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 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 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 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 MascotDatSummaryBuilderUI()
{
InitializeComponent();
columnSorter = new ListViewColumnSorter();
columnSorter.AttachToListView(lvDatFiles);
this.filterByScore = new RcpaCheckBox(this.cbFilterByScore, "FilterByScore", true);
AddComponent(this.filterByScore);
this.minScore = new RcpaDoubleField(this.txtMinScore, "MinScore", "Min score", 25, true);
AddComponent(this.minScore);
this.filterByExpectValue = new RcpaCheckBox(this.cbFilterByEvalue, "FilterByEvalue", false);
AddComponent(this.filterByExpectValue);
this.maxExpectValue = new RcpaDoubleField(this.txtMaxEvalue, "MaxEvalue", "Max Evalue", 0.05, false);
AddComponent(this.maxExpectValue);
this.datFiles = new RcpaListViewMultipleFileField(
this.btnAddFiles,
this.btnRemoveFiles,
this.btnLoad,
this.btnSave,
this.lvDatFiles,
"DatFiles",
new OpenFileArgument("Mascot Dat", "dat"),
true,
true);
AddComponent(this.datFiles);
Text = Constants.GetSQHTitle(title, UniformBuildSummaryUI.version);
}
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 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 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 MS3LibraryBuilderUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, Version);
rawFiles.FileArgument = new OpenFileArgument("Raw", "raw");
AddComponent(this.rawFiles);
this.precursorPPM = new RcpaDoubleField(txtPrecursorPPM, "PrecursorPPM", "Precursor PPM", 20, true);
AddComponent(this.precursorPPM);
this.fragmentPPM = new RcpaDoubleField(txtFragmentPPM, "FragmentPPM", "Fragment Ion PPM", 50, true);
AddComponent(this.fragmentPPM);
this.maxFragmentPeakCount = new RcpaIntegerField(txtMaxFragmentPeakCount, "MaxFragmentPeakCount", "Maximum Fragment Peak Count", 10, true);
AddComponent(this.maxFragmentPeakCount);
this.minSpectraPerPeptide = new RcpaIntegerField(txtMinIdentificationCount, "MinIdentificationCount", "Minimum Identified Spectra Per Peptide", 2, true);
AddComponent(this.minSpectraPerPeptide);
peptideFile.FileArgument = new OpenFileArgument("Peptide", "peptides");
outputFile.FileArgument = new SaveFileArgument("Output Library", "xml");
}
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 AbstractSequestDatasetPanel()
{
InitializeComponent();
this.filterByXcorr = new RcpaCheckBox(this.cbFilterByXcorr, "FilterByXcorr", false);
AddComponent(this.filterByXcorr);
this.minXcorr1 = new RcpaDoubleField(this.txtXcorr1, "MinXcorr1", "Min Xcorr for Charge 1", 1.0, false);
AddComponent(this.minXcorr1);
this.minXcorr2 = new RcpaDoubleField(this.txtXcorr2, "MinXcorr2", "Min Xcorr for Charge 2", 1.5, false);
AddComponent(this.minXcorr2);
this.minXcorr3 = new RcpaDoubleField(this.txtXcorr3, "MinXcorr3", "Min Xcorr for Charge 3", 2.0, false);
AddComponent(this.minXcorr3);
this.filterByDeltaCn = new RcpaCheckBox(this.cbFilterByDeltaCn, "FilterByDeltaCn", true);
AddComponent(this.filterByDeltaCn);
this.minDeltaCn = new RcpaDoubleField(this.txtMinDeltaCn, "MinDeltaCn", "Min DeltaCn", 0.1, true);
AddComponent(this.minDeltaCn);
this.filterBySpRank = new RcpaCheckBox(this.cbFilterBySpRank, "FilterBySpRank", false);
AddComponent(this.filterBySpRank);
this.maxSpRank = new RcpaIntegerField(this.txtSpRank, "MaxSpRank", "Max Sp Rank", 4, false);
AddComponent(this.maxSpRank);
}
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 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 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 SequestDatasetPanel()
{
InitializeComponent();
this.filterByXcorr = new RcpaCheckBox(this.cbFilterByXcorr, "FilterByXcorr", false);
AddComponent(this.filterByXcorr);
this.minXcorr1 = new RcpaDoubleField(this.txtXcorr1, "MinXcorr1", "Min Xcorr for Charge 1", 1.9, false);
AddComponent(this.minXcorr1);
this.minXcorr2 = new RcpaDoubleField(this.txtXcorr2, "MinXcorr2", "Min Xcorr for Charge 2", 2.2, false);
AddComponent(this.minXcorr2);
this.minXcorr3 = new RcpaDoubleField(this.txtXcorr3, "MinXcorr3", "Min Xcorr for Charge 3", 3.75, false);
AddComponent(this.minXcorr3);
this.filterByDeltaCn = new RcpaCheckBox(this.cbFilterByDeltaCn, "FilterByDeltaCn", true);
AddComponent(this.filterByDeltaCn);
this.minDeltaCn = new RcpaDoubleField(this.txtMinDeltaCn, "MinDeltaCn", "Min DeltaCn", 0.1, true);
AddComponent(this.minDeltaCn);
this.filterBySpRank = new RcpaCheckBox(this.cbFilterBySpRank, "FilterBySpRank", false);
AddComponent(this.filterBySpRank);
this.maxSpRank = new RcpaIntegerField(this.txtSpRank, "MaxSpRank", "Max Sp Rank", 4, false);
AddComponent(this.maxSpRank);
this.filterByEvalue = new RcpaCheckBox(this.cbFilterByEvalue, "FilterByEvalue", true);
AddComponent(this.filterByEvalue);
this.maxEvalue = new RcpaDoubleField(this.txtMaxEvalue, "MaxEvalue", "Max Evalue", 0.05, true);
