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 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 SequestSpectrumImageBuilderUI()
{
InitializeComponent();
dtaFile = new RcpaFileField(btnDtaFile, txtDtaFile, "DtaFile", new OpenFileArgument("sequest dta", "dta"), true);
AddComponent(dtaFile);
}
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 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 ProteinChromatographProcessorUI()
{
InitializeComponent();
ProteaseManager.Load();
SetFileArgument("PeptideFile", new OpenFileArgument("peptides", "peptides"));
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);
window = new RcpaDoubleField(txtWindow, "Window", "Elution Window", 1, true);
AddComponent(window);
lvcPeptides = new ListViewColumnField(lvPeptides, "LvPeptides");
AddComponent(lvcPeptides);
rawonly = new RcpaCheckBox(cbShowInRawFileOnly, "ShowRawFileOnly", true);
AddComponent(rawonly);
bFirstLoad = true;
}
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 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 IdentifiedPeptideSubtractorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
SetFileArgument("SubtractFile", new OpenFileArgument("Subtract Peptide", "peptides"));
this.sourceFile = new RcpaFileField(btnSource, txtSource, "SourceFile", new OpenFileArgument("Source Peptide", "peptides"), true);
AddComponent(this.sourceFile);
}
public IdentifiedPeptidesMergerUI()
{
InitializeComponent();
this.peptideFiles.FileArgument = new OpenFileArgument("Identified Peptide", "peptides");
AddComponent(new RcpaMultipleFileComponent(this.peptideFiles.GetItemInfos(), "PeptideFiles", "Peptide Files", false, true));
this.targetFile = new RcpaFileField(btnOriginalFile, txtOriginalFile, "TargetFile", new SaveFileArgument("Target Peptides", "peptides"), false);
Text = Constants.GetSQHTitle(title, version);
}
public ExtractProteinByIdProcessorUI()
{
InitializeComponent();
SetFileArgument("AccessNumberFile", new OpenFileArgument("Access Number", "txt"));
this.acFile = new RcpaFileField(btnAccessNumberFile, txtAccessNumberFile, "NoredundantFile", new OpenFileArgument("noredundant", "noredundant"), true);
this.AddComponent(this.acFile);
this.Text = Constants.GetSQHTitle(title, version);
}
public ITraqResultImageBuilderUI()
{
InitializeComponent();
base.SetFileArgument("ITraqFile", new OpenFileArgument("ITraq", "itraq"));
this.rLocation = new RcpaFileField(btnRLocation, txtRLocation, "RLocation", new OpenFileArgument("R execute", "exe"), false);
this.AddComponent(this.rLocation);
this.Text = Constants.GetSQHTitle(title, version);
}
public SpectrumSAPValidatorUI()
{
InitializeComponent();
peptideFile = new RcpaFileField(btnPeptideFile, txtPeptideFile, "PeptideFile", new OpenFileArgument("Peptides", "peptides"), true);
AddComponent(peptideFile);
imageDirectory = new RcpaDirectoryField(btnImageDirectory, txtImageDirectory, "ImageDirectory", "Images", true);
AddComponent(imageDirectory);
this.Text = Constants.GetSQHTitle(title, version);
}
public CombineQuantificationResultProcessorUI()
{
InitializeComponent();
base.SetFileArgument("PeptideFile", new OpenFileArgument("Single Aminoacid Polymorphism Peptides", "mut"));
this.itraqFile = new RcpaFileField(btnDatabase, txtDatabase, "IsobaricQuantificationPeptide", new OpenFileArgument("Isobaric Unique Peptide Quantification", "unique.itraq"), true);
AddComponent(this.itraqFile);
this.Text = Constants.GetSQHTitle(title, version);
}
public DatabaseSAPValidatorUI()
{
InitializeComponent();
base.SetFileArgument("PeptideFile", new OpenFileArgument("Peptides", "peptides"));
this.fastaFile = new RcpaFileField(btnDatabase, txtDatabase, "Database", new OpenFileArgument("Protein Fasta", "fasta"), true);
AddComponent(this.fastaFile);
this.Text = Constants.GetSQHTitle(title, version);
}
public ChromatographProfileBuilderUI()
{
InitializeComponent();
this.peptideFile = new RcpaFileField(btnPeptideFile, txtPeptideFile, "PeptideFile", new OpenFileArgument("peptides", "peptides"), true);
this.AddComponent(this.peptideFile);
this.rawDirectory = new RcpaDirectoryField(btnRawDirectory, txtRawDirectory, "RawDirectory", "Raw", true);
this.AddComponent(this.rawDirectory);
this.Text = Constants.GetSQHTitle(title, version);
}
public MaxQuantFileDistillerUI()
{
InitializeComponent();
base.SetFileArgument("SourceFile", new OpenFileArgument("Source MaxQuant", "txt"));
this.targetFile = new RcpaFileField(btnTarget, txtTarget, "TargetFile", new OpenFileArgument("Target MaxQuant", "txt"), true);
AddComponent(targetFile);
this.Roles = new MaxQuantTagMatchRoles();
Text = Constants.GetSQHTitle(title, version);
}
public SpectrumScanValidatorUI()
{
InitializeComponent();
ms3MatchedFile = new RcpaFileField(btnMatchFile, txtMatchFile, "PeptideFile", new OpenFileArgument("MS3 Match", "ms3match"), true);
AddComponent(ms3MatchedFile);
rawFile = new RcpaFileField(btnRawFile, txtRawFile, "RawFile", new OpenFileArgument("RAW", "raw"), true);
AddComponent(rawFile);
this.Text = Constants.GetSQHTitle(title, version);
