public MzIdentDatasetPanel()
{
InitializeComponent();
this.filterByScore = new RcpaCheckBox(this.cbFilterByScore, "FilterByScore", true);
AddComponent(this.filterByScore);
this.minScore = new RcpaDoubleField(this.txtMinScore, "MinScore", "Min score", 0, true);
AddComponent(this.minScore);
this.engines = new RcpaComboBox <SearchEngineType>(this.cbEngines, "SearchEngine", MzIdentParserFactory.Engines, 0, true, "Search engine that generated the result");
AddComponent(this.engines);
this.datFiles = new RcpaListViewMultipleFileField(
this.btnAddFiles,
this.btnRemoveFiles,
this.btnLoad,
this.btnSave,
this.lvDatFiles,
"MzIdentFiles",
new OpenFileArgument("MzIdent", "mzid"),
true,
false);
AddComponent(this.datFiles);
}
public IsobaricResultMultipleFileDistillerUI()
{
InitializeComponent();
rawFiles.FileArgument = new OpenFileArgument("Raw Files", rawExtentions);
RcpaMultipleFileComponent adaptor = new RcpaMultipleFileComponent(rawFiles.GetItemInfos(), "RawFiles", "Raw File", false, true);
AddComponent(adaptor);
minPeakCount = new RcpaIntegerField(txtMinPeakCount, "MinPeakCount", "Minmum peak count", 4, true);
AddComponent(minPeakCount);
plexTypes = new RcpaComboBox <IsobaricType>(cbPlexType, "PlexType", IsobaricTypeFactory.IsobaricTypes, 0);
AddComponent(plexTypes);
readers = new RcpaComboBox <IIsobaricRawReader>(cbScanMode, "ScanMode", new IIsobaricRawReader[] { new IsobaricRawHCDMS2Reader(), new IsobaricRawHCDMS3Reader(), new IsobaricRawHCDParallelMS3Reader(), new IsobaricRawPQDCIDReader(), new IsobaricRawPQDReader() }, 0);
AddComponent(readers);
precursorPPMTolerance = new RcpaDoubleField(txtPrecursorPPMTolerance, "precursorPPMTolerance", "Precursor Tolerance (ppm)", 10, true);
AddComponent(precursorPPMTolerance);
productPPMTolerance = new RcpaDoubleField(txtProductPPM, "productPPMTolerance", "Product Ion Tolerance (ppm)", 10, true);
AddComponent(productPPMTolerance);
this.Text = Constants.GetSQHTitle(title, version);
}
public ProteinChromatographViewer()
{
InitializeComponent();
ProteaseManager.Load();
proteases = new RcpaComboBox <string>(cbProtease, "ProteaseIndex", ProteaseManager.GetNames().ToArray(), 3);
AddComponent(proteases);
SetFileArgument("FastaFile", new OpenFileArgument("Fasta", "fasta"));
rawFile = new RcpaFileField(btnRawDirectory, txtRawDirectory, "RawFile", new OpenFileArgument("Thermo Raw", "raw"), true);
AddComponent(rawFile);
ppmTolerance = new RcpaDoubleField(txtPPMTolerance, "PPMTolerance", "Precursor PPM Tolerance", 10, true);
AddComponent(ppmTolerance);
rebuildAll = new RcpaCheckBox(cbRebuildAll, "RebuildAll", false);
AddComponent(rebuildAll);
noredundantFile = new RcpaFileField(btnNoredundant, txtNoredundant, "NoredundantFile", new OpenFileArgument("noredundant", "noredundant"), false);
AddComponent(noredundantFile);
//rawDirectory = new RcpaDirectoryField(btnRawDirectory, txtRawDirectory, "RawDirectory", "Thermo Fisher Raw", true);
//AddComponent(rawDirectory);
}
public O18QuantificationFileProcessorUI()
{
InitializeComponent();
base.SetFileArgument("MascotTextResult", new OpenFileArgument("Identified Result", new string[] { "txt", "noredundant" }));
this.Text = Constants.GetSQHTitle(title, version);
this.rawDir = new RcpaDirectoryField(btnRawDirectory, txtRawDirectory, "RawDir", "Raw File", false);
this.purityOfWater = new RcpaDoubleField(txtPurityOfO18Water, "PurityOfO18Water", "purity of O18 water", 0.95, true);
