public DatasetPanelBase()
{
InitializeComponent();
componentList = new RcpaComponentList();
this.enabled = new RcpaCheckBox(cbEnabled, "Enabled", true);
AddComponent(enabled);
this.datasetName = new RcpaTextField(txtDatasetName, "DatasetName", "Dataset Name", "", true);
AddComponent(datasetName);
this.filterPrecursorPPMTolerance = new RcpaCheckBox(this.cbFilterByPrecursor, "FilterPrecursor", false);
AddComponent(this.filterPrecursorPPMTolerance);
this.filterPrecursorIsotopic = new RcpaCheckBox(this.cbFilterByPrecursorIsotopic, "FilterPrecursorIsotopic", true);
AddComponent(this.filterPrecursorIsotopic);
this.precursorPPMTolerance = new RcpaDoubleField(this.txtPrecursorPPMTolerance, "PrecursorPPMTolerance", "Precursor Tolerance (ppm)", 10, false);
AddComponent(this.precursorPPMTolerance);
this.filterPrecursorByDynamicTolerance = new RcpaCheckBox(this.cbFilterByDynamicPrecursorTolerance, "FilterPrecursorByDynamicTolerance", true);
AddComponent(this.filterPrecursorByDynamicTolerance);
this.searchedByDifferentParameters = new RcpaCheckBox(this.cbSearchedByDifferentParameters, "SearchedByDifferentParameters", false);
AddComponent(this.searchedByDifferentParameters);
}
public TheoreticalDigestionStatisticCalculatorUI()
{
InitializeComponent();
SetFileArgument("FastaFile", new OpenFileArgument("Protein Sequence", "fasta"));
lbProteases.Items.AddRange(ProteaseManager.GetNames().ToArray());
AddComponent(lbSelectedProteases);
this.minLength = new RcpaIntegerField(txtMinLength, "minlength", "Minimum peptide length", 6, true);
AddComponent(minLength);
this.maxMissCleavage = new RcpaIntegerField(txtMaxMissCleavage, "maxmisscleavage", "Maximum miss cleavage", 2, true);
AddComponent(maxMissCleavage);
this.minMass = new RcpaDoubleField(txtMinMass, "minmass", "Minimum peptide mass", 400, true);
AddComponent(minMass);
this.maxMass = new RcpaDoubleField(txtMaxMass, "maxmass", "Maximum peptide mass", 5000, true);
AddComponent(maxMass);
ignoreAminoacids = new RcpaTextField(txtIgnoreAminoacids, "ignoreaminoacids", "Ignore amino acids", "XB", true);
AddComponent(ignoreAminoacids);
this.Text = Constants.GetSQHTitle(title, version);
}
public ReversedDatabaseBuilderUI()
{
InitializeComponent();
this.sourceDatabase.FileArgument = new OpenFileArgument("Source Database Fasta", new string[] { ".fasta", ".fa" });
reversedOnly = new RcpaCheckBox(cbReversedDatabaseOnly, "ReversedOnly", false);
AddComponent(reversedOnly);
includeContaminantProteins = new RcpaCheckBox(cbContaminantFile, "IncludeContaminantFile", false);
AddComponent(includeContaminantProteins);
contaminantFile = new RcpaFileField(btnContaminantFile, txtContaminantFile, "ContaminantFile", new OpenFileArgument("Contaminant Proteins (*.fasta)", "fasta"), false);
btnContaminantFile.Text = "...";
AddComponent(contaminantFile);
isPseudoAminoacid = new RcpaCheckBox(cbSwitch, "Switch", true);
AddComponent(isPseudoAminoacid);
pseudoAminoacids = new RcpaTextField(txtTermini, "Aminoacids", "Protease termini", "KR", true);
AddComponent(pseudoAminoacids);
isPseudoForward = new RcpaComboBox <string>(cbPrior, "Forward", new string[] { "previous", "next" }, 1);
AddComponent(isPseudoForward);
decoyTypes = new RcpaComboBox <DecoyType>(cbDecoyType, "DecoyType", DecoyType.Items, 0);
AddComponent(decoyTypes);
this.Text = Constants.GetSQHTitle(title, version);
}
public AbstractMultipleLabellingSeparatorUI()
{
InitializeComponent();
this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", DEFAULT_PATTERN, true);
this.AddComponent(this.modifiedAminoacids);
}
public AbstractITraqProteinStatisticBuilderUI()
{
InitializeComponent();
base.SetFileArgument("ProteinsFile", new OpenFileArgument("Proteins", "noredundant"));
this.iTraqFile = new RcpaFileField(btnRLocation, txtRLocation, "ITraqFile", new OpenFileArgument("iTRAQ", "itraq.xml"), true);
this.AddComponent(this.iTraqFile);
minProbability = new RcpaDoubleField(txtValidProbability, "MinValidProbability", "Minimum valid probability", 0.01, true);
AddComponent(minProbability);
normalize = new RcpaCheckBox(cbNormalize, "Normalize", false);
AddComponent(normalize);
builders = new RcpaComboBox <IRatioPeptideToProteinBuilder>(cbRatioCalculator, "RatioBuilder", RatioPeptideToProteinBuilderFactory.GetBuilders(), 0);
AddComponent(builders);
filterPeptide = new RcpaCheckBox(cbFilterPeptide, "FilterPeptide", true);
AddComponent(filterPeptide);
modifiedPeptideOnly = new RcpaCheckBox(cbModifiedOnly, "ModifiedOnly", false);
AddComponent(modifiedPeptideOnly);
