protected override IProcessor GetProcessor()
{
var options = new MS3LibraryPredictorOptions()
{
RawFiles = this.rawFiles.FileNames,
MinimumMS3PrecursorMz = this.minMS3PrecursorMz.Value,
MS2PrecursorPPMTolerance = this.ppmMS2Precursor.Value,
MS3PrecursorPPMTolerance = this.ppmMS3Precursor.Value,
MS3FragmentIonPPMTolerance = this.ppmMS3FragmentIon.Value,
MaximumFragmentPeakCount = this.maxFragmentIonCount.Value,
MinimumMatchedMS3SpectrumCount = this.minMatchedMS3SpectrumCount.Value,
MinimumMatchedMS3IonCount = this.minMatchedMS3FragmentIonCount.Value,
MinimumAminoacidSubstitutionDeltaMass = minAminoacidSubstitutionDeltaMass.Value,
IgnoreDeamidatedMutation = ignoreDeamidatedMutation.Checked,
IsSingleNucleotideMutationOnly = isSingleNucleotideMutationOnly.Checked,
AllowTerminalLoss = allowTerminalLoss.Checked,
AllowTerminalExtension = allowTerminalExtension.Checked,
LibraryFile = this.libraryFile.FullName,
PeptidesFile = this.peptidesFile.FullName,
DatabaseFastaFile = this.fastaFile.FullName,
OutputFile = this.outputFile.FullName
};
return(options.GetPredictor());
}
public MS3LibraryPredictorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, MS3LibraryBuilderUI.Version);
rawFiles.FileArgument = new OpenFileArgument("Raw", "raw");
AddComponent(this.rawFiles);
var dop = new MS3LibraryPredictorOptions();
this.ppmMS2Precursor = new RcpaDoubleField(txtMS2PrecursorPPM, "MS2PrecursorPPM", "MS2 Precursor PPM", dop.MS2PrecursorPPMTolerance, true);
AddComponent(this.ppmMS2Precursor);
this.ppmMS3Precursor = new RcpaDoubleField(txtMS3PrecursorPPM, "MS3PrecursorPPM", "MS3 Precursor PPM", dop.MS3PrecursorPPMTolerance, true);
AddComponent(this.ppmMS3Precursor);
this.ppmMS3FragmentIon = new RcpaDoubleField(txtMS3FragmentPPM, "MS3FragmentIonPPM", "MS3 Fragment Ion PPM", dop.MS3FragmentIonPPMTolerance, true);
AddComponent(this.ppmMS3FragmentIon);
this.maxFragmentIonCount = new RcpaIntegerField(txtMaximumMS3FragmentIonCount, "MaxFragmentIonCount", "Maximum Fragment Ion Count", dop.MaximumFragmentPeakCount, true);
AddComponent(this.maxFragmentIonCount);
this.minMS3PrecursorMz = new RcpaDoubleField(txtMinimumMS3PrecursorMz, "MinMS3PrecursorMz", "Minimum MS3 Precursor m/z", dop.MinimumMS3PrecursorMz, true);
AddComponent(this.minMS3PrecursorMz);
this.minMatchedMS3SpectrumCount = new RcpaIntegerField(txtMinimumMatchedMS3SpectrumCount, "MinMatchedMS3SpectrumCount", "Minimum Matched MS3 Spectrum Count", dop.MinimumMatchedMS3SpectrumCount, true);
AddComponent(this.minMatchedMS3SpectrumCount);
this.minMatchedMS3FragmentIonCount = new RcpaIntegerField(txtMinimumMatchedMS3FragmentIonCount, "MinimumMatchedMS3FragmentIonCount", "Minimum Matched MS3 Fragment Ion Count", dop.MinimumMatchedMS3IonCount, true);
AddComponent(this.minMatchedMS3FragmentIonCount);
this.minAminoacidSubstitutionDeltaMass = new RcpaDoubleField(txtMinimumSubstitutionDeltaMass, "MinimumSubstitutionDeltaMass", "Minimum Aminoacid Substitution Delta Mass", dop.MinimumAminoacidSubstitutionDeltaMass, true);
AddComponent(this.minAminoacidSubstitutionDeltaMass);
this.allowTerminalLoss.Checked = dop.AllowTerminalLoss;
this.allowTerminalExtension.Checked = dop.AllowTerminalExtension;
this.ignoreDeamidatedMutation.Checked = dop.IgnoreDeamidatedMutation;
this.isSingleNucleotideMutationOnly.Checked = dop.IsSingleNucleotideMutationOnly;
libraryFile.FileArgument = new OpenFileArgument("Library", "xml");
peptidesFile.FileArgument = new OpenFileArgument("Excluding Peptides", "peptides");
fastaFile.FileArgument = new OpenFileArgument("Database", "fasta");
outputFile.FileArgument = new SaveFileArgument("Output Database", "fasta");
}
public AbstractMS3LibraryPredictor(MS3LibraryPredictorOptions options)
{
this.options = options;
}
public MS3LibraryMS3FirstPredictor(MS3LibraryPredictorOptions options) : base(options)
{
}