGED_LOW_NEUTRAL_LOSS_CLEANING_WINDOW_MZ)
// {
// clean = true;
// }
// }
// if (clean)
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// // positive ETD
// else
// {
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// bool clean = false;
// for (int reduced_precursor_charge = 1; reduced_precursor_charge <= charge_i - 1; reduced_precursor_charge++)
// {
// if (mz >= MZFromMass(precursor_mass - LOW_NEUTRAL_LOSS_CLEANING_WINDOW_DA, reduced_precursor_charge) &&
// mz < MZFromMass(precursor_mass, reduced_precursor_charge) + HIGH_PRECURSOR_CLEANING_WINDOW_MZ)
// {
// clean = true;
// break;
// }
// }
// if (clean)
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// // TMT duplex cleaning
// if (cleanTmtDuplex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_duplex_tag_cleaning_mz = precursor_mz * reduced_charge_i - TMT_DUPLEX_CAD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_DUPLEX_CAD_REPORTER_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_DUPLEX_CAD_REPORTER_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_DUPLEX_CAD_TAG_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_DUPLEX_CAD_TAG_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_duplex_tag_cleaning_mz - TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_duplex_tag_cleaning_mz + TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// else if (fragmentation_method.StartsWith("ETD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_duplex_reporter_loss_cleaning_mz = precursor_mz * charge_i - TMT_DUPLEX_ETD_REPORTER_LOSS_DA / reduced_charge_i;
// double precursor_tmt_duplex_tag_loss_cleaning_mz = precursor_mz * charge_i - TMT_DUPLEX_ETD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_DUPLEX_ETD_REPORTER_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_DUPLEX_ETD_REPORTER_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_DUPLEX_ETD_TAG_MZ - TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_DUPLEX_ETD_TAG_MZ + TMT_DUPLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_duplex_reporter_loss_cleaning_mz - TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_duplex_reporter_loss_cleaning_mz + TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_duplex_tag_loss_cleaning_mz - TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_duplex_tag_loss_cleaning_mz + TMT_DUPLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// }
// // iTRAQ 4-plex cleaning
// if (cleanItraq4Plex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// double precursor_itraq_4plex_tag_cleaning_mz = precursor_mz * charge_i - ITRAQ_4PLEX_CAD_TAG_LOSS_DA;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_ITRAQ_4PLEX_CAD_REPORTER_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_ITRAQ_4PLEX_CAD_REPORTER_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= ITRAQ_4PLEX_CAD_TAG_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= ITRAQ_4PLEX_CAD_TAG_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_tag_cleaning_mz - ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_tag_cleaning_mz + ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// else if (fragmentation_method.StartsWith("ETD"))
// {
// double precursor_itraq_4plex_reporter_loss_cleaning_mz = precursor_mz * charge_i - ITRAQ_4PLEX_ETD_REPORTER_LOSS_DA;
