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) { }