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 TitleDatasetPanel()
{
InitializeComponent();
parsers = TitleParserUtils.GetTitleParsers().ToArray();
this.titleParsers = new RcpaComboBox <ITitleParser>(this.cbTitleFormat, "TitleFormat", parsers, parsers.Length - 1);
AddComponent(this.titleParsers);
}
protected override IFileProcessor GetFileProcessor()
{
return(new MultipleMgf2Ms2Processor(new MultipleMgf2Ms2ProcessorOptions()
{
InputFiles = mgfFiles.FileNames,
TargetDir = GetOriginFile(),
Parser = new DefaultTitleParser(TitleParserUtils.GetTitleParsers())
}));
}
public void TestUpdatePrecursor()
{
var pkl = new PeakList <Peak>();
pkl.Precursor = new PrecursorPeak(new Peak(1000.0, 1.0, 4));
pkl.FirstScan = 620;
pkl.Annotations["TITLE"] = "TCGA-AA-A01F-01A-23_W_VU_20120727_A0218_1B_R_FR04.620.620.4.dta";
var titleFormat = TitleParserUtils.FindByName("DTA");
MascotGenericFormatShiftPrecursorProcessor.UpdatePrecursor(titleFormat, pkl, -10.0, 10000);
Assert.AreEqual(10620, pkl.FirstScan);
Assert.AreEqual("TCGA-AA-A01F-01A-23_W_VU_20120727_A0218_1B_R_FR04.10620.10620.4.dta", pkl.Annotations["TITLE"]);
Assert.AreEqual(997.5, pkl.PrecursorMZ, 0.1);
}
private void btnFind_Click(object sender, EventArgs e)
{
var sample = GetTitleSample();
if (!string.IsNullOrEmpty(sample))
{
var guess = TitleParserUtils.GuessTitleParser(sample, parsers);
if (guess != null)
{
titleParsers.SelectedItem = guess;
}
else
{
MessageBox.Show(this, MyConvert.Format("Cannot find corresponding title parser for {0}", guess), "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
}
}
public override ISpectrumParser GetParser(string name, bool extractRank2)
{
if (extractRank2)
{
return(new CometXmlRank2Parser()
{
TitleParser = new DefaultTitleParser(TitleParserUtils.GetTitleParsers())
});
}
else
{
return(new CometXmlParser()
{
TitleParser = new DefaultTitleParser(TitleParserUtils.GetTitleParsers())
});
}
}
public void Test()
{
var spectra = new CometXmlRank2Parser()
{
TitleParser = TitleParserUtils.FindByName("DTA")
}.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/comet.pep.xml");
Assert.AreEqual(2, spectra.Count);
Assert.AreEqual("K.M*REGPAK.N", spectra[0].Sequence);
Assert.AreEqual(3, spectra[0].Rank);
Assert.AreEqual(0.743, spectra[0].Score, 0.001);
Assert.AreEqual(0.035, spectra[0].DeltaScore, 0.001);
Assert.AreEqual(66.0, spectra[0].SpScore, 0.01);
Assert.AreEqual(13, spectra[0].SpRank);
Assert.AreEqual(2.47E+01, spectra[0].ExpectValue, 0.01);
Assert.AreEqual(1077, spectra[0].Query.MatchCount);
Assert.AreEqual("Elite_CIDIT_Human.minus10dalton.2.2.2.dta", spectra[0].Query.FileScan.LongFileName);
}
public void Test()
{
var parser = TitleParserUtils.GetTitleParsers().Find(m => m.FormatName == "MaxQuant");
var format = new MaxQuantAplFormat(parser);
var pkls = format.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/maxquant.peak.apl");
Assert.AreEqual(562, pkls.Count);
Assert.AreEqual("20110915_iTRAQ_4plex_GK_6ug_Exp_1", pkls[0].Experimental);
Assert.AreEqual(10258, pkls[0].ScanTimes[0].Scan);
Assert.AreEqual("HCD", pkls[0].ScanMode);
Assert.AreEqual(301.68467, pkls[0].PrecursorMZ, 0.00001);
Assert.AreEqual(2, pkls[0].PrecursorCharge);
Assert.AreEqual(37, pkls[0].Count);
Assert.AreEqual(110.07127, pkls[0].First().Mz, 0.00001);