// double precursor_itraq_4plex_tag_loss_cleaning_mz = precursor_mz * charge_i - ITRAQ_4PLEX_ETD_TAG_LOSS_DA;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_ITRAQ_4PLEX_ETD_REPORTER_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_ITRAQ_4PLEX_ETD_REPORTER_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= ITRAQ_4PLEX_ETD_TAG_MZ - ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= ITRAQ_4PLEX_ETD_TAG_MZ + ITRAQ_4PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_reporter_loss_cleaning_mz - ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_reporter_loss_cleaning_mz + ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_tag_loss_cleaning_mz - ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_tag_loss_cleaning_mz + ITRAQ_4PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// // TMT 6-plex cleaning
// if (cleanTmt6Plex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_6plex_tag_cleaning_mz = precursor_mz * reduced_charge_i - TMT_6PLEX_CAD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_6PLEX_CAD_REPORTER_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_6PLEX_CAD_REPORTER_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_6PLEX_CAD_TAG_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_6PLEX_CAD_TAG_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_6plex_tag_cleaning_mz - TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_6plex_tag_cleaning_mz + TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// else if (fragmentation_method.StartsWith("ETD"))
// {
// for (int reduced_charge_i = charge_i - 1; reduced_charge_i >= 1; reduced_charge_i--)
// {
// double precursor_tmt_6plex_reporter_loss_cleaning_mz = precursor_mz * charge_i - TMT_6PLEX_ETD_REPORTER_LOSS_DA / reduced_charge_i;
// double precursor_tmt_6plex_tag_loss_cleaning_mz = precursor_mz * charge_i - TMT_6PLEX_ETD_TAG_LOSS_DA / reduced_charge_i;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_TMT_6PLEX_ETD_REPORTER_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_TMT_6PLEX_ETD_REPORTER_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= TMT_6PLEX_ETD_TAG_MZ - TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= TMT_6PLEX_ETD_TAG_MZ + TMT_6PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_6plex_reporter_loss_cleaning_mz - TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_6plex_reporter_loss_cleaning_mz + TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_tmt_6plex_tag_loss_cleaning_mz - TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_tmt_6plex_tag_loss_cleaning_mz + TMT_6PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// }
// // iTRAQ 8-plex cleaning
// if (cleanItraq8Plex)
// {
// if (fragmentation_method.StartsWith("CID") || fragmentation_method.StartsWith("PQD") || fragmentation_method.StartsWith("HCD"))
// {
// double precursor_itraq_4plex_tag_cleaning_mz = precursor_mz * charge_i - ITRAQ_8PLEX_CAD_TAG_LOSS_DA;
// int p1 = 0;
// while (p1 < peaks.Count)
// {
// double mz = peaks[p1].MZ;
// if ((mz >= MINIMUM_ITRAQ_8PLEX_CAD_REPORTER_MZ - ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= MAXIMUM_ITRAQ_8PLEX_CAD_REPORTER_MZ + ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= ITRAQ_8PLEX_CAD_TAG_MZ - ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ
// && mz <= ITRAQ_8PLEX_CAD_TAG_MZ + ITRAQ_8PLEX_CLEANING_MASS_TOLERANCE_MZ)
// || (mz >= precursor_itraq_4plex_tag_cleaning_mz - ITRAQ_8PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ
// && mz <= precursor_itraq_4plex_tag_cleaning_mz + ITRAQ_8PLEX_LOSS_CLEANING_MASS_TOLERANCE_MZ))
// {
// peaks.RemoveAt(p1);
// }
// else
// {
// p1++;
// }
// }
// }
// }
// MSPeak base_peak = null;
// foreach (MSPeak peak in peaks)
// {
// if (base_peak == null || peak.Intensity > base_peak.Intensity)
// {
// base_peak = peak;
// }
// }
// //if (omssaTxtOutput)
// //{
// //foreach (MSPeak peak in peaks)
// //{
// // dta_content_sb.AppendFormat(" {0:0.00000} {1:0.000}", peak.MZ, peak.Intensity).AppendLine();
// //dta_content_sb.AppendLine(string.Format(" {0:0.00000} {1:0.00}", peak.MZ, peak.Intensity));
