protected override void WriteTransition(TextWriter writer,
XmlFastaSequence sequence,
XmlPeptide peptide,
XmlTransition transition)
{
char separator = TextUtil.GetCsvSeparator(_cultureInfo);
writer.Write(transition.PrecursorMz.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(transition.ProductMz.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(Math.Round(transition.CollisionEnergy, 1).ToString(_cultureInfo));
writer.Write(separator);
if (MethodType == ExportMethodType.Scheduled)
{
if (!transition.StartRT.HasValue || !transition.StopRT.HasValue)
{
throw new InvalidOperationException(Resources.XmlThermoMassListExporter_WriteTransition_Attempt_to_write_scheduling_parameters_failed);
}
writer.Write(transition.StartRT.Value.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(transition.StopRT.Value.ToString(_cultureInfo));
writer.Write(separator);
writer.Write('1'); // Not L10N
writer.Write(separator);
}
writer.Write(peptide.Sequence);
writer.Write(separator);
writer.Write(sequence.Name);
writer.WriteLine();
}
protected override void WriteTransition(TextWriter writer,
XmlFastaSequence sequence,
XmlPeptide peptide,
XmlTransition transition)
{
char separator = TextUtil.GetCsvSeparator(_cultureInfo);
writer.Write(transition.PrecursorMz.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(transition.ProductMz.ToString(_cultureInfo));
writer.Write(separator);
if (MethodType == ExportMethodType.Standard)
{
writer.Write(Math.Round(DwellTime, 2).ToString(_cultureInfo));
}
else
{
if (!peptide.PredictedRetentionTime.HasValue)
{
throw new InvalidOperationException(Resources.XmlThermoMassListExporter_WriteTransition_Attempt_to_write_scheduling_parameters_failed);
}
writer.Write(peptide.PredictedRetentionTime.Value.ToString(_cultureInfo));
}
writer.Write(separator);
// Write special ID for ABI software
var fastaSequence = new FastaSequence(sequence.Name, sequence.Description, null, peptide.Sequence);
var newPeptide = new Peptide(fastaSequence, peptide.Sequence, 0, peptide.Sequence.Length, peptide.MissedCleavages);
var nodePep = new PeptideDocNode(newPeptide);
string modifiedPepSequence = AbiMassListExporter.GetSequenceWithModsString(nodePep, _document.Settings); // Not L10N;
string extPeptideId = string.Format("{0}.{1}.{2}.{3}", // Not L10N
sequence.Name,
modifiedPepSequence,
GetTransitionName(transition),
"light"); // Not L10N : file format
writer.WriteDsvField(extPeptideId, separator);
writer.Write(separator);
writer.Write(Math.Round(transition.DeclusteringPotential ?? 0, 1).ToString(_cultureInfo));
writer.Write(separator);
writer.Write(Math.Round(transition.CollisionEnergy, 1).ToString(_cultureInfo));
writer.WriteLine();
}
protected override void WriteTransition(TextWriter writer,
XmlFastaSequence sequence,
XmlPeptide peptide,
XmlTransition transition)
{
char separator = TextUtil.GetCsvSeparator(_cultureInfo);
writer.Write(transition.PrecursorMz.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(transition.ProductMz.ToString(_cultureInfo));
writer.Write(separator);
if (MethodType == ExportMethodType.Standard)
writer.Write(Math.Round(DwellTime, 2).ToString(_cultureInfo));
else
{
if (!peptide.PredictedRetentionTime.HasValue)
throw new InvalidOperationException(Resources.XmlThermoMassListExporter_WriteTransition_Attempt_to_write_scheduling_parameters_failed);
writer.Write(peptide.PredictedRetentionTime.Value.ToString(_cultureInfo));
}
writer.Write(separator);
// Write special ID for ABI software
var fastaSequence = new FastaSequence(sequence.Name, sequence.Description, null, peptide.Sequence);
var newPeptide = new Peptide(fastaSequence, peptide.Sequence, 0, peptide.Sequence.Length, peptide.MissedCleavages);
var nodePep = new PeptideDocNode(newPeptide);
string modifiedPepSequence = AbiMassListExporter.GetSequenceWithModsString(nodePep, _document.Settings); // Not L10N;
string extPeptideId = string.Format("{0}.{1}.{2}.{3}", // Not L10N
sequence.Name,
modifiedPepSequence,
GetTransitionName(transition),
"light"); // Not L10N : file format
writer.WriteDsvField(extPeptideId, separator);
writer.Write(separator);
writer.Write(Math.Round(transition.DeclusteringPotential ?? 0, 1).ToString(_cultureInfo));
writer.Write(separator);
writer.Write(Math.Round(transition.CollisionEnergy, 1).ToString(_cultureInfo));
writer.WriteLine();
}
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;
}
protected abstract void WriteTransition(TextWriter writer,
XmlFastaSequence sequence,
XmlPeptide peptide,
XmlTransition transition);
protected override void WriteTransition(TextWriter writer,
XmlFastaSequence sequence,
XmlPeptide peptide,
XmlTransition transition)
{
char separator = TextUtil.GetCsvSeparator(_cultureInfo);
writer.Write(transition.PrecursorMz.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(transition.ProductMz.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(Math.Round(transition.CollisionEnergy, 1).ToString(_cultureInfo));
writer.Write(separator);
if (MethodType == ExportMethodType.Scheduled)
{
if (!transition.StartRT.HasValue || !transition.StopRT.HasValue)
throw new InvalidOperationException(Resources.XmlThermoMassListExporter_WriteTransition_Attempt_to_write_scheduling_parameters_failed);
writer.Write(transition.StartRT.Value.ToString(_cultureInfo));
writer.Write(separator);
writer.Write(transition.StopRT.Value.ToString(_cultureInfo));
writer.Write(separator);
writer.Write('1'); // Not L10N
writer.Write(separator);
}
writer.Write(peptide.Sequence);
writer.Write(separator);
writer.Write(sequence.Name);
writer.WriteLine();
}
protected abstract void WriteTransition(TextWriter writer,
XmlFastaSequence sequence,
XmlPeptide peptide,
XmlTransition transition);