modifiedChar = new RcpaTextField(txtModifiedCharacter, "ModifiedChar", "Input modified characters which indicates isobaric labelling(such as @#)", "@#", false);
modifiedChar.PreCondition = cbModifiedOnly;
AddComponent(modifiedChar);
AddComponent(itraqIons);
AddComponent(pnlClassification);
}
public ExtendSilacQuantificationProteinFileProcessorUI()
{
InitializeComponent();
base.SetFileArgument("IdentificationResult", new OpenFileArgument("Identification Result", new string[] { "txt", "noredundant" }));
this.Text = Constants.GetSQHTitle(title, version);
rawDir = new RcpaDirectoryField(btnRawDirectory, txtRawDirectory, "RawDir", "Raw File", false);
rawFormats = new RcpaComboBox <IRawFormat>(comboBox1, "RawFormat", new IRawFormat[] { new ThermoRawFormat() }, 0);
precursorPPMTolerance = new RcpaDoubleField(txtPrecursorTolerance, "PrecursorPPMTolerance", "precursor PPM tolerance", 50, true);
silacFile = new RcpaFileField(btnSilacFile, txtSilacFile, "SilacFile", new OpenFileArgument("SILAC Configuration", "ini"), true);
searchEngine = new RcpaComboBox <SearchEngineType>(cbSearchEngine, "SearchEngine", new SearchEngineType[] { SearchEngineType.MASCOT, SearchEngineType.SEQUEST }, 0);
ignoreModifications = new RcpaTextField(textBox1, "IgnoreModifications", "Ignore Modifications (such like @ for Heavy labelling of Leu)", "", false);
minCorrelation = new RcpaDoubleField(txtMinPepRegCorrelation, "MinCorrelation", "Minimum Peptide Regression Correlation", 0.8, true);
_profileLength = new RcpaIntegerField(txtProfileLength, "ProfileLength", "Profile length used in calculation", 3, true);
this.AddComponent(rawDir);
this.AddComponent(rawFormats);
this.AddComponent(precursorPPMTolerance);
this.AddComponent(silacFile);
this.AddComponent(searchEngine);
this.AddComponent(ignoreModifications);
this.AddComponent(minCorrelation);
this.AddComponent(_profileLength);
this.AddComponent(datasetClassification);
this.AddComponent(rawPairClassification);
this.InsertButton(2, btnLoadParam);
this.InsertButton(3, btnSaveParam);
}
public AbstractDistributionUI()
{
InitializeComponent();
sourceFile = new RcpaFileField(btnProteinFile, txtProteinFile, "SourceFile", GetSourceFileArgument(), true);
AddComponent(sourceFile);
classificationTitle = new RcpaTextField(txtClassificationTitle, "ClassificationTitle", "Classification title", "", true);
AddComponent(classificationTitle);
filterType = new RcpaComboBox <PeptideFilterType>(cbFilterType, "FilterType", Enum.GetValues(typeof(PeptideFilterType)).Cast <PeptideFilterType>().ToArray(), 0);
AddComponent(filterType);
loopFrom = new RcpaIntegerField(txtLoopFrom, "LoopFrom", "Loop from", 1, true);
AddComponent(loopFrom);
loopTo = new RcpaIntegerField(txtLoopTo, "LoopTo", "Loop to", 2, true);
AddComponent(loopTo);
loopStep = new RcpaIntegerField(txtLoopStep, "LoopStep", "Loop step", 1, true);
AddComponent(loopStep);
modifiedOnly = new RcpaCheckBox(cbModifiedOnly, "ModifiedOnly", false);
AddComponent(modifiedOnly);
modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified aminoacids", "STY", false);
AddComponent(modifiedAminoacids);
AddComponent(pnlClassification);
}
public MascotSAPValidatorUI()
{
InitializeComponent();
base.SetFileArgument("PeptideFile", new OpenFileArgument("Peptides", "peptides"));
this.Text = Constants.GetSQHTitle(title, version);
this.mutationPattern = new RcpaTextField(txtPattern, "MutationPattern", "Mutation pattern", "MUL_", true);
AddComponent(this.mutationPattern);
this.fastaFile = new RcpaFileField(btnFastaFile, txtFastaFile, "FastaFile", new OpenFileArgument("Protein Fasta", "fasta"), true);
AddComponent(this.fastaFile);
this.acParsers = new RcpaComboBox <IAccessNumberParser>(cbAccessNumberPattern, "AccessNumberParser", AccessNumberParserFactory.GetParsers().ToArray(), -1);
AddComponent(this.acParsers);
dbFile = new RcpaFileField(btnBrowse, txtDBFile, "DBFile", new OpenFileArgument("Uniprot Xml Database", "xml"), false);
//dbFile.PreCondition = cbAnnotatedByDB;
AddComponent(dbFile);
pnovoFile = new RcpaFileField(btnPnovoPeptide, txtPnovoPeptide, "PNovoPeptide", new OpenFileArgument("PNovo Peptides", "peptides"), true);
AddComponent(pnovoFile);
AddComponent(pnlClassification);
}
public MascotResultHtmlDownloaderUI(bool fixPeptideDownload)
{
InitializeComponent();
base.SetFileArgument("MascotHtmlResult", new SaveFileArgument("Mascot Html Result", "html"));
this.Text = Constants.GetSQHTitle(title, version);
this.url = new RcpaTextField(txtUrl, "URL", "URL", "", true);
this.peptideFormat = new RcpaCheckBox(cbPeptideFormat, "PeptideFormat", true);
