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 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 MaxQuantMgfDistillerUI()
{
InitializeComponent();
this.SetFileArgument("PeptideFile", new OpenFileArgument("BuildSummary Peptides", "peptides"));
List <ITitleParser> allParsers = TitleParserUtils.GetTitleParsers();
this.titleParsers = new RcpaComboBox <ITitleParser>(this.cbTitleFormat, "TitleFormat", allParsers.ToArray(), 0);
AddComponent(this.titleParsers);
this.mgfFiles = new RcpaListViewMultipleFileField(
this.btnAddFiles,
this.btnRemoveFiles,
this.btnLoad,
this.btnSave,
this.lvMgfFiles,
"MgfFiles",
new OpenFileArgument("Mascot Generic Format", new string[] { "msm", "mgf" }),
true,
true);
AddComponent(this.mgfFiles);
this.singleFile = new RcpaCheckBox(cbSingleFile, "SingleFile", false);
AddComponent(this.singleFile);
this.singleFileName = new RcpaFileField(btnMgfFile, txtSingleFile, "SingleFilename", new SaveFileArgument("MGF", "mgf"), false);
AddComponent(this.singleFileName);
Text = Constants.GetSQHTitle(title, version);
}
public 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 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 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 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 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 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 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 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 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 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 ProteinDistributionUI()
{
InitializeComponent();
exportPeptideCountOnly = new RcpaCheckBox(cbPeptideCountOnly, "PeptideCountOnly", false);
AddComponent(exportPeptideCountOnly);
this.Text = Constants.GetSQHTitle(title, version);
}
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 MsfFileToNoredundantProcessorUI()
{
InitializeComponent();
base.SetFileArgument("MSFExcel", new OpenFileArgument("MSF Text/Excel/Msf", new string[] { "txt", "xls", "msf" }));
excelFormat = new RcpaCheckBox(cbExcelFormat, "ExcelFormat", false);
AddComponent(excelFormat);
this.Text = Constants.GetSQHTitle(title, version);
}
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 SrmExportForm()
{
InitializeComponent();
this.targetFile = new RcpaFileField(button1, textBox1, "TargetFile", new SaveFileArgument("Quantification Result", "csv"), true);
AddComponent(this.targetFile);
removeDecoy = new RcpaCheckBox(cbTargetOnly, "RemoveDecoy", true);
AddComponent(removeDecoy);
validOnly = new RcpaCheckBox(cbValidOnly, "ValidOnly", true);
AddComponent(validOnly);
}
public 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 ExportCompoundForm()
{
InitializeComponent();
FirstProductIonColumn = gvFiles.Columns.Count;
exportDecoy = new RcpaCheckBox(cbViewDecoy, "ViewDecoy", false);
AddComponent(exportDecoy);
exportEnabled = new RcpaCheckBox(cbViewValidOnly, "ViewVaidOnly", false);
AddComponent(exportEnabled);
exportInvalidCompoundAsNA = new RcpaCheckBox(cbInvalidCompoundAsNA, "ViewInvalidCompoundAsNA", true);
AddComponent(exportInvalidCompoundAsNA);
LoadOption();
}
public MaxQuantToMgfProcessorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
this.rawFiles.FileArgument = new OpenFileArgument("MaxQuant APL", ".apl");
this.rawFileComp = new RcpaMultipleFileComponent(this.rawFiles.GetItemInfos(), "AplFiles", "MaxQuant APL", false, true);
this.AddComponent(rawFileComp);
this.mergeFile = new RcpaCheckBox(cbMerge, "MergeFile", false);
AddComponent(this.mergeFile);
}
public TurboRaw2MzXmlProcessorUI()
{
InitializeComponent();
this.Text = Constants.GetSQHTitle(title, version);
this.targetDir = new RcpaDirectoryField(btnTarget, txtTarget, "TargetDir", "Target MzXml", true);
this.fullMsOnly = new RcpaCheckBox(cbFullMsOnly, "FullMsOnly", false);
this.centroid = new RcpaCheckBox(cbCentroid, "Centroid", true);
this.AddComponent(targetDir);
this.AddComponent(fullMsOnly);
this.AddComponent(centroid);
base.SetFileArgument("RawFile", new OpenFileArgument("Thermo Raw", "raw"));
base.SetDirectoryArgument("RawDir", "Raw");
}
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 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 ExtractFastaByAccessNumberProcessorUI()