Assert.AreEqual(2116.9580, pkls[0].First().Intensity, 0.0001);
Assert.AreEqual(590.83301, pkls[0].Last().Mz, 0.00001);
Assert.AreEqual(248.6751, pkls[0].Last().Intensity, 0.0001);
}
public override bool PrepareOptions()
{
if (!File.Exists(this.InputFile))
{
ParsingErrors.Add(string.Format("Input file not exists {0}.", this.InputFile));
}
if (TitleParserUtils.FindByName(TitleType) == null)
{
if (!string.IsNullOrEmpty(this.TitleType) && !this.TitleType.ToLower().Equals("help"))
{
ParsingErrors.Add(string.Format("Unknown title type {0}.", this.TitleType));
}
ParsingErrors.Add(" Those titles are valid:");
(from t in TitleParserUtils.GetTitleParsers()
select t.FormatName).ToList().ForEach(m => ParsingErrors.Add(" " + m));
}
return(ParsingErrors.Count == 0);
}
public override IEnumerable <string> Process()
{
var titleParser = TitleParserUtils.FindByName(options.TitleType);
Progress.SetMessage("Parsing " + options.InputFile + "...");
var outputFile = options.OutputFile + ".tmp";
new Mgf2Ms2Processor(outputFile, titleParser)
{
Progress = this.Progress
}.Process(options.InputFile);
if (File.Exists(outputFile))
{
File.Move(outputFile, options.OutputFile);
}
return(new[] { options.OutputFile });
}
public virtual ITitleParser GetTitleParser()
{
List <ITitleParser> allParsers = TitleParserUtils.GetTitleParsers();
foreach (ITitleParser parser in allParsers)
{
if (parser.FormatName.Equals(TitleParserName))
{
return(parser);
}
}
foreach (ITitleParser parser in allParsers)
{
if (parser.FormatName.Equals(DefaultTitleParser.FORMAT_NAME))
{
return(parser);
}
}
return(new DefaultTitleParser());
}
public void Test()
{
var spectra = new CometXmlParser()
{
TitleParser = TitleParserUtils.FindByName("DTA")
}.ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/comet.pep.xml");
Assert.AreEqual(2, spectra.Count);
Assert.AreEqual("R.HFM*LEMK.S", spectra[0].Sequence);
Assert.AreEqual(1, spectra[0].Rank);
Assert.AreEqual(0.778, spectra[0].Score, 0.001);
Assert.AreEqual(0.001, spectra[0].DeltaScore, 0.001);
Assert.AreEqual(80.2, spectra[0].SpScore, 0.01);
Assert.AreEqual(7, spectra[0].SpRank);
Assert.AreEqual(1.91E+01, spectra[0].ExpectValue, 0.01);
Assert.AreEqual("sp|Q9BV73|CP250_HUMAN", spectra[0].Proteins[0]);
Assert.AreEqual(4, spectra[0].MatchedIonCount);
Assert.AreEqual(10, spectra[0].TheoreticalIonCount);
Assert.AreEqual(803.399995, spectra[0].TheoreticalMass, 0.000001);
Assert.AreEqual(2, spectra[0].Query.FileScan.Charge);
Assert.AreEqual(1077, spectra[0].Query.MatchCount);
Assert.AreEqual("Elite_CIDIT_Human.minus10dalton.2.2.2.dta", spectra[0].Query.FileScan.LongFileName);
}
public override bool PrepareOptions()
{
foreach (var file in InputFiles)
{
if (!File.Exists(file))
{
ParsingErrors.Add(string.Format("File not exists {0}.", file));
}
}
if (!string.IsNullOrEmpty(OutputDirectory) && !Directory.Exists(OutputDirectory))
{
ParsingErrors.Add(string.Format("Directory not exists {0}.", OutputDirectory));
}
if (GetTitleParser() == null)
{
ParsingErrors.Add(string.Format("Title is not exists {0}, select one from following list:\n{1}",
TitleFormat,
TitleParserUtils.GetTitleParsers().ConvertAll(m => m.FormatName).Merge("\n")));
}
return(ParsingErrors.Count == 0);
}
public MascotDatToPepXmlConverterUI()
{
InitializeComponent();
