public DatasetPanelBase() { InitializeComponent(); componentList = new RcpaComponentList(); this.enabled = new RcpaCheckBox(cbEnabled, "Enabled", true); AddComponent(enabled); this.datasetName = new RcpaTextField(txtDatasetName, "DatasetName", "Dataset Name", "", true); AddComponent(datasetName); this.filterPrecursorPPMTolerance = new RcpaCheckBox(this.cbFilterByPrecursor, "FilterPrecursor", false); AddComponent(this.filterPrecursorPPMTolerance); this.filterPrecursorIsotopic = new RcpaCheckBox(this.cbFilterByPrecursorIsotopic, "FilterPrecursorIsotopic", true); AddComponent(this.filterPrecursorIsotopic); this.precursorPPMTolerance = new RcpaDoubleField(this.txtPrecursorPPMTolerance, "PrecursorPPMTolerance", "Precursor Tolerance (ppm)", 10, false); AddComponent(this.precursorPPMTolerance); this.filterPrecursorByDynamicTolerance = new RcpaCheckBox(this.cbFilterByDynamicPrecursorTolerance, "FilterPrecursorByDynamicTolerance", true); AddComponent(this.filterPrecursorByDynamicTolerance); this.searchedByDifferentParameters = new RcpaCheckBox(this.cbSearchedByDifferentParameters, "SearchedByDifferentParameters", false); AddComponent(this.searchedByDifferentParameters); }
public TheoreticalDigestionStatisticCalculatorUI() { InitializeComponent(); SetFileArgument("FastaFile", new OpenFileArgument("Protein Sequence", "fasta")); lbProteases.Items.AddRange(ProteaseManager.GetNames().ToArray()); AddComponent(lbSelectedProteases); this.minLength = new RcpaIntegerField(txtMinLength, "minlength", "Minimum peptide length", 6, true); AddComponent(minLength); this.maxMissCleavage = new RcpaIntegerField(txtMaxMissCleavage, "maxmisscleavage", "Maximum miss cleavage", 2, true); AddComponent(maxMissCleavage); this.minMass = new RcpaDoubleField(txtMinMass, "minmass", "Minimum peptide mass", 400, true); AddComponent(minMass); this.maxMass = new RcpaDoubleField(txtMaxMass, "maxmass", "Maximum peptide mass", 5000, true); AddComponent(maxMass); ignoreAminoacids = new RcpaTextField(txtIgnoreAminoacids, "ignoreaminoacids", "Ignore amino acids", "XB", true); AddComponent(ignoreAminoacids); this.Text = Constants.GetSQHTitle(title, version); }
public ReversedDatabaseBuilderUI() { InitializeComponent(); this.sourceDatabase.FileArgument = new OpenFileArgument("Source Database Fasta", new string[] { ".fasta", ".fa" }); reversedOnly = new RcpaCheckBox(cbReversedDatabaseOnly, "ReversedOnly", false); AddComponent(reversedOnly); includeContaminantProteins = new RcpaCheckBox(cbContaminantFile, "IncludeContaminantFile", false); AddComponent(includeContaminantProteins); contaminantFile = new RcpaFileField(btnContaminantFile, txtContaminantFile, "ContaminantFile", new OpenFileArgument("Contaminant Proteins (*.fasta)", "fasta"), false); btnContaminantFile.Text = "..."; AddComponent(contaminantFile); isPseudoAminoacid = new RcpaCheckBox(cbSwitch, "Switch", true); AddComponent(isPseudoAminoacid); pseudoAminoacids = new RcpaTextField(txtTermini, "Aminoacids", "Protease termini", "KR", true); AddComponent(pseudoAminoacids); isPseudoForward = new RcpaComboBox <string>(cbPrior, "Forward", new string[] { "previous", "next" }, 1); AddComponent(isPseudoForward); decoyTypes = new RcpaComboBox <DecoyType>(cbDecoyType, "DecoyType", DecoyType.Items, 0); AddComponent(decoyTypes); this.Text = Constants.GetSQHTitle(title, version); }
public AbstractMultipleLabellingSeparatorUI() { InitializeComponent(); this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", DEFAULT_PATTERN, true); this.AddComponent(this.modifiedAminoacids); }