this.threshold = new RcpaDoubleField(txtThreshold, "Threshold", "Peptide Identification Threshold (0~0.1)", 0.05, fixPeptideDownload);
this.minScore = new RcpaDoubleField(txtMinScore, "MinScore", "Min Score", 20, false);
this.AddComponent(url);
this.AddComponent(peptideFormat);
this.AddComponent(threshold);
this.AddComponent(minScore);
this.fixPeptideDownload = fixPeptideDownload;
if (fixPeptideDownload)
{
cbPeptideFormat.Checked = true;
cbPeptideFormat.Visible = false;
}
else
{
this.AfterLoadOption += new EventHandler(cbPeptideFormat_CheckedChanged);
}
}
public GenerateIsotopicFileUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
url = new RcpaTextField(txtUrl, "Url", "Url", "http://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl", true);
AddComponent(url);
}
public TargetPeptideDistillerUI()
{
InitializeComponent();
SetFileArgument("PeptideFile", new OpenFileArgument("Peptides", "peptides"));
this.decoyPattern = new RcpaTextField(txtDecoyPattern, "DecoyPattern", "Decoy pattern", "^REV", true);
AddComponent(this.decoyPattern);
this.Text = Constants.GetSQHTitle(title, version);
}
public SmallMoleculeDataMostIntensityBuilderUI()
{
InitializeComponent();
base.SetDirectoryArgument("RootRawDir", "Agilent .d root");
this.pattern = new RcpaTextField(textBox1, "NamePattern", "Name Pattern", @"(.+)\.d", true);
this.AddComponent(pattern);
this.Text = Constants.GetSQHTitle(title, version);
}
public SnpPeptideDistillerUI()
{
InitializeComponent();
SetFileArgument("PeptideFile", new OpenFileArgument("Peptide", "peptides"));
snpPattern = new RcpaTextField(txtSnpPattern, "SnpPattern", "SNP Pattern", @"_\S+\d+\S+", true);
AddComponent(snpPattern);
this.Text = Constants.GetSQHTitle(title, version);
}
public IdentifiedResultModificationSeparatorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
SetFileArgument("ProteinFile", new OpenFileArgument("Identified Protein", "noredundant"));
this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", true);
this.AddComponent(this.modifiedAminoacids);
}
public AbstractDatasetPanel()
{
InitializeComponent();
componentList = new RcpaComponentList();
this.enabled = new RcpaCheckBox(cbEnabled, "Enabled", true);
AddComponent(enabled);
this.datasetName = new RcpaTextField(txtDatasetName, "DatasetName", "Dataset Name", "", true);
AddComponent(datasetName);
this.filterPrecursorPPMTolerance = new RcpaCheckBox(this.cbFilterByPrecursor, "FilterPrecursor", false);
AddComponent(this.filterPrecursorPPMTolerance);
this.filterPrecursorIsotopic = new RcpaCheckBox(this.cbFilterByPrecursorIsotopic, "FilterPrecursorIsotopic", true);
AddComponent(this.filterPrecursorIsotopic);
this.precursorPPMTolerance = new RcpaDoubleField(this.txtPrecursorPPMTolerance, "PrecursorPPMTolerance", "Precursor Tolerance (ppm)", 10, false);
AddComponent(this.precursorPPMTolerance);
this.filterPrecursorByDynamicTolerance = new RcpaCheckBox(this.cbFilterByDynamicPrecursorTolerance, "FilterPrecursorByDynamicTolerance", true);
AddComponent(this.filterPrecursorByDynamicTolerance);
this.filterByScore = new RcpaCheckBox(this.cbFilterByScore, "FilterByScore", false);
AddComponent(this.filterByScore);
this.minScoreCharge1 = new RcpaDoubleField(this.txtScore1, "MinScore1", "Min Score for Charge 1", 1.0, false);
AddComponent(this.minScoreCharge1);
this.minScoreCharge2 = new RcpaDoubleField(this.txtScore2, "MinScore2", "Min Score for Charge 2", 1.5, false);
AddComponent(this.minScoreCharge2);
this.minScoreCharge3 = new RcpaDoubleField(this.txtScore3, "MinScore3", "Min Score for Charge 3", 2.0, false);
AddComponent(this.minScoreCharge3);
this.filterByDeltaScore = new RcpaCheckBox(this.cbFilterByDeltaScore, "FilterByDeltaScore", true);
AddComponent(this.filterByDeltaScore);
this.minDeltaScore = new RcpaDoubleField(this.txtMinDeltaScore, "MinDeltaScore", "Min Delta Score", 0.1, true);
AddComponent(this.minDeltaScore);
this.filterByEvalue = new RcpaCheckBox(this.cbFilterByEvalue, "FilterByEvalue", false);
AddComponent(this.filterByEvalue);
this.maxEvalue = new RcpaDoubleField(this.txtMaxEvalue, "MaxEvalue", "Max Evalue", 0.05, true);
AddComponent(this.maxEvalue);
this.dataFiles = InitializeDataFiles();
AddComponent(this.dataFiles);
}
public LabelledResultDistillerUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
SetFileArgument("ProteinFile", new OpenFileArgument("Protein", "noredundant"));
aminoAcids = new RcpaTextField(textBox1, "AminoAcids", "Labelled amino acids", "K", true);
AddComponent(aminoAcids);
