Ejemplo n.º 1
0
        private void AddPeptide(Library library, string[] line, int sequenceIndex, int pepMzIndex)
        {
            var peptide = new Library.Peptide();

            peptide.Id       = line[pepMzIndex].Replace(",", ".");
            peptide.Sequence = line[sequenceIndex];
            peptide.AssociatedTransitions = new List <Library.Transition>();
            library.PeptideList.Add(peptide.Id, peptide);
        }
Ejemplo n.º 2
0
        private void AddPeptide(Library library, XmlReader reader)
        {
            var peptide = new Library.Peptide();

            peptide.Id       = reader.GetAttribute("id");
            peptide.Sequence = reader.GetAttribute("sequence");
            peptide.AssociatedTransitionIds = new List <string>();
            bool cvParamsRead = false;

            while (reader.Read() && !cvParamsRead)
            {
                if (reader.IsStartElement())
                {
                    if (reader.LocalName == "cvParam")
                    {
                        switch (reader.GetAttribute("accession"))
                        {
                        case "MS:1000041":
                            peptide.ChargeState = Convert.ToInt32(reader.GetAttribute("value"));
                            break;

                        case "MS:1000893":
                            peptide.GroupLabel = reader.GetAttribute("value");
                            break;

                        case "MS:1000896":
                            peptide.RetentionTime = double.Parse(reader.GetAttribute("value"), System.Globalization.CultureInfo.InvariantCulture);
                            break;
                        }
                    }
                }
                else if (reader.NodeType == XmlNodeType.EndElement && reader.LocalName == "Peptide")
                {
                    cvParamsRead = true;
                }
            }

            library.PeptideList.Add(peptide.Id, peptide);
        }