public AbstractITraqProteinStatisticBuilderUI() { InitializeComponent(); base.SetFileArgument("ProteinsFile", new OpenFileArgument("Proteins", "noredundant")); this.iTraqFile = new RcpaFileField(btnRLocation, txtRLocation, "ITraqFile", new OpenFileArgument("iTRAQ", "itraq.xml"), true); this.AddComponent(this.iTraqFile); minProbability = new RcpaDoubleField(txtValidProbability, "MinValidProbability", "Minimum valid probability", 0.01, true); AddComponent(minProbability); normalize = new RcpaCheckBox(cbNormalize, "Normalize", false); AddComponent(normalize); builders = new RcpaComboBox <IRatioPeptideToProteinBuilder>(cbRatioCalculator, "RatioBuilder", RatioPeptideToProteinBuilderFactory.GetBuilders(), 0); AddComponent(builders); filterPeptide = new RcpaCheckBox(cbFilterPeptide, "FilterPeptide", true); AddComponent(filterPeptide); modifiedPeptideOnly = new RcpaCheckBox(cbModifiedOnly, "ModifiedOnly", false); AddComponent(modifiedPeptideOnly); modifiedChar = new RcpaTextField(txtModifiedCharacter, "ModifiedChar", "Input modified characters which indicates isobaric labelling(such as @#)", "@#", false); modifiedChar.PreCondition = cbModifiedOnly; AddComponent(modifiedChar); AddComponent(itraqIons); AddComponent(pnlClassification); }
public ExtendSilacQuantificationProteinFileProcessorUI() { InitializeComponent(); base.SetFileArgument("IdentificationResult", new OpenFileArgument("Identification Result", new string[] { "txt", "noredundant" })); this.Text = Constants.GetSQHTitle(title, version); rawDir = new RcpaDirectoryField(btnRawDirectory, txtRawDirectory, "RawDir", "Raw File", false); rawFormats = new RcpaComboBox <IRawFormat>(comboBox1, "RawFormat", new IRawFormat[] { new ThermoRawFormat() }, 0); precursorPPMTolerance = new RcpaDoubleField(txtPrecursorTolerance, "PrecursorPPMTolerance", "precursor PPM tolerance", 50, true); silacFile = new RcpaFileField(btnSilacFile, txtSilacFile, "SilacFile", new OpenFileArgument("SILAC Configuration", "ini"), true); searchEngine = new RcpaComboBox <SearchEngineType>(cbSearchEngine, "SearchEngine", new SearchEngineType[] { SearchEngineType.MASCOT, SearchEngineType.SEQUEST }, 0); ignoreModifications = new RcpaTextField(textBox1, "IgnoreModifications", "Ignore Modifications (such like @ for Heavy labelling of Leu)", "", false); minCorrelation = new RcpaDoubleField(txtMinPepRegCorrelation, "MinCorrelation", "Minimum Peptide Regression Correlation", 0.8, true); _profileLength = new RcpaIntegerField(txtProfileLength, "ProfileLength", "Profile length used in calculation", 3, true); this.AddComponent(rawDir); this.AddComponent(rawFormats); this.AddComponent(precursorPPMTolerance); this.AddComponent(silacFile); this.AddComponent(searchEngine); this.AddComponent(ignoreModifications); this.AddComponent(minCorrelation); this.AddComponent(_profileLength); this.AddComponent(datasetClassification); this.AddComponent(rawPairClassification); this.InsertButton(2, btnLoadParam); this.InsertButton(3, btnSaveParam); }
public AbstractDistributionUI() { InitializeComponent(); sourceFile = new RcpaFileField(btnProteinFile, txtProteinFile, "SourceFile", GetSourceFileArgument(), true); AddComponent(sourceFile); classificationTitle = new RcpaTextField(txtClassificationTitle, "ClassificationTitle", "Classification title", "", true); AddComponent(classificationTitle); filterType = new RcpaComboBox <PeptideFilterType>(cbFilterType, "FilterType", Enum.GetValues(typeof(PeptideFilterType)).Cast <PeptideFilterType>().ToArray(), 0); AddComponent(filterType); loopFrom = new RcpaIntegerField(txtLoopFrom, "LoopFrom", "Loop from", 1, true); AddComponent(loopFrom); loopTo = new RcpaIntegerField(txtLoopTo, "LoopTo", "Loop to", 2, true); AddComponent(loopTo); loopStep = new RcpaIntegerField(txtLoopStep, "LoopStep", "Loop step", 1, true); AddComponent(loopStep); modifiedOnly = new RcpaCheckBox(cbModifiedOnly, "ModifiedOnly", false); AddComponent(modifiedOnly); modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified aminoacids", "STY", false); AddComponent(modifiedAminoacids); AddComponent(pnlClassification); }
