public void TestBuild()
{
List <IIdentifiedSpectrum> spectra = new SequestPeptideTextFormat().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/TestBuilder.peptides");
Assert.AreEqual(4, spectra.Count);
IAccessNumberParser parser = AccessNumberParserFactory.FindOrCreateParser(@"(IPI\d+)", "IPI");
List <IIdentifiedProtein> proteins = new IdentifiedProteinBuilder().Build(spectra);
Assert.AreEqual(4, proteins.Count);
List <IIdentifiedProteinGroup> groups = new IdentifiedProteinGroupBuilder().Build(proteins);
Assert.AreEqual(2, groups.Count);
Assert.AreEqual(1, groups[0].Count);
Assert.AreEqual("IPI:IPI00784154.1|SW", groups[0][0].Name);
Assert.AreEqual(2, groups[1].Count);
Assert.AreEqual("REVERSED_00000001", groups[1][0].Name);
Assert.AreEqual("REVERSED_00000002", groups[1][1].Name);
IIdentifiedResult result = new IdentifiedResultBuilder(parser, "").Build(groups);
}
public ITraqUniquePeptideStatisticBuilderUI()
{
InitializeComponent();
base.SetFileArgument("PeptidesFile", new OpenFileArgument("Peptides", "peptides"));
fastaFile.FileArgument = new OpenFileArgument("Database", "fasta");
parsers = new RcpaComboBox <IAccessNumberParser>(cbAccessNumberParser, "AccessNumberParser", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(parsers);
this.Text = Constants.GetSQHTitle(title, version);
}
public ProteinLabelFreeQuantificationBuilderUI()
{
InitializeComponent();
SetFileArgument("ProteinFile", new OpenFileArgument("Protein", new string[] { "noredundant", "unduplicated" }));
calculators = new RcpaComboBox<IProteinLabelfreeQuantificationCalculator>(
cbFilterType,
"LabelfreeQuantificationCalculator",
new IProteinLabelfreeQuantificationCalculator[] {
new NSAFProteinLabelfreeQuantificationCalculator(),
new SInProteinLabelfreeQuantificationCalculator()
},
0);
AddComponent(calculators);
this.parsers = new RcpaComboBox<IAccessNumberParser>(cbAccessNumberParser, "Parser", AccessNumberParserFactory.GetParsers().ToArray(), 0);
AddComponent(this.parsers);
AddComponent(pnlClassification);
this.Text = Constants.GetSQHTitle(title, version);
}
protected override IEnumerable <string> DoProcess(string filename, List <string> result, Dictionary <IFilter <IIdentifiedSpectrum>, SpectrumEntry> map)
{
string database = filename + ".fasta";
if (!File.Exists(database))
{
throw new Exception("Fasta file not exists : " + database);
}
IAccessNumberParser acParser = AccessNumberParserFactory.GuessParser(database);
Dictionary <string, Sequence> seqMap = DatabaseUtils.GetAccessNumberMap(database, acParser);
try
{
using (IdentifiedProteinGroupEnumerator iter = new IdentifiedProteinGroupEnumerator(filename))
{
foreach (IFilter <IIdentifiedSpectrum> filter in map.Keys)
{
SpectrumEntry entry = map[filter];
entry.ResultWriter.WriteLine(iter.ProteinFormat.GetHeader());
entry.ResultWriter.WriteLine(iter.PeptideFormat.GetHeader());
}
while (iter.MoveNext())
{
IIdentifiedProteinGroup group = iter.Current;
List <IIdentifiedSpectrum> spectra = group[0].GetSpectra();
foreach (IFilter <IIdentifiedSpectrum> filter in map.Keys)
{
SpectrumEntry entry = map[filter];
entry.Spectra.Clear();
foreach (IIdentifiedSpectrum spectrum in spectra)
{
if (filter.Accept(spectrum))
{
entry.Spectra.Add(spectrum);
}
}
if (entry.Spectra.Count > 0)
{
for (int i = 0; i < group.Count; i++)
{
entry.ResultWriter.WriteLine("${0}-{1}{2}", group.Index, i + 1, iter.ProteinFormat.GetString(group[i]));
string ac = acParser.GetValue(group[i].Name);
Sequence seq = seqMap[ac];
entry.FastaWriter.WriteLine(">" + seq.Reference);
entry.FastaWriter.WriteLine(seq.SeqString);
}
foreach (IIdentifiedSpectrum spectrum in entry.Spectra)
{
entry.ResultWriter.WriteLine(iter.PeptideFormat.GetString(spectrum));
}
}
}
}
return(result);
}
}
finally
{
foreach (SpectrumEntry entry in map.Values)
{
entry.Dispose();
}
}
}
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 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);
}
protected override void InitializeFromOption(string optionFile)
{
base.InitializeFromOption(optionFile);
parser = AccessNumberParserFactory.GetAutoParser();
}
public static void FillSequenceFromFasta(string fastaFilename, IIdentifiedResult t, IProgressCallback progress)
{
IAccessNumberParser acParser = AccessNumberParserFactory.GuessParser(fastaFilename);
FillSequenceFromFasta(acParser, fastaFilename, t, progress);
}
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 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 IAccessNumberParser GetAccessNumberParser()
{
return AccessNumberParserFactory.FindOrCreateParser(AccessNumberPattern, AccessNumberPattern);
}