labelPosition = new RcpaComboBox <LabelPosition>(comboBox1, "Position", new LabelPosition[] { LabelPosition.ALL, LabelPosition.CTERM, LabelPosition.NTERM }, 0);
AddComponent(labelPosition);
}
public FastaDatabaseDistillerUI()
{
InitializeComponent();
SetFileArgument("Database", new OpenFileArgument("Source Database (*.fasta)", "fasta"));
dbName = new RcpaTextField(txtName, "DbName", "Database Name", "HUMAN", true);
AddComponent(dbName);
dbPattern = new RcpaTextField(txtPattern, "DbPattern", "Entry Name Pattern", "_HUMAN", true);
AddComponent(dbPattern);
this.Text = Constants.GetSQHTitle(title, version);
}
public NGlycanPeptideMassCalculatorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
this.peptideSequence = new RcpaTextField(txtPeptideSequence, "PeptideSequence", "Peptide Sequence", "", false);
this.peptideModification = new RcpaTextField(txtPeptideModification, "PeptideModification", "Peptide Modification", "(STY* +79.96633) (M# +15.99492) C=160.16523", false);
this.glycanStructure = new RcpaTextField(txtGlycanStructure, "GlycanStructure", "Glycan Structure", "", false);
this.AddComponent(peptideSequence);
this.AddComponent(peptideModification);
this.AddComponent(glycanStructure);
}
public QuantificationExportForm()
{
InitializeComponent();
this.proteinName = new RcpaCheckBox(cbProteinName, "ProteinName", false);
AddComponent(this.proteinName);
this.proteinNamePattern = new RcpaTextField(txtProteinNamePattern, "ProteinNamePattern", "Keep only one protein name based on Regex Patterns, separated by ';' : (for example: _RAT ; _MOUSE)", "_RAT ; _MOUSE", false);
AddComponent(this.proteinNamePattern);
this.singleFile = new RcpaCheckBox(cbSingleFile, "SingleFile", true);
AddComponent(this.singleFile);
this.exportScan = new RcpaCheckBox(cbExportScan, "ExportScan", false);
AddComponent(this.exportScan);
}
public MassCalculatorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(Title, Version);
sequence = new RcpaTextField(txtSequence, "Sequence", "Peptide Sequence", "", true);
AddComponent(sequence);
modification = new RcpaTextField(txtModification, "Modification", "Modification Definition", "(STY* +79.96633) (M# +15.99492) C=160.16523", false);
AddComponent(modification);
isMonoisotopic = new RcpaCheckBox(cbIsMonoisotopic, "IsMonoisotopic", false);
AddComponent(isMonoisotopic);
isMH = new RcpaCheckBox(cbIsMH, "IsMH", false);
AddComponent(isMH);
}
public ITraqPeptideRsdFilterUI()
{
InitializeComponent();
base.SetFileArgument("PeptidesFile", new OpenFileArgument("Peptides", "peptides"));
this.iTraqFile = new RcpaFileField(btnRLocation, txtRLocation, "ITraqFile", new OpenFileArgument("iTRAQ", "itraq"), true);
this.AddComponent(this.iTraqFile);
Func <string, bool> validator = (m =>
{
string[] parts = m.Split(new char[] { ',' });
if (parts.Length != 2)
{
return(false);
}
int intResult;
return(int.TryParse(parts[0].Trim(), out intResult) && int.TryParse(parts[1].Trim(), out intResult));
});
this.referenceIndecies = new RcpaTextField(txtReferences, "referenceIndecies", "Reference Indecies", "114,115", true)
{
ValidateFunc = validator
};
this.AddComponent(referenceIndecies);
this.sampleIndecies = new RcpaTextField(txtSamples, "sampleIndecies", "Sample Indecies", "116,117", true)
{
ValidateFunc = validator
};
this.AddComponent(sampleIndecies);
this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", false);
this.AddComponent(modifiedAminoacids);
this.rsd = new RcpaDoubleField(txtMaxRsd, "RSD", "Max RSD in Group", 0.4, true);
this.AddComponent(rsd);
fold = new RcpaDoubleField(txtFold, "Fold", "Significance Tolerance (fold)", 2, true);
AddComponent(fold);
this.Text = Constants.GetSQHTitle(title, version);
}
public MaxQuantSiteToPeptideProcessorUI()
{
InitializeComponent();
siteFile.FileArgument = new OpenFileArgument("MaxQuant Sites", new string[] { "txt" });
msmsFile.FileArgument = new OpenFileArgument("MaxQuant MSMS", new string[] { "txt" });
this.minLocalizationProbability = new RcpaDoubleField(txtMinProbability, "minLocalizationProbability", "Minmum Localization Probability", 0.75, true);
AddComponent(this.minLocalizationProbability);
this.minScoreDiff = new RcpaDoubleField(txtMinScoreDiff, "minScoreDiff", "Minmum Score Diff", 5.0, true);
AddComponent(this.minScoreDiff);
this.silacAminoacids = new RcpaTextField(txtSILACAminoacids, "SILACAminoacids", "SILAC amino acids", "KR", false);
this.silacAminoacids.PreCondition = cbSILAC;
AddComponent(this.silacAminoacids);
this.Text = Constants.GetSQHTitle(title, version);
}
public SmallMoleculeDataImageBuilderUI()