public MascotSAPValidatorUI() { InitializeComponent(); base.SetFileArgument("PeptideFile", new OpenFileArgument("Peptides", "peptides")); this.Text = Constants.GetSQHTitle(title, version); this.mutationPattern = new RcpaTextField(txtPattern, "MutationPattern", "Mutation pattern", "MUL_", true); AddComponent(this.mutationPattern); this.fastaFile = new RcpaFileField(btnFastaFile, txtFastaFile, "FastaFile", new OpenFileArgument("Protein Fasta", "fasta"), true); AddComponent(this.fastaFile); this.acParsers = new RcpaComboBox <IAccessNumberParser>(cbAccessNumberPattern, "AccessNumberParser", AccessNumberParserFactory.GetParsers().ToArray(), -1); AddComponent(this.acParsers); dbFile = new RcpaFileField(btnBrowse, txtDBFile, "DBFile", new OpenFileArgument("Uniprot Xml Database", "xml"), false); //dbFile.PreCondition = cbAnnotatedByDB; AddComponent(dbFile); pnovoFile = new RcpaFileField(btnPnovoPeptide, txtPnovoPeptide, "PNovoPeptide", new OpenFileArgument("PNovo Peptides", "peptides"), true); AddComponent(pnovoFile); AddComponent(pnlClassification); }
public MascotResultHtmlDownloaderUI(bool fixPeptideDownload) { InitializeComponent(); base.SetFileArgument("MascotHtmlResult", new SaveFileArgument("Mascot Html Result", "html")); this.Text = Constants.GetSQHTitle(title, version); this.url = new RcpaTextField(txtUrl, "URL", "URL", "", true); this.peptideFormat = new RcpaCheckBox(cbPeptideFormat, "PeptideFormat", true); this.threshold = new RcpaDoubleField(txtThreshold, "Threshold", "Peptide Identification Threshold (0~0.1)", 0.05, fixPeptideDownload); this.minScore = new RcpaDoubleField(txtMinScore, "MinScore", "Min Score", 20, false); this.AddComponent(url); this.AddComponent(peptideFormat); this.AddComponent(threshold); this.AddComponent(minScore); this.fixPeptideDownload = fixPeptideDownload; if (fixPeptideDownload) { cbPeptideFormat.Checked = true; cbPeptideFormat.Visible = false; } else { this.AfterLoadOption += new EventHandler(cbPeptideFormat_CheckedChanged); } }
public GenerateIsotopicFileUI() { InitializeComponent(); this.Text = Constants.GetSQHTitle(title, version); url = new RcpaTextField(txtUrl, "Url", "Url", "http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl", true); AddComponent(url); }
public TargetPeptideDistillerUI() { InitializeComponent(); SetFileArgument("PeptideFile", new OpenFileArgument("Peptides", "peptides")); this.decoyPattern = new RcpaTextField(txtDecoyPattern, "DecoyPattern", "Decoy pattern", "^REV", true); AddComponent(this.decoyPattern); this.Text = Constants.GetSQHTitle(title, version); }
public SmallMoleculeDataMostIntensityBuilderUI() { InitializeComponent(); base.SetDirectoryArgument("RootRawDir", "Agilent .d root"); this.pattern = new RcpaTextField(textBox1, "NamePattern", "Name Pattern", @"(.+)\.d", true); this.AddComponent(pattern); this.Text = Constants.GetSQHTitle(title, version); }
public SnpPeptideDistillerUI() { InitializeComponent(); SetFileArgument("PeptideFile", new OpenFileArgument("Peptide", "peptides")); snpPattern = new RcpaTextField(txtSnpPattern, "SnpPattern", "SNP Pattern", @"_\S+\d+\S+", true); AddComponent(snpPattern); this.Text = Constants.GetSQHTitle(title, version); }
public IdentifiedResultModificationSeparatorUI() { InitializeComponent(); this.Text = Constants.GetSQHTitle(title, version); SetFileArgument("ProteinFile", new OpenFileArgument("Identified Protein", "noredundant")); this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", true); this.AddComponent(this.modifiedAminoacids); }
public AbstractDatasetPanel() { InitializeComponent(); componentList = new RcpaComponentList(); this.enabled = new RcpaCheckBox(cbEnabled, "Enabled", true); AddComponent(enabled); this.datasetName = new RcpaTextField(txtDatasetName, "DatasetName", "Dataset Name", "", true); AddComponent(datasetName); this.filterPrecursorPPMTolerance = new RcpaCheckBox(this.cbFilterByPrecursor, "FilterPrecursor", false); AddComponent(this.filterPrecursorPPMTolerance); this.filterPrecursorIsotopic = new RcpaCheckBox(this.cbFilterByPrecursorIsotopic, "FilterPrecursorIsotopic", true); AddComponent(this.filterPrecursorIsotopic); this.precursorPPMTolerance = new RcpaDoubleField(this.txtPrecursorPPMTolerance, "PrecursorPPMTolerance", "Precursor Tolerance (ppm)", 10, false); AddComponent(this.precursorPPMTolerance); this.filterPrecursorByDynamicTolerance = new RcpaCheckBox(this.cbFilterByDynamicPrecursorTolerance, "FilterPrecursorByDynamicTolerance", true); AddComponent(this.filterPrecursorByDynamicTolerance); this.filterByScore = new RcpaCheckBox(this.cbFilterByScore, "FilterByScore", false); AddComponent(this.filterByScore); this.minScoreCharge1 = new RcpaDoubleField(this.txtScore1, "MinScore1", "Min Score for Charge 1", 1.0, false); AddComponent(this.minScoreCharge1); this.minScoreCharge2 = new RcpaDoubleField(this.txtScore2, "MinScore2", "Min Score for Charge 2", 1.5, false); AddComponent(this.minScoreCharge2); this.minScoreCharge3 = new RcpaDoubleField(this.txtScore3, "MinScore3", "Min Score for Charge 3", 2.0, false); AddComponent(this.minScoreCharge3); this.filterByDeltaScore = new RcpaCheckBox(this.cbFilterByDeltaScore, "FilterByDeltaScore", true); AddComponent(this.filterByDeltaScore); this.minDeltaScore = new RcpaDoubleField(this.txtMinDeltaScore, "MinDeltaScore", "Min Delta Score", 0.1, true); AddComponent(this.minDeltaScore); this.filterByEvalue = new RcpaCheckBox(this.cbFilterByEvalue, "FilterByEvalue", false); AddComponent(this.filterByEvalue); this.maxEvalue = new RcpaDoubleField(this.txtMaxEvalue, "MaxEvalue", "Max Evalue", 0.05, true); AddComponent(this.maxEvalue); this.dataFiles = InitializeDataFiles(); AddComponent(this.dataFiles); }
public LabelledResultDistillerUI() { InitializeComponent(); this.Text = Constants.GetSQHTitle(title, version); SetFileArgument("ProteinFile", new OpenFileArgument("Protein", "noredundant")); aminoAcids = new RcpaTextField(textBox1, "AminoAcids", "Labelled amino acids", "K", true); AddComponent(aminoAcids); labelPosition = new RcpaComboBox <LabelPosition>(comboBox1, "Position", new LabelPosition[] { LabelPosition.ALL, LabelPosition.CTERM, LabelPosition.NTERM }, 0); AddComponent(labelPosition); }
public FastaDatabaseDistillerUI() { InitializeComponent(); SetFileArgument("Database", new OpenFileArgument("Source Database (*.fasta)", "fasta")); dbName = new RcpaTextField(txtName, "DbName", "Database Name", "HUMAN", true); AddComponent(dbName); dbPattern = new RcpaTextField(txtPattern, "DbPattern", "Entry Name Pattern", "_HUMAN", true); AddComponent(dbPattern); this.Text = Constants.GetSQHTitle(title, version); }
public NGlycanPeptideMassCalculatorUI() { InitializeComponent(); this.Text = Constants.GetSQHTitle(title, version); this.peptideSequence = new RcpaTextField(txtPeptideSequence, "PeptideSequence", "Peptide Sequence", "", false); this.peptideModification = new RcpaTextField(txtPeptideModification, "PeptideModification", "Peptide Modification", "(STY* +79.96633) (M# +15.99492) C=160.16523", false); this.glycanStructure = new RcpaTextField(txtGlycanStructure, "GlycanStructure", "Glycan Structure", "", false); this.AddComponent(peptideSequence); this.AddComponent(peptideModification); this.AddComponent(glycanStructure); }
public QuantificationExportForm() { InitializeComponent(); this.proteinName = new RcpaCheckBox(cbProteinName, "ProteinName", false); AddComponent(this.proteinName); this.proteinNamePattern = new RcpaTextField(txtProteinNamePattern, "ProteinNamePattern", "Keep only one protein name based on Regex Patterns, separated by ';' : (for example: _RAT ; _MOUSE)", "_RAT ; _MOUSE", false); AddComponent(this.proteinNamePattern); this.singleFile = new RcpaCheckBox(cbSingleFile, "SingleFile", true); AddComponent(this.singleFile); this.exportScan = new RcpaCheckBox(cbExportScan, "ExportScan", false); AddComponent(this.exportScan); }
public MassCalculatorUI() { InitializeComponent(); this.Text = Constants.GetSQHTitle(Title, Version); sequence = new RcpaTextField(txtSequence, "Sequence", "Peptide Sequence", "", true); AddComponent(sequence); modification = new RcpaTextField(txtModification, "Modification", "Modification Definition", "(STY* +79.96633) (M# +15.99492) C=160.16523", false); AddComponent(modification); isMonoisotopic = new RcpaCheckBox(cbIsMonoisotopic, "IsMonoisotopic", false); AddComponent(isMonoisotopic); isMH = new RcpaCheckBox(cbIsMH, "IsMH", false); AddComponent(isMH); }