this.precursorPPMTolerance = new RcpaDoubleField(txtPrecursorTolerance, "PrecursorPPMTolerance", "precursor PPM tolerance", 50, true);
this.postDigestionLabelling = new RcpaCheckBox(cbPostDigestionLabelling, "PostDigestionLabelling", false);
this.limitScanRange = new RcpaCheckBox(cbScanRange, "LimitScanRange", false);
this.scanStart = new RcpaDoubleField(txtScanStart, "ScanStart", "Limit scan start percentage", 20, false);
this.scanEnd = new RcpaDoubleField(txtScanEnd, "ScanEnd", "Limit scan end percentage", 80, false);
this.rawExtensions = new RcpaComboBox<string>(cbRawFormat, "RawFormat", new string[] { ".raw", ".mzXML", ".mzData", ".mzData.xml" }, 0);
this.scanStart.MinValue = 0.0;
this.scanStart.MaxValue = 100.0;
this.scanEnd.MinValue = 0.0;
this.scanEnd.MaxValue = 100.0;
this.AddComponent(rawDir);
this.AddComponent(purityOfWater);
this.AddComponent(precursorPPMTolerance);
this.AddComponent(postDigestionLabelling);
this.AddComponent(limitScanRange);
this.AddComponent(scanStart);
this.AddComponent(scanEnd);
AddComponent(this.rawExtensions);
}
public PNovoSAPValidatorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
pNovoFiles.FileArgument = new OpenFileArgument("pNovo Result", "txt");
AddComponent(this.pNovoFiles);
this.minScore = new RcpaDoubleField(txtMinScore, "MinScore", "Minmum score", 0.65, true);
AddComponent(this.minScore);
this.threadCount = new RcpaIntegerField(txtThreadCount, "ThreadCount", "Thread count", Environment.ProcessorCount - 1, true);
AddComponent(this.threadCount);
toolTip1.SetToolTip(txtThreadCount, MyConvert.Format("Suggest max value = {0}", Environment.ProcessorCount + 1));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), -1);
AddComponent(this.titleParsers);
fastaFile.FileArgument = new OpenFileArgument("Fasta To Find Mutation", "fasta");
databaseFile.FileArgument = new OpenFileArgument("Fasta To Merge Mutated Peptide", "fasta");
this.acParsers = new RcpaComboBox <IAccessNumberParser>(cbAccessNumberPattern, "AccessNumberParser", AccessNumberParserFactory.GetParsers().ToArray(), -1);
AddComponent(this.acParsers);
this.proteases = new RcpaComboBox <string>(cbProtease, "Protease", ProteaseManager.GetNames().ToArray(), -1);
AddComponent(this.proteases);
this.minLength = new RcpaIntegerField(txtMinLength, "MinLength", "Minimum Peptide Length", 6, true);
AddComponent(this.minLength);
}
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 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 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 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 MaxQuantMgfDistillerUI()
{
InitializeComponent();
this.SetFileArgument("PeptideFile", new OpenFileArgument("BuildSummary Peptides", "peptides"));
List <ITitleParser> allParsers = TitleParserUtils.GetTitleParsers();
this.titleParsers = new RcpaComboBox <ITitleParser>(this.cbTitleFormat, "TitleFormat", allParsers.ToArray(), 0);
AddComponent(this.titleParsers);
this.mgfFiles = new RcpaListViewMultipleFileField(
this.btnAddFiles,
this.btnRemoveFiles,
this.btnLoad,
this.btnSave,
this.lvMgfFiles,
"MgfFiles",
new OpenFileArgument("Mascot Generic Format", new string[] { "msm", "mgf" }),
true,
true);
AddComponent(this.mgfFiles);
this.singleFile = new RcpaCheckBox(cbSingleFile, "SingleFile", false);
AddComponent(this.singleFile);