{
InitializeComponent();
base.SetFileArgument("SigFile", new OpenFileArgument("Result", ".sig"));
sampleFile = new RcpaDirectoryField(button1, textBox1, "SampleDir", "Sample Data", true);
AddComponent(sampleFile);
refFile = new RcpaDirectoryField(button2, textBox2, "RefDir", "Reference Data", true);
AddComponent(refFile);
targetDir = new RcpaDirectoryField(button3, textBox3, "TargetDir", "Target Image", true);
AddComponent(targetDir);
peakPattern = new RcpaTextField(textBox4, "PeakPattern", "Peak Pattern (P for positive, N for negative)", "P", true);
AddComponent(peakPattern);
this.Text = Constants.GetSQHTitle(title, version);
}
public BuildSummaryResultParserUI()
{
InitializeComponent();
this.decoyPattern = new RcpaTextField(this.txtDecoyPattern, "DecoyPattern", "Decoy Database Pattern", "^REVERSED_", false);
AddComponent(this.decoyPattern);
this.fdrType = new RcpaComboBox <IFalseDiscoveryRateCalculator>(this.cbFdrType, "FdrType",
new IFalseDiscoveryRateCalculator[]
{
new TargetFalseDiscoveryRateCalculator(),
new TotalFalseDiscoveryRateCalculator()
},
new[]
{
"Target : N(decoy) / N(target)",
"Global : N(decoy) * 2 / (N(decoy) + N(target))"
}, 0);
AddComponent(this.fdrType);
Text = Constants.GetSQHTitle(Title, Version);
}
public ITraqPhosphoPeptideStatisticBuilderUI()
{
InitializeComponent();
base.SetFileArgument("PeptidesFile", new OpenFileArgument("Peptides", "peptides"));
this.iTraqFile = new RcpaFileField(btnRLocation, txtRLocation, "ITraqFile", new OpenFileArgument("iTRAQ", "itraq"), true);
this.AddComponent(this.iTraqFile);
Func <string, bool> validator = (m =>
{
string[] parts = m.Split(new char[] { ',' });
if (parts.Length != 2)
{
return(false);
}
int intResult;
return(int.TryParse(parts[0].Trim(), out intResult) && int.TryParse(parts[1].Trim(), out intResult));
});
this.normalIndecies = new RcpaTextField(txtNormal, "NormalIndecies", "Normal Indecies", "114,115", true)
{
ValidateFunc = validator
};
this.AddComponent(normalIndecies);
this.modificationIndecies = new RcpaTextField(txtModifications, "ModificationIndecies", "Modification Indecies", "116,117", true)
{
ValidateFunc = validator
};
this.AddComponent(modificationIndecies);
this.modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", true);
this.AddComponent(modifiedAminoacids);
this.Text = Constants.GetSQHTitle(title, version);
}
public IsobaricPeptideStatisticBuilderUI()
{
InitializeComponent();
peptideFile = new RcpaFileField(btnPeptideFile, txtPeptideFile, "PeptideFile", new OpenFileArgument("Peptides", "peptides"), true);
AddComponent(this.peptideFile);
designFile = new RcpaFileField(btnDesignFile, txtDesignFile, "IsobaricDesignFile", new OpenFileArgument("Isobaric Labeling Experimental Design", "experimental.xml"), true);
AddComponent(this.designFile);
normalize = new RcpaCheckBox(cbNormalize, "Normalize", false);
AddComponent(normalize);
modes = new RcpaComboBox <QuantifyMode>(cbQuantifyMode, "QuantifyMode", EnumUtils.EnumToArray <QuantifyMode>(), 0, true);
AddComponent(modes);
modifiedAminoacids = new RcpaTextField(txtModifiedAminoacids, "ModifiedAminoacids", "Input modified amino acids", "STY", false);
AddComponent(modifiedAminoacids);
minimumSiteProbability = new RcpaDoubleField(txtMinimumSiteProbability, "MinimumSiteProbability", "Input minimum phosphylation site probability", 0.9, false);
AddComponent(minimumSiteProbability);
this.Text = Constants.GetSQHTitle(title, version);
}
public SrmDistillerUI()
{
InitializeComponent();
base.SetDirectoryArgument("TargetDirectory", "Target");
this.dataDirs = new RcpaListViewMultipleFileDirectoryField(
this.btnAddFiles,
this.btnAddDirectory,
this.btnAddSubdirectory,
this.btnRemove,
this.btnLoad,
this.btnSave,
this.lvDirectories,
"Files",
new OpenFileArgument("mzXml / mzData / Thermo Raw", new string[] { "mzXml", "mzData", "raw" }),
"Agilent .d directory",
true,
true);
AddComponent(this.dataDirs);
this.rtToleranceInSecond = new RcpaDoubleField(txtRetentionTimeTolerance, "RTToleranceSecond", "Retention Time Tolerance in Second", 1.0, true);
AddComponent(this.rtToleranceInSecond);
this.signalToNoise = new RcpaDoubleField(txtSignalToNoise, "SignalToNoise", "Signal to Noise", 3.0, true);
AddComponent(this.signalToNoise);
this.precursorMassDistance = new RcpaTextField(txtPrecursorTolerance, "PrecursorMassDistance", "Distance between light and heavy precursor mass", "7,8,10", true);
AddComponent(this.precursorMassDistance);
this.smooth = new RcpaCheckBox(cbSmooth, "Smooth", true);
AddComponent(this.smooth);
