private void addPeptideValue() { MsRun msRun1 = new MsRun(1); Assay assay1 = new Assay(1); Assay assay2 = new Assay(2); StudyVariable studyVariable1 = new StudyVariable(1); MZTabColumnFactory factory = MZTabColumnFactory.GetInstance(Section.Peptide_Header); factory.AddOptionalColumn(PeptideColumn.SEARCH_ENGINE_SCORE, msRun1); factory.AddAbundanceOptionalColumn(assay1); factory.AddAbundanceOptionalColumn(studyVariable1); factory.AddAbundanceOptionalColumn(assay2); factory.AddOptionalColumn(msRun1, "my_value", typeof (string)); CVParam param = new CVParam("MS", "MS:1002217", "decoy peptide", null); factory.AddOptionalColumn(param, typeof (string)); Metadata metadata = new Metadata(); metadata.AddMsRunLocation(2, new Url("file://C:\\path\\to\\my\\file")); Console.WriteLine(factory); Peptide peptide = new Peptide(factory, metadata); peptide.Sequence = "KVPQVSTPTLVEVSR"; peptide.Accession = "P02768"; peptide.SetUnique("0"); peptide.Database = "UniProtKB"; peptide.DatabaseVersion = "2011_11"; peptide.SetSearchEngine("[MS,MS:1001207,Mascot,]|[MS,MS:1001208,Sequest,]"); peptide.SetBestSearchEngineScore("[MS,MS:1001155,Sequest:xcorr,2]"); peptide.Reliability = Reliability.findReliability("3"); peptide.SetModifications( "3[MS,MS:1001876, modification probability, 0.8]|4[MS,MS:1001876, modification probability, 0.2]-MOD:00412,8[MS,MS:1001876, modification probability, 0.3]-MOD:00412"); peptide.AddRetentionTime(10.2); peptide.AddRetentionTimeWindow(1123.2); peptide.AddRetentionTimeWindow(1145.3); peptide.Charge = new Integer(2); peptide.MassToCharge = 1234.4; peptide.URI = new Uri("http://www.ebi.ac.uk/pride/link/to/peptide"); peptide.SetSpectraRef("ms_run[2]:index=7|ms_run[2]:index=9"); Console.WriteLine(peptide); }
/** * Translate the data line to a {@link MZTabRecord}. * * NOTICE: Normally, we suggest user do convert operation after validate successfully. * * @see #parse(int, string, uk.ac.ebi.pride.jmztab.utils.errors.MZTabErrorList) */ protected MZTabRecord getRecord(Section section, string line) { MZTabRecord record = null; if (section.Equals(Section.Protein)){ record = new Protein(factory); } else if (section.Equals(Section.Peptide)){ record = new Peptide(factory, metadata); } else if (section.Equals(Section.PSM)){ record = new PSM(factory, metadata); } else if (section.Equals(Section.Small_Molecule)){ record = new SmallMolecule(factory, metadata); } int offset = loadStableData(record, line); if (offset == _items.Length - 1){ return record; } loadOptionalData(record, offset); return record; }
public object Clone() { Peptide peptide = new Peptide(base.factory, this.metadata); peptide.Sequence = Sequence; peptide.Accession = Accession; peptide.Unique = Unique; peptide.Database = Database; peptide.DatabaseVersion = DatabaseVersion; peptide.SearchEngine = SearchEngine; peptide.BestSearchEngineScore = BestSearchEngineScore; //TODO: peptide.setSearchEngineScore(); peptide.Reliability = Reliability; peptide.Modifications = Modifications; peptide.RetentionTime = RetentionTime; peptide.RetentionTimeWindow = RetentionTimeWindow; peptide.Charge = Charge; peptide.MassToCharge = MassToCharge; peptide.URI = URI; peptide.SpectraRef = SpectraRef; return peptide; }
/** * Add a Peptide record. * * @param peptide SHOULD NOT set null. */ public void addPeptide(Peptide peptide) { if (peptide == null){ throw new NullReferenceException("Peptide record is null!"); } int position = peptides.Count == 0 ? 1 : peptides.Last().Key + 1; peptides.Add(position, peptide); }
/** * Add a Peptide record. * * @param lineNumber SHOULD be positive integer * @param peptide SHOULD NOT set null. * * @throws ArgumentException if there exists Peptide object for assigned lineNumber */ public void addPeptide(int lineNumber, Peptide peptide) { if (peptide == null){ throw new NullReferenceException("Peptide record is null!"); } if (lineNumber <= 0){ throw new ArgumentException("Line number should be positive integer"); } if (peptides.ContainsKey(lineNumber)){ throw new ArgumentException("There already exist peptide record in line number " + lineNumber); } peptides.Add(lineNumber, peptide); }