this.singleFileName = new RcpaFileField(btnMgfFile, txtSingleFile, "SingleFilename", new SaveFileArgument("MGF", "mgf"), false);
AddComponent(this.singleFileName);
Text = Constants.GetSQHTitle(title, version);
}
public TitleDatasetPanel()
{
InitializeComponent();
parsers = TitleParserUtils.GetTitleParsers().ToArray();
this.titleParsers = new RcpaComboBox <ITitleParser>(this.cbTitleFormat, "TitleFormat", parsers, parsers.Length - 1);
AddComponent(this.titleParsers);
}
protected virtual void DoAfterSettingOptions()
{
if (this.options != null)
{
RemoveComponent(this.scoreFunctions);
this.scoreFunctions = new RcpaComboBox <IScoreFunction>(cbScoreFunctions, "ScoreFunction", this.options.SearchEngine.GetFactory().GetScoreFunctions(), 0, true);
AddComponent(this.scoreFunctions);
}
}
public ITraqUniquePeptideStatisticBuilderUI()
{
InitializeComponent();
base.SetFileArgument("PeptidesFile", new OpenFileArgument("Peptides", "peptides"));
fastaFile.FileArgument = new OpenFileArgument("Database", "fasta");
parsers = new RcpaComboBox <IAccessNumberParser>(cbAccessNumberParser, "AccessNumberParser", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(parsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public MascotGenericFormatShiftPrecursorProcessorUI()
{
InitializeComponent();
this.datFiles.FileArgument = new OpenFileArgument("Mascot MGF", new string[] { "mgf", "msm" });
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "MGFFiles", "Mgf Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.targetDirectory.SetDirectoryArgument("TargetDirectory", "Target");
this.Text = Constants.GetSQHTitle(Title, Version);
}
public MascotDatToPepXmlConverterUI()
{
InitializeComponent();
this.minPeptideLength.DefaultValue = MascotDatToPepXmlConverterOptions.DEFAULT_MinPeptideLength.ToString();
this.targetDir.SetDirectoryArgument("TargetDir", "Target PepXML");
this.datFiles.FileArgument = new OpenFileArgument("Mascot Dat", "dat");
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "DatFiles", "Dat Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public UpdatePepXmlModificationProcessorUI()
{
InitializeComponent();
this.SetDirectoryArgument("TargetDir", "Target DAT");
this.datFiles.FileArgument = new OpenFileArgument("PepXml", new string[] { "pepXml", "pep.xml" });
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "PepXml", "PepXml Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public MappedCountProcessorUI()
{
InitializeComponent();
bamFile.FileArgument = new OpenFileArgument("BAM/SAM", new string[] { "bam", "sam" });
gffFile.FileArgument = new OpenFileArgument("GFF", new string[] { "gff3", "bed" });
fileFastq.FileArgument = new OpenFileArgument("FASTQ", new string[] { "fastq", "fq" });
countFile.FileArgument = new OpenFileArgument("Count", "dupcount");
engines = new RcpaComboBox <string>(cbEngine, "Engine", new string[] { "Bowtie1", "Bowtie2", "BWA" }, 0);
AddComponent(engines);
this.Text = Constants.GetSqhVanderbiltTitle(title, version);
}
public UpdateMascotDatTitleFormatProcessorUI()
{
InitializeComponent();
this.SetDirectoryArgument("TargetDir", "Target DAT");
this.datFiles.FileArgument = new OpenFileArgument("Mascot Dat", "dat");
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "DatFiles", "Dat Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.Text = Constants.GetSQHTitle(title, version);
