public Raw2MzXMLProcessor(MultipleRaw2MgfOptions options) : base(options) { this.options = options; this.dataProcessingOperations = new Dictionary <string, string>(); this.scanIndeies = new List <Pair <int, long> >(); }
public Raw2MgfProcessor(MultipleRaw2MgfOptions options) : base(options) { this.options = options; this.Writer = options.GetMGFWriter(); this.swMap = new Dictionary <string, StreamWriter>(); this.outputFiles = new List <string>(); }
public override IEnumerable <string> Process() { var runOptions = new MultipleRaw2MgfOptions(); if (options.Create) { runOptions.RawFiles = new[] { "sample1.raw", "sample2.raw" }; runOptions.SaveToFile(options.InputFile); return(new[] { options.InputFile }); } runOptions.LoadFromFile(options.InputFile); return(new MultipleRaw2MgfProcessor(runOptions).Process(runOptions.TargetDirectory)); }
private void btnLoad_Click(object sender, EventArgs e) { var dlg = this.openParamFile.GetFileDialog(); if (dlg.ShowDialog() == DialogResult.OK) { var options = new MultipleRaw2MgfOptions(); try { options.LoadFromFile(dlg.FileName); OptionsToForm(options); } catch (Exception ex) { MessageBox.Show(this, "Failed to load parameters from " + dlg.FileName + "\nError:" + ex.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error); } } }
private void OptionsToForm(MultipleRaw2MgfOptions options) { originalFile.FullName = options.TargetDirectory; rawFiles.FileNames = options.RawFiles; titleFormat.SelectedItem = titleFormat.Items.Where(l => l.FormatName.Equals(options.MascotTitleName)).First(); minMassRange.Value = options.PrecursorMassRange.From; maxMassRange.Value = options.PrecursorMassRange.To; minIonIntensity.Value = options.MinimumIonIntensity; minIonCount.Value = options.MinimumIonCount; minTotalIonIntensity.Value = options.MinimumTotalIonIntensity; defaultCharge.SelectedItem = defaultCharge.Items.Where(l => l.ToString().Equals(options.DefaultCharges.ToString())).First(); productIonPPM.Value = options.ProductIonPPM; cbDeisotopic.Checked = options.Deisotopic; cbDeconvolution.Checked = options.ChargeDeconvolution; cbKeepTopX.Checked = options.KeepTopX; topX.Value = options.TopX; cbGroupByMode.Checked = options.GroupByMode; cbGroupByMsLevel.Checked = options.GroupByMsLevel; cbParallelMode.Checked = options.ParallelMode; cbExtractRawMS3.Checked = options.ExtractRawMS3; cbOverwrite.Checked = options.Overwrite; cbOutputMzXmlFormat.Checked = options.OutputMzXmlFormat; cbRemoveIons.Checked = options.RemoveIons; removeIonWindow.Value = options.RemoveIonWindow; cbRemoveSpecialIons.Checked = options.RemoveSpecialIons; txtSpecialIons.Text = options.SpecialIons; cbRemoveIsobaricIons.Checked = options.RemoveIsobaricIons; isobaricTypes.SelectedItem = options.IsobaricType; proteases.SelectedItem = proteases.Items.Where(l => l.ToString().Equals(options.ProteaseName)).First(); rbRemoveReporters.Checked = options.RemoveIsobaricIonsReporters; cbRemoveIsobaricIonsInLowRange.Checked = options.RemoveIsobaricIonsInLowRange; cbRemoveIsobaricIonsInHighRange.Checked = options.RemoveIsobaricIonsInHighRange; cbRemovePrecursor.Checked = options.PrecursorOptions.RemovePrecursor; txtPrecursorPPM.Text = options.PrecursorOptions.PPMTolerance.ToString(); cbRemoveNeutralLoss.Checked = options.PrecursorOptions.RemoveNeutralLoss; txtNeutralLoss.Text = options.PrecursorOptions.NeutralLoss; cbRemovePrecursorIsotopicIons.Checked = options.PrecursorOptions.RemoveIsotopicIons; cbRemovePrecursorMinus1ChargeIon.Checked = options.PrecursorOptions.RemoveChargeMinus1Precursor; cbRemovePrecursorLargeIons.Checked = options.PrecursorOptions.RemoveIonLargerThanPrecursor; }
private MultipleRaw2MgfOptions FormToOptions() { var result = new MultipleRaw2MgfOptions(); result.ConverterName = Title; result.ConverterVersion = Version; result.TargetDirectory = GetOriginFile(); result.RawFiles = rawFiles.FileNames; result.MascotTitleName = titleFormat.SelectedItem.FormatName; result.PrecursorMassRange = new MassRange(minMassRange.Value, maxMassRange.Value); result.MinimumIonIntensity = minIonIntensity.Value; result.MinimumIonCount = minIonCount.Value; result.MinimumTotalIonIntensity = minTotalIonIntensity.Value; result.DefaultCharges = defaultCharge.SelectedItem; result.ProductIonPPM = productIonPPM.Value; result.Deisotopic = cbDeisotopic.Checked; result.ChargeDeconvolution = cbDeconvolution.Checked; result.KeepTopX = cbKeepTopX.Checked; result.TopX = topX.Value; result.GroupByMode = cbGroupByMode.Checked; result.GroupByMsLevel = cbGroupByMsLevel.Checked; result.ParallelMode = cbParallelMode.Checked; result.ExtractRawMS3 = cbExtractRawMS3.Checked; result.Overwrite = cbOverwrite.Checked; result.OutputMzXmlFormat = cbOutputMzXmlFormat.Checked; result.RemoveIons = cbRemoveIons.Checked; result.RemoveIonWindow = removeIonWindow.Value; result.RemoveSpecialIons = cbRemoveSpecialIons.Checked; result.SpecialIons = txtSpecialIons.Text; result.RemoveIsobaricIons = cbRemoveIsobaricIons.Checked; result.IsobaricType = isobaricTypes.SelectedItem; result.ProteaseName = proteases.SelectedItem.ToString(); result.RemoveIsobaricIonsInLowRange = cbRemoveIsobaricIonsInLowRange.Checked; result.RemoveIsobaricIonsInHighRange = cbRemoveIsobaricIonsInHighRange.Checked; result.RemoveIsobaricIonsReporters = rbRemoveReporters.Checked; result.PrecursorOptions = GetPrecursorOptions(); return(result); }