this.minPeptideLength.DefaultValue = MascotDatToPepXmlConverterOptions.DEFAULT_MinPeptideLength.ToString();
this.targetDir.SetDirectoryArgument("TargetDir", "Target PepXML");
this.datFiles.FileArgument = new OpenFileArgument("Mascot Dat", "dat");
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "DatFiles", "Dat Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public ReplaceMascotGenericFormatProcessorUI()
{
InitializeComponent();
base.SetFileArgument("TargetFile", new SaveFileArgument("Target MGF", "mgf"));
fileHeader.FileArgument = new OpenFileArgument("Precursor Info MGF", "mgf");
this.titleHeaderParser = new RcpaComboBox <ITitleParser>(cbHeaderFormat, "HeaderTitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleHeaderParser);
filePeak.FileArgument = new OpenFileArgument("Peak Info MGF", "mgf");
this.titlePeakParser = new RcpaComboBox <ITitleParser>(cbPeakFormat, "PeakTitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titlePeakParser);
this.titleFormat = new RcpaComboBox <ITitleFormat>(cbTitleFormat, "TitleFormat", MascotTitleFactory.Titles, 0);
AddComponent(this.titleFormat);
this.Text = Constants.GetSQHTitle(title, version);
lblInfo.Text = info;
}
public MascotGenericFormatShiftPrecursorProcessorUI()
{
InitializeComponent();
this.datFiles.FileArgument = new OpenFileArgument("Mascot MGF", new string[] { "mgf", "msm" });
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "MGFFiles", "Mgf Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.targetDirectory.SetDirectoryArgument("TargetDirectory", "Target");
this.Text = Constants.GetSQHTitle(Title, Version);
}
public override bool PrepareOptions()
{
foreach (var file in InputFiles)
{
if (!File.Exists(file))
{
ParsingErrors.Add(string.Format("File not exists {0}.", file));
}
}
if (!string.IsNullOrEmpty(OutputDirectory) && !Directory.Exists(OutputDirectory))
{
ParsingErrors.Add(string.Format("Directory not exists {0}.", OutputDirectory));
}
if (GetTitleParser() == null)
{
ParsingErrors.Add(string.Format("Title is not exists {0}.", TitleFormat));
Console.WriteLine("Valid title format names : \n" + StringUtils.Merge(TitleParserUtils.GetTitleParsers().ConvertAll(m => m.FormatName), "\n") + "\n");
}
return(ParsingErrors.Count == 0);
}
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 UpdatePepXmlModificationProcessorUI()
{
InitializeComponent();
this.SetDirectoryArgument("TargetDir", "Target DAT");
this.datFiles.FileArgument = new OpenFileArgument("PepXml", new string[] { "pepXml", "pep.xml" });
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "PepXml", "PepXml Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public UpdateMascotDatTitleFormatProcessorUI()
{
InitializeComponent();
this.SetDirectoryArgument("TargetDir", "Target DAT");
this.datFiles.FileArgument = new OpenFileArgument("Mascot Dat", "dat");
AddComponent(new RcpaMultipleFileComponent(this.datFiles.GetItemInfos(), "DatFiles", "Dat Files", false, true));
this.titleParsers = new RcpaComboBox <ITitleParser>(cbTitleFormat, "TitleFormat", TitleParserUtils.GetTitleParsers().ToArray(), 0);
AddComponent(this.titleParsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public ITitleParser GetTitleParser()
{
return(TitleParserUtils.FindByName(this.TitleFormat));
}