{
InitializeComponent();
SetFileArgument("AccessNumberFile", new OpenFileArgument("Access Number", "txt"));
fastaFile = new RcpaFileField(btnFastaFile, textBox1, "FastaFile", new OpenFileArgument("Database", "fasta"), true);
AddComponent(fastaFile);
replaceName = new RcpaCheckBox(cbReplaceName, "ReplaceName", false);
AddComponent(replaceName);
parsers = new RcpaComboBox <IAccessNumberParser>(cbAccessNumberParser, "AccessNumberParser", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(parsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public CensusResultFileMergerUI()
{
InitializeComponent();
targetFile = new SaveFileArgument("Merged Census Result", "txt");
this.isLabelFree = new RcpaCheckBox(cbLabelFree, "IsLabelFree", false);
AddComponent(this.isLabelFree);
this.isPeptideLevel = new RcpaCheckBox(cbPeptideLevel, "IsPeptideLevel", false);
AddComponent(this.isPeptideLevel);
this.resultFiles = new RcpaListBoxMultipleFileField(btnAdd, btnRemove, null, null, null, lbResultFiles, "ResultFile", new OpenFileArgument("Census Result", "txt"), true, true);
AddComponent(this.resultFiles);
this.Text = Constants.GetSQHTitle(Title, Version);
}
public ITraqResultMultipleFileDistillerUI()
{
InitializeComponent();
rawFiles.FileArgument = new OpenFileArgument("Raw Files", rawExtentions);
RcpaMultipleFileComponent adaptor = new RcpaMultipleFileComponent(rawFiles.GetItemInfos(), "RawFiles", "Raw File", false, true);
AddComponent(adaptor);
individual = new RcpaCheckBox(cbIndividual, "Individual", false);
AddComponent(individual);
minPeakCount = new RcpaIntegerField(txtMinPeakCount, "MinPeakCount", "Minmum peak count", 4, true);
AddComponent(minPeakCount);
plexFiles = new string[] {
new FileInfo(Application.ExecutablePath).Directory.FullName + "\\itraq-4plex.csv",
new FileInfo(Application.ExecutablePath).Directory.FullName + "\\itraq-8plex.csv",
new FileInfo(Application.ExecutablePath).Directory.FullName + "\\tmt-6plex.csv"
};
plexTypes = new RcpaComboBox <IsobaricType>(cbPlexType, "PlexType", EnumUtils.EnumToArray <IsobaricType>(), 0);
AddComponent(plexTypes);
txtIsotopeFileName.Items.AddRange(plexFiles);
isotopeFile = new RcpaFileField2 <ComboBox>(btnIsotopeFile, txtIsotopeFileName, "IsotopeFile", new OpenFileArgument("Isotope Impurity Correction Table", "csv"), plexFiles[0], true, m => m.Text, (m, value) => m.Text = value);
AddComponent(isotopeFile);
readers = new RcpaComboBox <IITraqRawReader>(cbScanMode, "ScanMode", new IITraqRawReader[] { new ITraqRawHCDMS2Reader(), new ITraqRawHCDMS3Reader(), new ITraqRawHCDParallelMS3Reader(), new ITraqRawPQDCIDReader(), new ITraqRawPQDReader() }, 0);
AddComponent(readers);
normalizationBuilders = new RcpaComboBox <IITraqNormalizationBuilder>(cbNormalizationType, "NormalizationType",
new IITraqNormalizationBuilder[] { new ITraqNormalizationByMedianIntensityBuilder(), new ITraqNormalizationByTotalIntensityBuilder(), new ITraqNormalizationNoneBuilder() }, 1);
AddComponent(normalizationBuilders);
normalizationByIonInjectionTime = new RcpaCheckBox(cbNormalizeByIonInjectionTime, "normalizationByIonInjectionTime", false);
AddComponent(normalizationByIonInjectionTime);
precursorPPMTolerance = new RcpaDoubleField(txtPrecursorPPMTolerance, "precursorPPMTolerance", "Precursor Tolerance (ppm)", 10, true);
AddComponent(precursorPPMTolerance);
this.Text = Constants.GetSQHTitle(title, version);
}
public 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 One2AllProcessorUI()
{
InitializeComponent();
this.SetFileArgument("Peptides", new OpenFileArgument("BuildSummary Peptides", "peptides"));
lbDtaFiles.FileArgument = new OpenFileArgument("Sequest Dtas", "dtas");
this.dtasFiles = new RcpaMultipleFileComponent(lbDtaFiles.GetItemInfos(), "DtasFiles", "Sequest Dtas File", false, true);
this.AddComponent(this.dtasFiles);
this.targetDir = new RcpaDirectoryField(btnTargetDirectory, txtTargetDirectory, "TargetDirectory", "Target Directory", true);
this.AddComponent(this.targetDir);
this.extractToSameDirectory = new RcpaCheckBox(cbExtractToSameDirectory, "ExtractToSameDirectory", false);
this.AddComponent(this.extractToSameDirectory);
this.Text = Constants.GetSQHTitle(title, version);
}