public ITraqPeptideRsdFilterUI() { InitializeComponent(); base.SetFileArgument("PeptidesFile", new OpenFileArgument("Peptides", "peptides")); this.iTraqFile = new RcpaFileField(btnRLocation, txtRLocation, "ITraqFile", new OpenFileArgument("iTRAQ", "itraq"), true); this.AddComponent(this.iTraqFile); Func <string, bool> validator = (m => { string[] parts = m.Split(new char[] { ',' }); if (parts.Length != 2) { return(false); } int intResult; return(int.TryParse(parts[0].Trim(), out intResult) && int.TryParse(parts[1].Trim(), out intResult)); }); this.referenceIndecies = new RcpaTextField(txtReferences, "referenceIndecies", "Reference Indecies", "114,115", true) { ValidateFunc = validator }; this.AddComponent(referenceIndecies); this.sampleIndecies = new RcpaTextField(txtSamples, "sampleIndecies", "Sample Indecies", "116,117", true) { ValidateFunc = validator }; this.AddComponent(sampleIndecies); this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", false); this.AddComponent(modifiedAminoacids); this.rsd = new RcpaDoubleField(txtMaxRsd, "RSD", "Max RSD in Group", 0.4, true); this.AddComponent(rsd); fold = new RcpaDoubleField(txtFold, "Fold", "Significance Tolerance (fold)", 2, true); AddComponent(fold); this.Text = Constants.GetSQHTitle(title, version); }
public MaxQuantSiteToPeptideProcessorUI() { InitializeComponent(); siteFile.FileArgument = new OpenFileArgument("MaxQuant Sites", new string[] { "txt" }); msmsFile.FileArgument = new OpenFileArgument("MaxQuant MSMS", new string[] { "txt" }); this.minLocalizationProbability = new RcpaDoubleField(txtMinProbability, "minLocalizationProbability", "Minmum Localization Probability", 0.75, true); AddComponent(this.minLocalizationProbability); this.minScoreDiff = new RcpaDoubleField(txtMinScoreDiff, "minScoreDiff", "Minmum Score Diff", 5.0, true); AddComponent(this.minScoreDiff); this.silacAminoacids = new RcpaTextField(txtSILACAminoacids, "SILACAminoacids", "SILAC amino acids", "KR", false); this.silacAminoacids.PreCondition = cbSILAC; AddComponent(this.silacAminoacids); this.Text = Constants.GetSQHTitle(title, version); }
public SmallMoleculeDataImageBuilderUI() { InitializeComponent(); base.SetFileArgument("SigFile", new OpenFileArgument("Result", ".sig")); sampleFile = new RcpaDirectoryField(button1, textBox1, "SampleDir", "Sample Data", true); AddComponent(sampleFile); refFile = new RcpaDirectoryField(button2, textBox2, "RefDir", "Reference Data", true); AddComponent(refFile); targetDir = new RcpaDirectoryField(button3, textBox3, "TargetDir", "Target Image", true); AddComponent(targetDir); peakPattern = new RcpaTextField(textBox4, "PeakPattern", "Peak Pattern (P for positive, N for negative)", "P", true); AddComponent(peakPattern); this.Text = Constants.GetSQHTitle(title, version); }
public BuildSummaryResultParserUI() { InitializeComponent(); this.decoyPattern = new RcpaTextField(this.txtDecoyPattern, "DecoyPattern", "Decoy Database Pattern", "^REVERSED_", false); AddComponent(this.decoyPattern); this.fdrType = new RcpaComboBox <IFalseDiscoveryRateCalculator>(this.cbFdrType, "FdrType", new IFalseDiscoveryRateCalculator[] { new TargetFalseDiscoveryRateCalculator(), new TotalFalseDiscoveryRateCalculator() }, new[] { "Target : N(decoy) / N(target)", "Global : N(decoy) * 2 / (N(decoy) + N(target))" }, 0); AddComponent(this.fdrType); Text = Constants.GetSQHTitle(Title, Version); }
public ITraqPhosphoPeptideStatisticBuilderUI() { InitializeComponent(); base.SetFileArgument("PeptidesFile", new OpenFileArgument("Peptides", "peptides")); this.iTraqFile = new RcpaFileField(btnRLocation, txtRLocation, "ITraqFile", new OpenFileArgument("iTRAQ", "itraq"), true); this.AddComponent(this.iTraqFile); Func <string, bool> validator = (m => { string[] parts = m.Split(new char[] { ',' }); if (parts.Length != 2) { return(false); } int intResult; return(int.TryParse(parts[0].Trim(), out intResult) && int.TryParse(parts[1].Trim(), out intResult)); }); this.normalIndecies = new RcpaTextField(txtNormal, "NormalIndecies", "Normal Indecies", "114,115", true) { ValidateFunc = validator }; this.AddComponent(normalIndecies); this.modificationIndecies = new RcpaTextField(txtModifications, "ModificationIndecies", "Modification Indecies", "116,117", true) { ValidateFunc = validator }; this.AddComponent(modificationIndecies); this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", true); this.AddComponent(modifiedAminoacids); this.Text = Constants.GetSQHTitle(title, version); }