AddComponent(this.maxEvalue);
this.dataDirs = new RcpaListViewMultipleDirectoryField(
this.btnAddFiles,
this.btnRemoveFiles,
this.btnLoad,
this.btnSave,
this.lvDirectories,
"Directories",
"SEQUEST out/outs directory",
true,
false);
dataDirs.Validator.ValidateFunc = (m =>
{
if (m.ToLower().EndsWith(".zip") || m.ToLower().EndsWith(".xml") || m.ToLower().EndsWith(".msf"))
{
return(File.Exists(m));
}
else
{
return(Directory.Exists(m));
}
});
AddComponent(this.dataDirs);
}
public ScoreDatasetPanel()
{
InitializeComponent();
this.filterByScore = new RcpaCheckBox(this.cbFilterByScore, "FilterByScore", false);
AddComponent(this.filterByScore);
this.minScore = new RcpaDoubleField(this.txtMinScore, "MinScore", "Min score", 1.0, false);
AddComponent(this.minScore);
}
public ExpectValueDatasetPanel()
{
InitializeComponent();
this.filterByExpectValue = new RcpaCheckBox(this.cbFilterByEvalue, "FilterByEvalue", false);
AddComponent(this.filterByExpectValue);
this.maxExpectValue = new RcpaDoubleField(this.txtMaxEvalue, "MaxEvalue", "Max Evalue", 0.05, false);
AddComponent(this.maxExpectValue);
}
public ProteinProphetToSummaryProcessorUI()
{
InitializeComponent();
this.SetFileArgument("SourceFile", new OpenFileArgument("ProteinProphet Xml", "xml"));
this.minProbability = new RcpaDoubleField(txtMinProbability, "MinProbability", "Min Probability", 0.9, true);
AddComponent(this.minProbability);
this.Text = Constants.GetSQHTitle(title, version);
}
public MascotGenericFormatSplitterUI()
{
InitializeComponent();
this.SetFileArgument("MGFFile", new OpenFileArgument("Mascot Generic Format", new string[] { "msm", "mgf" }));
this.fileSize = new RcpaDoubleField(txtFileSize, "FileSize", "file size", 100.0, true);
AddComponent(this.fileSize);
this.Text = Constants.GetSQHTitle(title, version);
}
public TripleTOFTextToMGFMainProcessorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
this.SetDirectoryArgument("TargetDir", "Target MGF");
this.precursorTolerance = new RcpaDoubleField(txtPrecursorTolerance, "PrecursorTolerance", "Use precursor tolerance to find precursor from MS1 spectrum", 200, true);
AddComponent(this.precursorTolerance);
this.rawFiles.FileArgument = new OpenFileArgument("TripleTOF Peak List Text", "txt");
}
public PeptideProphetDatasetPanel()
{
InitializeComponent();
this.xmlFiles.FileArgument = new OpenFileArgument("PeptidePhophet XML", "xml");
AddComponent(new RcpaMultipleFileComponent(this.xmlFiles.GetItemInfos(), "XmlFiles", "PeptidePhophet Xml Files", false, true));
this.filterByMinPvalue = new RcpaCheckBox(cbFilterByPValue, "FilterByPValue", true);
AddComponent(this.filterByMinPvalue);
this.minPvalue = new RcpaDoubleField(txtMinProbabilityValue, "MinPValue", "Minimum Probability Value", 0.5, true);
AddComponent(this.minPvalue);
}
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 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 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 PrecursorOffsetStatisticMainBuilderUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
this.SetDirectoryArgument("TargetDir", "Target");
this.productIonPPM = new RcpaDoubleField(txtProductIonPPM, "ProductIonPPMTolerance", "Product Ion PPM Tolerance", 20, true);
AddComponent(this.productIonPPM);
this.minRelativeIntensity = new RcpaDoubleField(txtMinimumIonRelativeIntensity, "MinimumIonRelativeIntensity", "Minimum Ion Relative Intensity", 0.05, true);
AddComponent(this.minRelativeIntensity);
this.rawFiles.FileArgument = new OpenFileArgument("Raw", RawFileFactory.GetSupportedRawFormats());
}
public MassOffsetCalculatorUI()
{
InitializeComponent();
base.SetFileArgument("RawFile", new OpenFileArgument("RAW", "raw"));
this.Text = Constants.GetSQHTitle(title, version);
maxShiftPPM = new RcpaDoubleField(txtInitPPM, "InitPPM", "Maximum shift ppm", 50, true);
AddComponent(maxShiftPPM);
precursorPPM = new RcpaDoubleField(txtPrecursorPPM, "PrecursorPPM", "Maximum precursor ppm", 10, true);
AddComponent(precursorPPM);
rtWindow = new RcpaDoubleField(txtRtWindow, "RtWindow", "Smoothing retention time window in mintue", 0.5, true);
AddComponent(rtWindow);
}
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 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 LipidQuantificationProcessorUI()
{
InitializeComponent();
SetFileArgument("QueryItem", new OpenFileArgument("Query Item", ".txt"));
rawFile = new RcpaFileField(btnRawFile, txtRawFile, "RawFile", new OpenFileArgument("Raw", rawExtentions), true);
AddComponent(rawFile);
productIonPPM = new RcpaDoubleField(txtProductPPM, "ProductIonPPM", "Product Ion Tolerance (ppm)", 20, true);
AddComponent(productIonPPM);
precursorPPM = new RcpaDoubleField(txtPrecursorPPM, "PrecursorPPM", "Precursor Ion Tolerance (ppm)", 20, true);
AddComponent(precursorPPM);
this.Text = Constants.GetSQHTitle(title, version);
AddButton(btnSmooth);
AddButton(btnSave);
AddButton(btnExport);
}