// //}
// //}
// if (mascotMgfOutput)
// {
// foreach (MSPeak peak in peaks)
// {
// mgf_content_sb.AppendLine(string.Format("{0:0.00000} {1:0.00}", peak.MZ, peak.Intensity));
// }
// }
// if (sequestDtaOutput)
// {
// StreamWriter dta = new StreamWriter(Path.Combine(outputFolder, dta_filepath));
// if (dta_content_sb.Length > 0)
// {
// dta.Write(dta_content_sb.ToString());
// }
// dta.Close();
// }
// if (omssaTxtOutput)
// {
// string txt_filepath = Path.Combine(outputFolder,
// base_output_filename + ".txt");
// if (!txt_outputs.ContainsKey(txt_filepath))
// {
// txt_outputs.Add(txt_filepath, new StreamWriter(txt_filepath));
// }
// StreamWriter txt = txt_outputs[txt_filepath];
// txt.WriteLine("<dta id=\"" + scan_number.ToString() + "\" name=\"" + dta_filepath + "\">");
// txt.WriteLine();
// foreach (MSPeak peak in peaks)
// {
// txt.WriteLine(" {0:0.00000} {1:0.000}", peak.MZ, peak.Intensity);
// // dta_content_sb.AppendFormat(" {0:0.00000} {1:0.000}", peak.MZ, peak.Intensity).AppendLine();
// //dta_content_sb.AppendLine(string.Format(" {0:0.00000} {1:0.00}", peak.MZ, peak.Intensity));
// }
// // if(dta_content_sb.Length > 0)
// // {
// // txt.Write(dta_content_sb.ToString());
// // }
// txt.WriteLine();
// txt.WriteLine();
// }
// if (mascotMgfOutput)
// {
// string mgf_filepath = Path.Combine(outputFolder,
// base_output_filename + ".mgf");
// if (!mgf_outputs.ContainsKey(mgf_filepath))
// {
// mgf_outputs.Add(mgf_filepath, new StreamWriter(mgf_filepath));
// }
// StreamWriter mgf = mgf_outputs[mgf_filepath];
// if (mgf_content_sb.Length > 0)
// {
// mgf.Write(mgf_content_sb.ToString());
// }
// mgf.WriteLine("END IONS");
// mgf.WriteLine();
// }
// }
// }
// }
// // Perform update progress every 100 scans so not to slow down with all the callbacks
// if (scan_number % 100 == 0)
// {
// double progress = (double)(scan_number - first_scan_number + 1) / (last_scan_number - first_scan_number + 1);
// onUpdateProgress(new ProgressEventArgs((int)(progress * 100)));
// }
//}
//raw.Close();
//if (txt_outputs != null)
//{
// foreach (StreamWriter sw in txt_outputs.Values)
// {
// if (sw != null)
// {
// sw.Close();
// }
// }
//}
//if (mgf_outputs != null)
//{
// foreach (StreamWriter sw in mgf_outputs.Values)
// {
// if (sw != null)
// {
// sw.Close();
// }
// }
//}
//using (StreamWriter log = new StreamWriter(Path.Combine(LogFolder, Path.GetFileNameWithoutExtension(filepath) + "_log.txt")))
//{
// log.WriteLine("DTA Generator PARAMETERS");
// log.WriteLine("Assumed Precursor Charge State Range: " + minimumAssumedPrecursorChargeState.ToString() + '-' + maximumAssumedPrecursorChargeState.ToString());
// log.WriteLine("Clean Precursor: " + cleanPrecursor.ToString());
// log.WriteLine("Enable ETD Pre-Processing: " + enableEtdPreProcessing.ToString());
// log.WriteLine("Clean TMT Duplex: " + cleanTmtDuplex.ToString());
// log.WriteLine("Clean iTRAQ 4-Plex: " + cleanItraq4Plex.ToString());
// log.WriteLine("Clean TMT 6-Plex: " + cleanTmt6Plex.ToString());
// log.WriteLine("Clean iTRAQ 8-Plex: " + cleanItraq8Plex.ToString());
// log.WriteLine();
// log.WriteLine("Spectrum Type\tNumber of Scans");
// foreach (KeyValuePair<string, int> kvp in spectrum_counts)
// {
// log.WriteLine(kvp.Key + '\t' + kvp.Value.ToString());
// }
// log.WriteLine();
// log.WriteLine("Spectrum Type\tNumber of DTAs");
// foreach (KeyValuePair<string, int> kvp in dta_counts)
// {
// log.WriteLine(kvp.Key + '\t' + kvp.Value.ToString());
// }
// log.WriteLine();
// double? min_elapsed = null;
// double? max_elapsed = null;
// double mean_elapsed = 0.0;