public IsobaricPeptideStatisticBuilderUI() { InitializeComponent(); peptideFile = new RcpaFileField(btnPeptideFile, txtPeptideFile, "PeptideFile", new OpenFileArgument("Peptides", "peptides"), true); AddComponent(this.peptideFile); designFile = new RcpaFileField(btnDesignFile, txtDesignFile, "IsobaricDesignFile", new OpenFileArgument("Isobaric Labeling Experimental Design", "experimental.xml"), true); AddComponent(this.designFile); normalize = new RcpaCheckBox(cbNormalize, "Normalize", false); AddComponent(normalize); modes = new RcpaComboBox <QuantifyMode>(cbQuantifyMode, "QuantifyMode", EnumUtils.EnumToArray <QuantifyMode>(), 0, true); AddComponent(modes); modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Input modified amino acids", "STY", false); AddComponent(modifiedAminoacids); minimumSiteProbability = new RcpaDoubleField(txtMinimumSiteProbability, "MinimumSiteProbability", "Input minimum phosphylation site probability", 0.9, false); AddComponent(minimumSiteProbability); this.Text = Constants.GetSQHTitle(title, version); }
public SrmDistillerUI() { InitializeComponent(); base.SetDirectoryArgument("TargetDirectory", "Target"); this.dataDirs = new RcpaListViewMultipleFileDirectoryField( this.btnAddFiles, this.btnAddDirectory, this.btnAddSubdirectory, this.btnRemove, this.btnLoad, this.btnSave, this.lvDirectories, "Files", new OpenFileArgument("mzXml / mzData / Thermo Raw", new string[] { "mzXml", "mzData", "raw" }), "Agilent .d directory", true, true); AddComponent(this.dataDirs); this.rtToleranceInSecond = new RcpaDoubleField(txtRetentionTimeTolerance, "RTToleranceSecond", "Retention Time Tolerance in Second", 1.0, true); AddComponent(this.rtToleranceInSecond); this.signalToNoise = new RcpaDoubleField(txtSignalToNoise, "SignalToNoise", "Signal to Noise", 3.0, true); AddComponent(this.signalToNoise); this.precursorMassDistance = new RcpaTextField(txtPrecursorTolerance, "PrecursorMassDistance", "Distance between light and heavy precursor mass", "7,8,10", true); AddComponent(this.precursorMassDistance); this.smooth = new RcpaCheckBox(cbSmooth, "Smooth", true); AddComponent(this.smooth); this.refinePeakPicking = new RcpaCheckBox(cbRefinePeakPicking, "RefinePeakPicking", true); AddComponent(this.refinePeakPicking); this.deductBaseLine = new RcpaCheckBox(cbBaseLineExtraction, "DeductBaseLine", false); AddComponent(this.deductBaseLine); this.mzTolerance = new RcpaDoubleField(txtMzTolerance, "MzTolerance", "Product ion m/z tolerance", 0.1, true); AddComponent(this.mzTolerance); this.validateSignalToNoise = new RcpaDoubleField(txtValidateSignalToNoise, "ValidateSignalToNoise", "Validation signal to noise", 2, true); AddComponent(this.validateSignalToNoise); this.validateCorrel = new RcpaDoubleField(txtValidateCorrel, "ValidateCorrel", "Validation regression correlation", 0.5, true); AddComponent(this.validateCorrel); this.minValidTransactionPair = new RcpaIntegerField(txtMinValidTransactionPair, "minValidTransactionPair", "Minimum valid transaction pair count", 2, true); AddComponent(this.minValidTransactionPair); this.clusterByPredefine = new RcpaRadioButton(rbClusterByPredefine, "ClusterByPredefined", true); AddComponent(this.clusterByPredefine); this.clusterByRealData = new RcpaRadioButton(rbClusterByRealData, "ClusterByRealData", false); AddComponent(this.clusterByRealData); this.predefinedFile = new RcpaFileField(btnPredefined, txtPredefinedFile, "PredefinedFile", new OpenFileArgument("Predefined SRM Transaction File", ".txt"), false); AddComponent(this.predefinedFile); this.peakPickingByBaseline = new RcpaRadioButton(rbBaseline, "PeakPickingByBaseline", true); AddComponent(this.peakPickingByBaseline); this.peakPickingByHighestPeak = new