this.refinePeakPicking = new RcpaCheckBox(cbRefinePeakPicking, "RefinePeakPicking", true);
AddComponent(this.refinePeakPicking);
this.deductBaseLine = new RcpaCheckBox(cbBaseLineExtraction, "DeductBaseLine", false);
AddComponent(this.deductBaseLine);
this.mzTolerance = new RcpaDoubleField(txtMzTolerance, "MzTolerance", "Product ion m/z tolerance", 0.1, true);
AddComponent(this.mzTolerance);
this.validateSignalToNoise = new RcpaDoubleField(txtValidateSignalToNoise, "ValidateSignalToNoise", "Validation signal to noise", 2, true);
AddComponent(this.validateSignalToNoise);
this.validateCorrel = new RcpaDoubleField(txtValidateCorrel, "ValidateCorrel", "Validation regression correlation", 0.5, true);
AddComponent(this.validateCorrel);
this.minValidTransactionPair = new RcpaIntegerField(txtMinValidTransactionPair, "minValidTransactionPair", "Minimum valid transaction pair count", 2, true);
AddComponent(this.minValidTransactionPair);
this.clusterByPredefine = new RcpaRadioButton(rbClusterByPredefine, "ClusterByPredefined", true);
AddComponent(this.clusterByPredefine);
this.clusterByRealData = new RcpaRadioButton(rbClusterByRealData, "ClusterByRealData", false);
AddComponent(this.clusterByRealData);
this.predefinedFile = new RcpaFileField(btnPredefined, txtPredefinedFile, "PredefinedFile", new OpenFileArgument("Predefined SRM Transaction File", ".txt"), false);
AddComponent(this.predefinedFile);
this.peakPickingByBaseline = new RcpaRadioButton(rbBaseline, "PeakPickingByBaseline", true);
AddComponent(this.peakPickingByBaseline);
this.peakPickingByHighestPeak = new RcpaRadioButton(rbHighestPeak, "PeakPickingByHighestPeak", false);
AddComponent(this.peakPickingByHighestPeak);
this.baseLinePercentage = new RcpaDoubleField(txtBaselinePercentage, "BaselinePercentage", "Baseline percentage", 5, true);
AddComponent(this.baseLinePercentage);
this.highestPeakPercentage = new RcpaDoubleField(txtHighestPeakPercentage, "HighestPeakPercentage", "Highest peak percentage", 5, false);
AddComponent(this.highestPeakPercentage);
this.precursorDistance = new RcpaDoubleField(txtMaxPrecursorDistance, "precursorDistance", "Maximum Precursor Distance", 20, true);
AddComponent(this.precursorDistance);
this.formats = new RcpaComboBox <IFileReader2 <List <SrmTransition> > >(cbFormat, "FileFormat", SrmFormatFactory.GetReaders().ToArray(), 0);
AddComponent(this.formats);
this.minEnabledScan = new RcpaIntegerField(txtMinEnabledScan, "MinValidScan", "Minimum valid scan count", 5, true);
AddComponent(this.minEnabledScan);
this.hasDecoy = new RcpaCheckBox(cbDecoyPattern, "HasDecoy", false);
AddComponent(this.hasDecoy);
this.ratioByArea = new RcpaCheckBox(cbRatioByArea, "ratioByArea", true);
AddComponent(this.ratioByArea);
this.decoyPattern = new RcpaTextField(txtDecoyPattern, "DecoyPattern", "Decoy pattern", "DECOY", false);
this.decoyPattern.ValidateFunc = m =>
{
try
{
new Regex(m);
return(true);
}
catch (Exception)
{
return(false);
}
};
AddComponent(this.decoyPattern);
this.Text = Constants.GetSQHTitle(title, version);
}
public MultipleRaw2MgfProcessorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(Title, Version);
this.SetDirectoryArgument("TargetDir", "Target MGF");
var options = new MultipleRaw2MgfOptions();
this.titleFormat = new RcpaComboBox <ITitleFormat>(cbTitleFormat, "TitleFormat", MascotTitleFactory.Titles, 0);
this.minMassRange = new RcpaDoubleField(txtMWRangeFrom, "MWRangeFrom", "Min Mass", options.PrecursorMassRange.From, true);
this.maxMassRange = new RcpaDoubleField(txtMWRangeTo, "MWRangeTo", "Max Mass", options.PrecursorMassRange.To, true);
this.minIonIntensity = new RcpaDoubleField(txtMinIonIntensity, "MinIonIntensity", "Min Ion Intensity", options.MinimumIonIntensity, true);
this.minIonCount = new RcpaIntegerField(txtMinIonCount, "MinIonCount", "Min Ion Count", options.MinimumIonCount, true);
this.minTotalIonIntensity = new RcpaDoubleField(txtMinIonIntensityThreshold, "MinTotalIonIntensity", "Min Total Ion Intensity", options.MinimumTotalIonIntensity, true);
this.defaultCharge = new RcpaComboBox <ChargeClass>(cbDefaultCharge, "DefaultCharge",
new ChargeClass[] {
new ChargeClass(new int[] {}),
new ChargeClass(new int[] { 2, 3 })
},
1);
this.rawFiles.FileArgument = new OpenFileArgument("Raw", RawFileFactory.GetSupportedRawFormats());
//high resolution MS/MS
productIonPPM = new RcpaDoubleField(txtDeisotopic, "DeisotopicPPM", "Deisotopic Product Ion Tolerance (ppm)", options.ProductIonPPM, false);
AddComponent(productIonPPM);
cbDeisotopic.Checked = options.Deisotopic;