public MultipleRaw2MgfProcessorUI() { InitializeComponent(); this.Text = Constants.GetSQHTitle(Title, Version); this.SetDirectoryArgument("TargetDir", "Target MGF"); var options = new MultipleRaw2MgfOptions(); this.titleFormat = new RcpaComboBox <ITitleFormat>(cbTitleFormat, "TitleFormat", MascotTitleFactory.Titles, 0); this.minMassRange = new RcpaDoubleField(txtMWRangeFrom, "MWRangeFrom", "Min Mass", options.PrecursorMassRange.From, true); this.maxMassRange = new RcpaDoubleField(txtMWRangeTo, "MWRangeTo", "Max Mass", options.PrecursorMassRange.To, true); this.minIonIntensity = new RcpaDoubleField(txtMinIonIntensity, "MinIonIntensity", "Min Ion Intensity", options.MinimumIonIntensity, true); this.minIonCount = new RcpaIntegerField(txtMinIonCount, "MinIonCount", "Min Ion Count", options.MinimumIonCount, true); this.minTotalIonIntensity = new RcpaDoubleField(txtMinIonIntensityThreshold, "MinTotalIonIntensity", "Min Total Ion Intensity", options.MinimumTotalIonIntensity, true); this.defaultCharge = new RcpaComboBox <ChargeClass>(cbDefaultCharge, "DefaultCharge", new ChargeClass[] { new ChargeClass(new int[] {}), new ChargeClass(new int[] { 2, 3 }) }, 1); this.rawFiles.FileArgument = new OpenFileArgument("Raw", RawFileFactory.GetSupportedRawFormats()); //high resolution MS/MS productIonPPM = new RcpaDoubleField(txtDeisotopic, "DeisotopicPPM", "Deisotopic Product Ion Tolerance (ppm)", options.ProductIonPPM, false); AddComponent(productIonPPM); cbDeisotopic.Checked = options.Deisotopic; cbDeconvolution.Checked = options.ChargeDeconvolution; cbKeepTopX.Checked = options.KeepTopX; topX = new RcpaIntegerField(txtTopX, "TopX", "Top X Peaks in 100 dalton window", options.TopX, false); topX.PreCondition = cbKeepTopX; AddComponent(topX); cbGroupByMode.Checked = options.GroupByMode; cbGroupByMsLevel.Checked = options.GroupByMsLevel; cbParallelMode.Checked = options.ParallelMode; removeIonWindow = new RcpaDoubleField(txtRemoveMassWindow, "removeMassWindow", "Remove Mass Window", options.RemoveIonWindow, false); removeIonWindow.PreCondition = cbRemoveIons; AddComponent(removeIonWindow); isobaricTypes = new RcpaComboBox <IsobaricType>(cbxIsobaricTypes, "IsobaricType", IsobaricTypeFactory.IsobaricTypes, 0); isobaricTypes.PreCondition = cbRemoveIsobaricIons; AddComponent(isobaricTypes); proteases = new RcpaComboBox <IIsobaricLabellingProtease>(cbProteases, "Protease", IsobaricLabellingProteaseFactory.Proteases, 0); proteases.PreCondition = cbRemoveIsobaricIons; AddComponent(proteases); this.AddComponent(titleFormat); this.AddComponent(minMassRange); this.AddComponent(maxMassRange); this.AddComponent(minIonIntensity); this.AddComponent(minIonCount); this.AddComponent(minTotalIonIntensity); this.AddComponent(defaultCharge); cbRemoveSpecialIons.PreCondition = cbRemoveIons; specialIons = new RcpaTextField(txtSpecialIons, "RemoveIonMzRange", "Remove special mz range, for example, 113.5-117.5,145.5.0-155.5 for iTRAQ plex 4", options.SpecialIons, false); specialIons.PreCondition = cbRemoveSpecialIons; AddComponent(specialIons); cbRemoveIsobaricIons.PreCondition = cbRemoveIons; cbRemoveIsobaricIonsInLowRange.PreCondition = cbRemoveIsobaricIons; cbRemoveIsobaricIonsInHighRange.PreCondition = cbRemoveIsobaricIons; retentionTimeWindow = new RcpaDoubleField(txtRetentionTimeWindow, "RetentionTimeWindow", "Retention time window for smoothing offset", 0.5, false); AddComponent(retentionTimeWindow); cbRemovePrecursorLargeIons.PreCondition = cbRemovePrecursor; precursorPPM = new RcpaDoubleField(txtPrecursorPPM, "PrecursorPPM", "Precursor PPM", 50, false); precursorPPM.PreCondition = cbRemovePrecursor; AddComponent(precursorPPM); neutralLoss = new RcpaTextField(txtNeutralLoss, "NeutralLoss", "Neutral loss atom composition", "NH3,H2O,", false); neutralLoss.PreCondition = cbRemovePrecursor; AddComponent(neutralLoss); InsertButton(0, btnSave); InsertButton(0, btnLoad); }
public MultipleRaw2MgfProcessor(MultipleRaw2MgfOptions options) : base(options.RawFiles) { this.options = options; this.ParallelMode = options.ParallelMode; }