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 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 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 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 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 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 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 DtaselectFileSplitterUI()
{
InitializeComponent();
base.SetFileArgument("Dtaselect", new OpenFileArgument("Dtaselect", "txt"));
this.Text = Constants.GetSQHTitle(Title, Version);
this.resultCount = new RcpaIntegerField(txtResultCount, "ResultCount", "Split Result Count", 4, true);
this.AddComponent(resultCount);
}
public CensusChroFileSplitterUI()
{
InitializeComponent();
base.SetFileArgument("CensusChroFile", new OpenFileArgument("Census Chro", "xml"));
this.Text = Constants.GetSQHTitle(title, version);
this.resultCount = new RcpaIntegerField(txtResultCount, "ResultCount", "Split Result Count", 4, true);
this.AddComponent(resultCount);
}
public CensusResultUniquePeptideCountFilterUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
SetFileArgument("CensusResult", new OpenFileArgument("Census Result", "txt"));
this.uniqueCount = new RcpaIntegerField(txtUniquePeptide, "UniqueCount", "Minimum Unique Peptide Count", 2, true);
this.AddComponent(this.uniqueCount);
}
public RawFileViewerUI()
{
InitializeComponent();
base.SetFileArgument("RawFile", new OpenFileArgument("Raw", new[] { "raw", "mzData.xml", "mzData", "mzXML" }));
_scan = new RcpaIntegerField(txtScan, "Scan", "Scan", 0, false);
_msLevel = new RcpaIntegerField(txtMslevel, "MSLevel", "MS Level (0 ~ any level)", 0, false);
zgcScan.InitGraph("Scan", "M/Z", "Intensity", true, 0.0);
zgcScan.GraphPane.XAxis.Scale.Min = 0;
zgcScan.GraphPane.XAxis.Scale.Max = 2000;
Text = Constants.GetSQHTitle(Title, Version);
}
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 ProteinXPeptideDistillerUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
SetFileArgument("ProteinFile", new OpenFileArgument("Protein", "noredundant"));
this.uniqueCount = new RcpaIntegerField(txtUniquePeptide, "UniqueCount", "Unique Peptide Count", 2, true);
this.uniqueOnly = new RcpaCheckBox(cbUniquePeptideOnly, "UniqueOnly", false);
this.AddComponent(this.uniqueCount);
this.AddComponent(this.uniqueOnly);
}
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 RcpaGrouperUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
group = new RcpaIntegerField(txtGroupCount, "group", "Group Count", 4, true);
AddComponent(group);
AddButton(btnCopy);
string namesFile = new FileInfo(Application.ExecutablePath).DirectoryName + "\\names.txt";
if (File.Exists(namesFile))
{
var names = File.ReadAllLines(namesFile);
txtNames.Lines = names;
}
else
{
File.WriteAllLines(namesFile, txtNames.Lines);
}
}
public MaxQuantPeptideRatioDistillerUI()
{
InitializeComponent();
base.SetFileArgument("SourceFile", new OpenFileArgument("MaxQuant Peptide", "txt"));
this.minCount = new RcpaIntegerField(txtCount, "MinCount", "Minimum quantified experiment count", 1, true);
AddComponent(this.minCount);
var funcs = new[] {
new MaxQuantItemFunc()
{
ItemFunc = m => m.Ratio,
Name = "Ratio H/L"
},
new MaxQuantItemFunc()
{
ItemFunc = m => m.Ratio_Norm,
Name = "Ratio H/L Normalized"
},
new MaxQuantItemFunc()
{
ItemFunc = m => m.IntensityL,
Name = "Intensity L"
},
new MaxQuantItemFunc()
{
ItemFunc = m => m.IntensityH,
Name = "Intensity H"
}
};
this.lbFuncItems.Items.AddRange(funcs);
this.lbFuncItems.SetItemChecked(0, true);
Text = Constants.GetSQHTitle(title, version);
}
public ShuffleDatabaseBuilderUI()
{
InitializeComponent();
SetFileArgument("Database", new OpenFileArgument("Source Database (*.fasta)", "fasta"));
reversedOnly = new RcpaCheckBox(cbReversedDatabaseOnly, "ShuffledOnly", false);
AddComponent(reversedOnly);
includeContaminantProteins = new RcpaCheckBox(cbContaminantFile, "IncludeContaminantFile", false);
AddComponent(includeContaminantProteins);
klet = new RcpaIntegerField(txtKlet, "Klet", "Klet", 1, true);
AddComponent(klet);
repeat = new RcpaIntegerField(txtRepeat, "Repeat", "Repeat", 1, true);
AddComponent(repeat);
contaminantFile = new RcpaFileField(btnContaminantFile, txtContaminantFile, "ContaminantFile", new OpenFileArgument("Contaminant Proteins (*.fasta)", "fasta"), false);
btnContaminantFile.Text = "...";
AddComponent(contaminantFile);
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();
}
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);
}