}
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 MappedCountProcessorUI()
{
InitializeComponent();
bamFile.FileArgument = new OpenFileArgument("BAM/SAM", new string[] { "bam", "sam" });
gffFile.FileArgument = new OpenFileArgument("GFF", new string[] { "gff3", "bed" });
fileFastq.FileArgument = new OpenFileArgument("FASTQ", new string[] { "fastq", "fq" });
countFile.FileArgument = new OpenFileArgument("Count", "dupcount");
engines = new RcpaComboBox<string>(cbEngine, "Engine", new string[] { "Bowtie1", "Bowtie2", "BWA" }, 0);
AddComponent(engines);
this.Text = Constants.GetSqhVanderbiltTitle(title, version);
}
public ExtractFastaByAccessNumberProcessorUI()
{
InitializeComponent();
SetFileArgument("AccessNumberFile", new OpenFileArgument("Access Number", "txt"));
fastaFile = new RcpaFileField(btnFastaFile, textBox1, "FastaFile", new OpenFileArgument("Database", "fasta"), true);
AddComponent(fastaFile);
replaceName = new RcpaCheckBox(cbReplaceName, "ReplaceName", false);
AddComponent(replaceName);
parsers = new RcpaComboBox <IAccessNumberParser>(cbAccessNumberParser, "AccessNumberParser", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(parsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public ITraqResultMultipleFileDistillerUI()
{
InitializeComponent();
rawFiles.FileArgument = new OpenFileArgument("Raw Files", rawExtentions);
RcpaMultipleFileComponent adaptor = new RcpaMultipleFileComponent(rawFiles.GetItemInfos(), "RawFiles", "Raw File", false, true);
AddComponent(adaptor);
individual = new RcpaCheckBox(cbIndividual, "Individual", false);
AddComponent(individual);
minPeakCount = new RcpaIntegerField(txtMinPeakCount, "MinPeakCount", "Minmum peak count", 4, true);
AddComponent(minPeakCount);
plexFiles = new string[] {
new FileInfo(Application.ExecutablePath).Directory.FullName + "\\itraq-4plex.csv",
new FileInfo(Application.ExecutablePath).Directory.FullName + "\\itraq-8plex.csv",
new FileInfo(Application.ExecutablePath).Directory.FullName + "\\tmt-6plex.csv"
};
plexTypes = new RcpaComboBox <IsobaricType>(cbPlexType, "PlexType", EnumUtils.EnumToArray <IsobaricType>(), 0);
AddComponent(plexTypes);
txtIsotopeFileName.Items.AddRange(plexFiles);
isotopeFile = new RcpaFileField2 <ComboBox>(btnIsotopeFile, txtIsotopeFileName, "IsotopeFile", new OpenFileArgument("Isotope Impurity Correction Table", "csv"), plexFiles[0], true, m => m.Text, (m, value) => m.Text = value);
AddComponent(isotopeFile);
readers = new RcpaComboBox <IITraqRawReader>(cbScanMode, "ScanMode", new IITraqRawReader[] { new ITraqRawHCDMS2Reader(), new ITraqRawHCDMS3Reader(), new ITraqRawHCDParallelMS3Reader(), new ITraqRawPQDCIDReader(), new ITraqRawPQDReader() }, 0);
AddComponent(readers);
normalizationBuilders = new RcpaComboBox <IITraqNormalizationBuilder>(cbNormalizationType, "NormalizationType",
new IITraqNormalizationBuilder[] { new ITraqNormalizationByMedianIntensityBuilder(), new ITraqNormalizationByTotalIntensityBuilder(), new ITraqNormalizationNoneBuilder() }, 1);
AddComponent(normalizationBuilders);
normalizationByIonInjectionTime = new RcpaCheckBox(cbNormalizeByIonInjectionTime, "normalizationByIonInjectionTime", false);
AddComponent(normalizationByIonInjectionTime);
precursorPPMTolerance = new RcpaDoubleField(txtPrecursorPPMTolerance, "precursorPPMTolerance", "Precursor Tolerance (ppm)", 10, true);