RcpaRadioButton(rbHighestPeak, "PeakPickingByHighestPeak", false); AddComponent(this.peakPickingByHighestPeak); this.baseLinePercentage = new RcpaDoubleField(txtBaselinePercentage, "BaselinePercentage", "Baseline percentage", 5, true); AddComponent(this.baseLinePercentage); this.highestPeakPercentage = new RcpaDoubleField(txtHighestPeakPercentage, "HighestPeakPercentage", "Highest peak percentage", 5, false); AddComponent(this.highestPeakPercentage); this.precursorDistance = new RcpaDoubleField(txtMaxPrecursorDistance, "precursorDistance", "Maximum Precursor Distance", 20, true); AddComponent(this.precursorDistance); this.formats = new RcpaComboBox <IFileReader2 <List <SrmTransition> > >(cbFormat, "FileFormat", SrmFormatFactory.GetReaders().ToArray(), 0); AddComponent(this.formats); this.minEnabledScan = new RcpaIntegerField(txtMinEnabledScan, "MinValidScan", "Minimum valid scan count", 5, true); AddComponent(this.minEnabledScan); this.hasDecoy = new RcpaCheckBox(cbDecoyPattern, "HasDecoy", false); AddComponent(this.hasDecoy); this.ratioByArea = new RcpaCheckBox(cbRatioByArea, "ratioByArea", true); AddComponent(this.ratioByArea); this.decoyPattern = new RcpaTextField(txtDecoyPattern, "DecoyPattern", "Decoy pattern", "DECOY", false); this.decoyPattern.ValidateFunc = m => { try { new Regex(m); return(true); } catch (Exception) { return(false); } }; AddComponent(this.decoyPattern); this.Text = Constants.GetSQHTitle(title, version); }
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 UniformSummaryBuilderUI() { InitializeComponent(); Option = new BuildSummaryOptions(); InsertButton(2, btnNew); InsertButton(3, this.btnLoadParam); InsertButton(4, this.btnSaveParam); this.minDecoyScan.DefaultValue = MascotGenericFormatShiftPrecursorProcessorOptions.DEFAULT_ShiftScan.ToString(); this.decoyPattern = new RcpaTextField(this.txtDecoyPattern, "DecoyPattern", "Decoy Database Pattern", "^REVERSED_", false); AddComponent(this.decoyPattern); this.removeContamination = new RcpaCheckBox(cbRemoveContamination, "RemoveContamination", false); AddComponent(this.removeContamination); this.contaminationNamePattern = new RcpaTextField(this.txtContaminantString, "ContaminationNamePattern", "Contaminant Name Pattern", "CON_", false); AddComponent(this.contaminationNamePattern); this.contaminationDescriptionPattern = new RcpaTextField(this.txtContaminantDescriptionPattern, "ContaminantDescriptionPattern", "Contaminant Description Pattern", "KERATIN", false); AddComponent(this.contaminationDescriptionPattern); this.filterByFdr = new RcpaCheckBox(this.cbFilterByFDR, "FilterByFDR", true); AddComponent(this.filterByFdr); this.maxFdr = new RcpaDoubleField(this.txtMaxFdr, "MaxFdr", "Max False Discovery Rate", 0.01, true); AddComponent(this.maxFdr); this.maxPeptideFdr = new RcpaDoubleField(this.txtMaxPeptideFdr, "MaxPeptideFdr", "Max Peptide FDR", 0.01, true); AddComponent(this.maxPeptideFdr); this.filterProteinByPeptideCount = new RcpaCheckBox(this.cbPeptideCount, "FilterProteinByPeptideCount", false); AddComponent(this.filterProteinByPeptideCount); this.fdrLevel = new RcpaComboBox <FalseDiscoveryRateLevel>(this.cbFdrLevel, "FdrLevel", new[] { FalseDiscoveryRateLevel.Peptide, FalseDiscoveryRateLevel.Protein, FalseDiscoveryRateLevel.SimpleProtein, FalseDiscoveryRateLevel.UniquePeptide }, 1); AddComponent(this.fdrLevel); this.peptideRetrieval = new RcpaCheckBox(this.cbPeptideRetrieval, "PeptideRetrieval", true); AddComponent(this.peptideRetrieval); this.fdrType = new RcpaComboBox <FalseDiscoveryRateType>(this.cbFdrType, "FdrType", new[] { FalseDiscoveryRateType.Target, FalseDiscoveryRateType.Total }, new[] { "Target : N(decoy) / N(target)", "Global : N(decoy) * 2 / (N(decoy) + N(target))" }, 0); AddComponent(this.fdrType); this.classifyByCharge = new RcpaCheckBox(this.cbClassifyByCharge, "ClassifyByCharge", ClassificationOptions.DEFAULT_ClassifyByCharge); AddComponent(this.classifyByCharge); this.classifyByMissCleavage = new RcpaCheckBox(this.cbClassifyByMissCleavage, "ClassifyByMissCleavage", ClassificationOptions.DEFAULT_ClassifyByMissCleavage); AddComponent(this.classifyByMissCleavage); this.classifyByNumberOfProteaseTermini = new RcpaCheckBox(this.cbClassifyByPreteaseTermini, "ClassifyByNumberOfProteaseTermini", ClassificationOptions.DEFAULT_ClassifyByNumProteaseTermini); AddComponent(this.classifyByNumberOfProteaseTermini); this.classifyByModification = new RcpaCheckBox(this.cbClassifyByModification, "ClassifyByModification", ClassificationOptions.DEFAULT_ClassifyByModification); AddComponent(this.classifyByModification); this.modifiedAminoacids = new RcpaTextField(this.txtFdrModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", true); this.modifiedAminoacids.PreCondition = this.cbClassifyByModification; AddComponent(this.modifiedAminoacids); this.classifyByProteinTag = new RcpaCheckBox(this.cbClassifyByProteinTag, "ClassifyByProteinTag", ClassificationOptions.DEFAULT_ClassifyByProteinTag); AddComponent(this.classifyByProteinTag); this.proteinTag = new RcpaTextField(this.txtProteinTag, "ProteinTag", "Protein Tag", "", false); this.proteinTag.PreCondition = this.cbClassifyByProteinTag; AddComponent(this.proteinTag); this.minimumSpectraPerGroup = new RcpaIntegerField(this.txtMinimumSpectraPerGroup, "MinimumSpectraPerGroup", "MinimumSpectraPerGroup", ClassificationOptions.DEFAULT_MinimumSpectraPerGroup, true); AddComponent(this.minimumSpectraPerGroup); this.filterSequenceLength = new RcpaCheckBox(this.cbSequenceLength, "FilterSequenceLength", false); AddComponent(this.filterSequenceLength); this.minSequenceLength = new RcpaIntegerField(this.txtMinSequenceLength, "MinSequenceLength", "Minmum Sequence Length", PeptideFilterOptions.DEFAULT_MinSequenceLength, false); this.minSequenceLength.PreCondition = cbSequenceLength; AddComponent(this.minSequenceLength); this.filterMaxMissCleavage = new RcpaCheckBox(this.cbMaxMissCleavage, "FilterMaxMisscleavage", false); AddComponent(this.filterMaxMissCleavage); this.maxMissCleagage = new RcpaIntegerField(this.txtMaxMissCleavage, "MaxMissCleavage", "Maximum Number of Internal Missed Cleavage", PeptideFilterOptions.DEFAULT_MaxMissCleavage, false); this.maxMissCleagage.PreCondition = cbMaxMissCleavage; AddComponent(this.maxMissCleagage); this.removeDecoyEntry = new RcpaCheckBox(this.cbRemoveDecoyEntry, "RemovePeptideFromDecoyDB", false); AddComponent(this.removeDecoyEntry); this.database = new RcpaFileField(btnDatabase, txtDatabase, "Database", new OpenFileArgument("Protein Database", "fasta"), "", true); AddComponent(this.database); this.acParsers = new RcpaComboBox <IAccessNumberParser>(this.cbAccessNumberPattern, "AccessNumberPattern", AccessNumberParserFactory.GetParsers().ToArray(), 0); AddComponent(this.acParsers); this.seConflictType = new RcpaComboBox <IResolveSearchEngineConflictType>(cbConflict, "ConflictType", ResolveSearchEngineConflictTypeFactory.GetTypes(), 1); AddComponent(this.seConflictType); this.conflictAsDecoy = new RcpaComboBox <ITargetDecoyConflictType>(cbConflictAsDecoy, "ConflictAsDecoy", ResolveTargetDecoyConflictTypeFactory.GetTypes(), 0); AddComponent(this.conflictAsDecoy); this.minAgreeCount = new RcpaIntegerField(txtMinAgreeCount, "MinAgreeCount", "Minimum agree count of engines", 1, true); AddComponent(this.minAgreeCount); minOneHitWonderPeptideCount = new RcpaIntegerField(txtMinOneHitWonderPeptideCount, "MinOneHitWonderPeptideCount", "minimum one-hit-wonder peptide count", 2, false); AddComponent(minOneHitWonderPeptideCount); minOneHitWonderPeptideCount.PreCondition = FilterOneHitWonder; this.AfterLoadOption += DoAfterLoadOption; Text = Constants.GetSQHTitle(title, version); var engines = EnumUtils.EnumToArray <SearchEngineType>().OrderByDescending(m => m.ToString()).ToArray(); foreach (var engine in engines) { if (engine.HasFactory()) { var button = new Button(); pnlAdd.Controls.Add(button); button.Dock = System.Windows.Forms.DockStyle.Top; button.UseVisualStyleBackColor = true; button.Text = "Add " + engine.ToString(); button.Name = "btnAdd" + engine.ToString(); button.Tag = engine; button.Click += button_Click; } } pnlAdd.Update(); }