// foreach (double elapsed_scan_time in elapsed_scan_times.Values)
// {
// if (!min_elapsed.HasValue || elapsed_scan_time < min_elapsed)
// {
// min_elapsed = elapsed_scan_time;
// }
// if (!max_elapsed.HasValue || elapsed_scan_time > max_elapsed)
// {
// max_elapsed = elapsed_scan_time;
// }
// mean_elapsed += elapsed_scan_time;
// }
// mean_elapsed /= elapsed_scan_times.Count;
// if (min_elapsed.HasValue)
// {
// log.WriteLine("Minimum Fragmentation Elapsed Scan Time (sec): " + min_elapsed.Value.ToString());
// }
// if (max_elapsed.HasValue)
// {
// log.WriteLine("Maximum Fragmentation Elapsed Scan Time (sec): " + max_elapsed.Value.ToString());
// }
// if (!Double.IsNaN(mean_elapsed))
// {
// log.WriteLine("Average Fragmentation Elapsed Scan Time (sec): " + mean_elapsed.ToString());
// }
// log.WriteLine();
// double? min_injection = null;
// double? max_injection = null;
// double mean_injection = 0.0;
// foreach (double ion_injection_time in ion_injection_times.Values)
// {
// if (!min_injection.HasValue || ion_injection_time < min_injection)
// {
// min_injection = ion_injection_time;
// }
// if (!max_injection.HasValue || ion_injection_time > max_injection)
// {
// max_injection = ion_injection_time;
// }
// mean_injection += ion_injection_time;
// }
// mean_injection /= ion_injection_times.Count;
// if (min_injection.HasValue)
// {
// log.WriteLine("Minimum Fragmentation Ion Injection Time (msec): " + min_injection.Value.ToString());
// }
// if (max_injection.HasValue)
// {
// log.WriteLine("Maximum Fragmentation Ion Injection Time (msec): " + max_injection.Value.ToString());
// }
// if (!Double.IsNaN(mean_injection))
// {
// log.WriteLine("Average Fragmentation Ion Injection Time (msec): " + mean_injection.ToString());
// }
// log.WriteLine();
// log.WriteLine("Fragmentation Scan Summary");
// log.Write("Fragmentation Scan Number\t");
// log.Write("Retention Time (min.)\t");
// log.Write("Scan Filter m/z\t");
// log.Write("Precursor m/z\t");
// log.Write("Precursor Intensity\t");
// log.Write("Precursor Denormalized Intensity\t");
// log.Write("Precursor Charge State\t");
// log.Write("Precursor S/N Ratio\t");
// log.Write("Precursor Peak Depth\t");
// log.Write("Fragmentation Method\t");
// log.Write("Elapsed Scan Time (sec)\t");
// log.Write("Ion Injection Time (msec)");
// log.WriteLine();
// foreach (int sn2 in retention_times.Keys)
// {
// log.Write(sn2.ToString() + '\t');
// log.Write(retention_times[sn2].ToString("0.00") + '\t');
// log.Write(scan_filter_mzs[sn2].ToString("0.00") + '\t');
// log.Write((precursor_mzs.ContainsKey(sn2) ? precursor_mzs[sn2].ToString("0.00000") : "n/a") + '\t');
// log.Write((precursor_intensities.ContainsKey(sn2) ? precursor_intensities[sn2].ToString("0.0") : "n/a") + '\t');
// log.Write((precursor_denormalized_intensities.ContainsKey(sn2) ? precursor_denormalized_intensities[sn2].ToString("0.0") : "n/a") + '\t');
// log.Write((precursor_charge_states.ContainsKey(sn2) ? precursor_charge_states[sn2].ToString() : "n/a") + '\t');
// log.Write((precursor_sns.ContainsKey(sn2) && precursor_sns[sn2].HasValue ? precursor_sns[sn2].Value.ToString() : "n/a") + '\t');
// log.Write((precursor_peak_depths.ContainsKey(sn2) ? precursor_peak_depths[sn2].ToString() : "n/a") + '\t');
// log.Write((precursor_fragmentation_methods.ContainsKey(sn2) ? precursor_fragmentation_methods[sn2] : "n/a") + '\t');
// log.Write((elapsed_scan_times.ContainsKey(sn2) ? elapsed_scan_times[sn2].ToString() : "n/a") + '\t');
// log.Write((ion_injection_times.ContainsKey(sn2) ? ion_injection_times[sn2].ToString() : "n/a") + '\t');
// log.WriteLine();
// }
//}
onFinishedFile(new FilepathEventArgs(filepath));
}