cbDeconvolution.Checked = options.ChargeDeconvolution;
cbKeepTopX.Checked = options.KeepTopX;
topX = new RcpaIntegerField(txtTopX, "TopX", "Top X Peaks in 100 dalton window", options.TopX, false);
topX.PreCondition = cbKeepTopX;
AddComponent(topX);
cbGroupByMode.Checked = options.GroupByMode;
cbGroupByMsLevel.Checked = options.GroupByMsLevel;
cbParallelMode.Checked = options.ParallelMode;
removeIonWindow = new RcpaDoubleField(txtRemoveMassWindow, "removeMassWindow", "Remove Mass Window", options.RemoveIonWindow, false);
removeIonWindow.PreCondition = cbRemoveIons;
AddComponent(removeIonWindow);
isobaricTypes = new RcpaComboBox <IsobaricType>(cbxIsobaricTypes, "IsobaricType", IsobaricTypeFactory.IsobaricTypes, 0);
isobaricTypes.PreCondition = cbRemoveIsobaricIons;
AddComponent(isobaricTypes);
proteases = new RcpaComboBox <IIsobaricLabellingProtease>(cbProteases, "Protease", IsobaricLabellingProteaseFactory.Proteases, 0);
proteases.PreCondition = cbRemoveIsobaricIons;
AddComponent(proteases);
this.AddComponent(titleFormat);
this.AddComponent(minMassRange);
this.AddComponent(maxMassRange);
this.AddComponent(minIonIntensity);
this.AddComponent(minIonCount);
this.AddComponent(minTotalIonIntensity);
this.AddComponent(defaultCharge);
cbRemoveSpecialIons.PreCondition = cbRemoveIons;
specialIons = new RcpaTextField(txtSpecialIons, "RemoveIonMzRange", "Remove special mz range, for example, 113.5-117.5,145.5.0-155.5 for iTRAQ plex 4", options.SpecialIons, false);
specialIons.PreCondition = cbRemoveSpecialIons;
AddComponent(specialIons);
cbRemoveIsobaricIons.PreCondition = cbRemoveIons;
cbRemoveIsobaricIonsInLowRange.PreCondition = cbRemoveIsobaricIons;
cbRemoveIsobaricIonsInHighRange.PreCondition = cbRemoveIsobaricIons;
retentionTimeWindow = new RcpaDoubleField(txtRetentionTimeWindow, "RetentionTimeWindow", "Retention time window for smoothing offset", 0.5, false);
AddComponent(retentionTimeWindow);
cbRemovePrecursorLargeIons.PreCondition = cbRemovePrecursor;
precursorPPM = new RcpaDoubleField(txtPrecursorPPM, "PrecursorPPM", "Precursor PPM", 50, false);
precursorPPM.PreCondition = cbRemovePrecursor;
AddComponent(precursorPPM);
neutralLoss = new RcpaTextField(txtNeutralLoss, "NeutralLoss", "Neutral loss atom composition", "NH3,H2O,", false);
neutralLoss.PreCondition = cbRemovePrecursor;
AddComponent(neutralLoss);
InsertButton(0, btnSave);
InsertButton(0, btnLoad);
}
public UniformSummaryBuilderUI()
{
InitializeComponent();
Option = new BuildSummaryOptions();
InsertButton(2, btnNew);
InsertButton(3, this.btnLoadParam);
InsertButton(4, this.btnSaveParam);
this.minDecoyScan.DefaultValue = MascotGenericFormatShiftPrecursorProcessorOptions.DEFAULT_ShiftScan.ToString();
this.decoyPattern = new RcpaTextField(this.txtDecoyPattern, "DecoyPattern", "Decoy Database Pattern", "^REVERSED_", false);
AddComponent(this.decoyPattern);
this.removeContamination = new RcpaCheckBox(cbRemoveContamination, "RemoveContamination", false);
AddComponent(this.removeContamination);
this.contaminationNamePattern = new RcpaTextField(this.txtContaminantString, "ContaminationNamePattern", "Contaminant Name Pattern", "CON_", false);
AddComponent(this.contaminationNamePattern);
this.contaminationDescriptionPattern = new RcpaTextField(this.txtContaminantDescriptionPattern, "ContaminantDescriptionPattern", "Contaminant Description Pattern", "KERATIN", false);
AddComponent(this.contaminationDescriptionPattern);
this.filterByFdr = new RcpaCheckBox(this.cbFilterByFDR, "FilterByFDR", true);
AddComponent(this.filterByFdr);
this.maxFdr = new RcpaDoubleField(this.txtMaxFdr, "MaxFdr", "Max False Discovery Rate", 0.01, true);
AddComponent(this.maxFdr);
this.maxPeptideFdr = new RcpaDoubleField(this.txtMaxPeptideFdr, "MaxPeptideFdr", "Max Peptide FDR", 0.01, true);
AddComponent(this.maxPeptideFdr);
this.filterProteinByPeptideCount = new RcpaCheckBox(this.cbPeptideCount, "FilterProteinByPeptideCount", false);
AddComponent(this.filterProteinByPeptideCount);
this.fdrLevel = new RcpaComboBox <FalseDiscoveryRateLevel>(this.cbFdrLevel, "FdrLevel",
new[]
{
FalseDiscoveryRateLevel.Peptide,
FalseDiscoveryRateLevel.Protein,
FalseDiscoveryRateLevel.SimpleProtein,
FalseDiscoveryRateLevel.UniquePeptide
}, 1);
AddComponent(this.fdrLevel);
this.peptideRetrieval = new RcpaCheckBox(this.cbPeptideRetrieval, "PeptideRetrieval", true);
AddComponent(this.peptideRetrieval);
this.fdrType = new RcpaComboBox <FalseDiscoveryRateType>(this.cbFdrType, "FdrType",
new[]
{
FalseDiscoveryRateType.Target,
