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;
}