this.reader = null;
}
public DeuteriumCalculatorUI()
{
InitializeComponent();
this.noredundantFile = new RcpaFileField(btnNoredundantFile, txtNoredundantFile, "NoredundantFile", new OpenFileArgument("Noredundant/Peptide", new string[] { "noredundant", "peptides" }), true);
this.AddComponent(this.noredundantFile);
this.rawFiles.FileArgument = new OpenFileArgument("Raw", RawFileFactory.GetSupportedRawFormats(), true);
this.rawFiles.FileDescription = "Input raw files (" + RawFileFactory.SupportedRawFormatString + ")";
this.Text = Constants.GetSQHTitle(title, version);
}
public IsobaricLabelingExperimentalDesignBuilderUI()
{
InitializeComponent();
this.dataFile = new RcpaFileField(btnDataFile, txtDataFile, "DataFile", new OpenFileArgument("Peptides/Proteins", new[] { "peptides", "noredundant" }), true);
this.dataFile.AfterBrowseFileEvent += btnLoad_Click;
this.AddComponent(this.dataFile);
this.iTraqFile = new RcpaFileField(btnIsobaricXmlFile, txtIsobaricXmlFile, "IsobaricXmlFile", new OpenFileArgument("Isobaric XML", "isobaric.xml"), true);
this.AddComponent(this.iTraqFile);
this.Text = Constants.GetSQHTitle(title, version);
}
public ScoreComparisonBuilderUI()
{
InitializeComponent();
base.SetFileArgument("FirstPeptideFile", new OpenFileArgument("First Identified Peptides", "peptides"));
this.targetFastaFile = new RcpaFileField(btnFastaFile, txtFastaFile, "SecondPeptideFile", new OpenFileArgument("Second Identified Peptides", "peptides"), true);
AddComponent(this.targetFastaFile);
saveFile = new SaveFileArgument("Output Data", ".txt");
this.Text = Constants.GetSQHTitle(title, version);
}
public SilacResultSplitterUI()
{
InitializeComponent();
base.SetFileArgument("BuildSummaryProteinsFile", new OpenFileArgument("BuildSummary Proteins", "noredundant"));
this.Text = Constants.GetSQHTitle(title, version);
this.lightFile = new RcpaFileField(btnLight, txtLightFile, "Light", new OpenFileArgument("Light Sequest Param", "params"), true);
this.heavyFile = new RcpaFileField(btnHeavy, txtHeavyFile, "Heavy", new OpenFileArgument("Heavy Sequest Param", "params"), true);
this.AddComponent(lightFile);
this.AddComponent(heavyFile);
}
public MicroarrayDataSummaryBuilderUI()
{
InitializeComponent();
base.SetDirectoryArgument("DataDirectory", "Microarray Level3 Data Root");
this.itraqFile = new RcpaFileField(btnDatabase, txtDatabase, "SdrfFile", new OpenFileArgument("Metadata Sdrf", "sdrf.txt"), true);
AddComponent(this.itraqFile);
this.targetFile = new SaveFileArgument("Result", "tsv");
this.Text = Constants.GetSQHTitle(title, version);
}
public SrmExportForm()
{
InitializeComponent();
this.targetFile = new RcpaFileField(button1, textBox1, "TargetFile", new SaveFileArgument("Quantification Result", "csv"), true);
AddComponent(this.targetFile);
removeDecoy = new RcpaCheckBox(cbTargetOnly, "RemoveDecoy", true);
AddComponent(removeDecoy);
validOnly = new RcpaCheckBox(cbValidOnly, "ValidOnly", true);
AddComponent(validOnly);
}
public SmallMoleculeSignificantPeakFinderUI()
{
InitializeComponent();
base.SetFileArgument("SaveFile", new SaveFileArgument("Result", ".sig"));
sampleFile = new RcpaFileField(button1, textBox1, "SampleFile", new OpenFileArgument("Sample Data", ".data"), true);
AddComponent(sampleFile);
refFile = new RcpaFileField(button2, textBox2, "RefFile", new OpenFileArgument("Reference Data", ".data"), true);
AddComponent(refFile);
this.Text = Constants.GetSQHTitle(title, version);
}
public SmallMoleculeQuantificationViewerUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
resultFile = new RcpaFileField(button1, textBox1, "ResultFile", new OpenFileArgument("Significance", "sig"), true);
AddComponent(resultFile);
sampleFiles.FileArgument = new OpenFileArgument("Sample", "txt");
AddComponent(new RcpaMultipleFileComponent(sampleFiles.GetItemInfos(), "SampleFiles", "Sample", false, false));
referenceFiles.FileArgument = new OpenFileArgument("Reference", "txt");
AddComponent(new RcpaMultipleFileComponent(referenceFiles.GetItemInfos(), "ReferenceFiles", "Reference", false, false));
InsertButton(2, btnExport);
}
public AminoacidInsertionBuilderUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
this.peptideFile = new RcpaFileField(btnPeptideFile, txtPeptideFile, "PeptideFile", new OpenFileArgument("Peptide", "peptides"), true);
AddComponent(this.peptideFile);
this.databaseFile = new RcpaFileField(btnDatabaseFile, txtDatabaseFile, "DatabaseFile", new OpenFileArgument("Database", new[] { "fa", "fasta" }), true);
AddComponent(this.databaseFile);
this.outputFile = new RcpaFileField(btnOutputFile, txtOutputFile, "OutputFile", new SaveFileArgument("Output Database", "fasta"), true);
AddComponent(this.outputFile);
}
public ITraqPeptideStatisticBuilderUI()
{
InitializeComponent();
base.SetFileArgument("PeptidesFile", new OpenFileArgument("Peptides", "peptides"));
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);
this.AddComponent(itraqIons);
this.Text = Constants.GetSQHTitle(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);
}
