public XmlFastaSequence(FastaSeqV01 sequence, XmlPeptide[] peptides) { Name = sequence.Id; if (sequence.Descriptions.Length > 0) { Description = sequence.Descriptions[0]; List<XmlAlternativeProtein> alternatives = new List<XmlAlternativeProtein>(); for (int i = 1; i < sequence.Descriptions.Length; i++) { string desc = sequence.Descriptions[i].Trim(); int space = desc.IndexOf(' '); if (space > 0) alternatives.Add(new XmlAlternativeProtein(desc.Substring(0, space), desc.Substring(space + 1))); else alternatives.Add(new XmlAlternativeProtein(desc, null)); } if (alternatives.Count > 0) Alternatives = alternatives.ToArray(); } PeptideList = sequence.PeptideList; Sequence = FormatAA(sequence.AA); Peptides = peptides; }
public PepV01(FastaSeqV01 fastaSequence, int begin, int end, int missedCleavages, double mh, double? rt) : this(fastaSequence, begin, end, missedCleavages) { MassH = mh; PredictedRetentionTime = rt; }
public PepV01(FastaSeqV01 fastaSequence, int begin, int end, int missedCleavages) { _fastaSequence = fastaSequence; Begin = begin; End = end; MissedCleavages = missedCleavages; // Derived value Sequence = _fastaSequence.AA.Substring(Begin, End - Begin); }
public PepV01 GetModel(FastaSeqV01 sequence) { double mh = NeutralMass + BioMassCalc.MassProton; return new PepV01(sequence, Begin, End, MissedCleavages, mh, PredictedRetentionTime); }