AddComponent(precursorPPMTolerance);
this.Text = Constants.GetSQHTitle(title, version);
}
public PeptideSpectrumMatchDistillerUI()
{
InitializeComponent();
this.searchResultFiles.FileArgument = new OpenFileArgument("Search Result", "*");
var parsers = TitleParserUtils.GetTitleParsers().ToArray();
this.titleParsers = new RcpaComboBox <ITitleParser>(this.cbTitleFormat, "TitleFormat", parsers, parsers.Length - 1, true);
AddComponent(this.titleParsers);
var engineNames = PeptideSpectrumMatchDistillerOptions.GetValidEngines();
this.engines = new RcpaComboBox <string>(this.cbEngines, "Engine", engineNames, 0);
AddComponent(this.engines);
this.Text = Constants.GetSQHTitle(Title, Version);
}
public IsobaricProteinStatisticBuilderUI()
{
InitializeComponent();
this.proteinFile = new RcpaFileField(btnProteinFile, txtProteinFile, "ProteinFile", new OpenFileArgument("Proteins", "noredundant"), true);
this.AddComponent(this.proteinFile);
this.designFile = new RcpaFileField(btnDesignFile, txtIsobaricXmlFile, "IsobaricDesignFile", new OpenFileArgument("Isobaric Labeling Experimental Design", "experimental.xml"), true);
this.AddComponent(this.designFile);
this.quanPeptideFile = new RcpaFileField(btnQuanPeptideFile, txtQuanPeptideFile, "QuanPeptideFile", new OpenFileArgument("Quantified Peptide", "quan.tsv"), true);
this.AddComponent(this.quanPeptideFile);
this.methods = new RcpaComboBox <string>(cbRatioCalculator, "PeptideToProteinMethod", new[] { "Median", "Sum" }, 0, true, "How to calculate protein ratio from peptide?");
this.AddComponent(methods);
this.Text = Constants.GetSQHTitle(title, version);
}
public ReplaceMascotGenericFormatProcessorUI()
{
InitializeComponent();
base.SetFileArgument("TargetFile", new SaveFileArgument("Target MGF", "mgf"));
fileHeader.FileArgument = new OpenFileArgument("Precursor Info MGF", "mgf");
this.titleHeaderParser = new RcpaComboBox <ITitleParser>(cbHeaderFormat, "HeaderTitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleHeaderParser);
filePeak.FileArgument = new OpenFileArgument("Peak Info MGF", "mgf");
this.titlePeakParser = new RcpaComboBox <ITitleParser>(cbPeakFormat, "PeakTitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titlePeakParser);
this.titleFormat = new RcpaComboBox <ITitleFormat>(cbTitleFormat, "TitleFormat", MascotTitleFactory.Titles, 0);
AddComponent(this.titleFormat);
this.Text = Constants.GetSQHTitle(title, version);
lblInfo.Text = info;
}
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 ProteinLabelFreeQuantificationBuilderUI()
{
InitializeComponent();
SetFileArgument("ProteinFile", new OpenFileArgument("Protein", new string[] { "noredundant", "unduplicated" }));
calculators = new RcpaComboBox<IProteinLabelfreeQuantificationCalculator>(
cbFilterType,
"LabelfreeQuantificationCalculator",
new IProteinLabelfreeQuantificationCalculator[] {
new NSAFProteinLabelfreeQuantificationCalculator(),
new SInProteinLabelfreeQuantificationCalculator()
},
0);
AddComponent(calculators);
this.parsers = new RcpaComboBox<IAccessNumberParser>(cbAccessNumberParser, "Parser", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(this.parsers);
AddComponent(pnlClassification);
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 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();
}
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);
}