FalseDiscoveryRateType.Total
},
new[]
{
"Target : N(decoy) / N(target)",
"Global : N(decoy) * 2 / (N(decoy) + N(target))"
}, 0);
AddComponent(this.fdrType);
this.classifyByCharge = new RcpaCheckBox(this.cbClassifyByCharge, "ClassifyByCharge", ClassificationOptions.DEFAULT_ClassifyByCharge);
AddComponent(this.classifyByCharge);
this.classifyByMissCleavage = new RcpaCheckBox(this.cbClassifyByMissCleavage, "ClassifyByMissCleavage", ClassificationOptions.DEFAULT_ClassifyByMissCleavage);
AddComponent(this.classifyByMissCleavage);
this.classifyByNumberOfProteaseTermini = new RcpaCheckBox(this.cbClassifyByPreteaseTermini, "ClassifyByNumberOfProteaseTermini", ClassificationOptions.DEFAULT_ClassifyByNumProteaseTermini);
AddComponent(this.classifyByNumberOfProteaseTermini);
this.classifyByModification = new RcpaCheckBox(this.cbClassifyByModification, "ClassifyByModification", ClassificationOptions.DEFAULT_ClassifyByModification);
AddComponent(this.classifyByModification);
this.modifiedAminoacids = new RcpaTextField(this.txtFdrModifiedAminoacids, "ModifiedAminoacids", "Modified Aminoacids", "STY", true);
this.modifiedAminoacids.PreCondition = this.cbClassifyByModification;
AddComponent(this.modifiedAminoacids);
this.classifyByProteinTag = new RcpaCheckBox(this.cbClassifyByProteinTag, "ClassifyByProteinTag", ClassificationOptions.DEFAULT_ClassifyByProteinTag);
AddComponent(this.classifyByProteinTag);
this.proteinTag = new RcpaTextField(this.txtProteinTag, "ProteinTag", "Protein Tag", "", false);
this.proteinTag.PreCondition = this.cbClassifyByProteinTag;
AddComponent(this.proteinTag);
this.minimumSpectraPerGroup = new RcpaIntegerField(this.txtMinimumSpectraPerGroup, "MinimumSpectraPerGroup", "MinimumSpectraPerGroup", ClassificationOptions.DEFAULT_MinimumSpectraPerGroup, true);
AddComponent(this.minimumSpectraPerGroup);
this.filterSequenceLength = new RcpaCheckBox(this.cbSequenceLength, "FilterSequenceLength", false);
AddComponent(this.filterSequenceLength);
this.minSequenceLength = new RcpaIntegerField(this.txtMinSequenceLength, "MinSequenceLength", "Minmum Sequence Length", PeptideFilterOptions.DEFAULT_MinSequenceLength, false);
this.minSequenceLength.PreCondition = cbSequenceLength;
AddComponent(this.minSequenceLength);
this.filterMaxMissCleavage = new RcpaCheckBox(this.cbMaxMissCleavage, "FilterMaxMisscleavage", false);
AddComponent(this.filterMaxMissCleavage);
this.maxMissCleagage = new RcpaIntegerField(this.txtMaxMissCleavage, "MaxMissCleavage", "Maximum Number of Internal Missed Cleavage", PeptideFilterOptions.DEFAULT_MaxMissCleavage, false);
this.maxMissCleagage.PreCondition = cbMaxMissCleavage;
AddComponent(this.maxMissCleagage);
this.removeDecoyEntry = new RcpaCheckBox(this.cbRemoveDecoyEntry, "RemovePeptideFromDecoyDB", false);
AddComponent(this.removeDecoyEntry);
this.database = new RcpaFileField(btnDatabase, txtDatabase, "Database", new OpenFileArgument("Protein Database", "fasta"), "", true);
AddComponent(this.database);
this.acParsers = new RcpaComboBox <IAccessNumberParser>(this.cbAccessNumberPattern, "AccessNumberPattern", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(this.acParsers);
this.seConflictType = new RcpaComboBox <IResolveSearchEngineConflictType>(cbConflict, "ConflictType", ResolveSearchEngineConflictTypeFactory.GetTypes(), 1);
AddComponent(this.seConflictType);
this.conflictAsDecoy = new RcpaComboBox <ITargetDecoyConflictType>(cbConflictAsDecoy, "ConflictAsDecoy", ResolveTargetDecoyConflictTypeFactory.GetTypes(), 0);
AddComponent(this.conflictAsDecoy);
this.minAgreeCount = new RcpaIntegerField(txtMinAgreeCount, "MinAgreeCount", "Minimum agree count of engines", 1, true);
AddComponent(this.minAgreeCount);
minOneHitWonderPeptideCount = new RcpaIntegerField(txtMinOneHitWonderPeptideCount, "MinOneHitWonderPeptideCount", "minimum one-hit-wonder peptide count", 2, false);
AddComponent(minOneHitWonderPeptideCount);
minOneHitWonderPeptideCount.PreCondition = FilterOneHitWonder;
this.AfterLoadOption += DoAfterLoadOption;
Text = Constants.GetSQHTitle(title, version);
var engines = EnumUtils.EnumToArray <SearchEngineType>().OrderByDescending(m => m.ToString()).ToArray();
foreach (var engine in engines)
{
if (engine.HasFactory())
{
var button = new Button();
pnlAdd.Controls.Add(button);
button.Dock = System.Windows.Forms.DockStyle.Top;
button.UseVisualStyleBackColor = true;
button.Text = "Add " + engine.ToString();
button.Name = "btnAdd" + engine.ToString();
button.Tag = engine;
button.Click += button_Click;
}
}
pnlAdd.Update();
}
