public void WriteTransition(AbstractMassListExporter exporter,
PeptideGroupDocNode seq,
PeptideDocNode peptide,
TransitionGroupDocNode group,
TransitionGroupDocNode groupPrimary,
TransitionDocNode transition,
int step)
{
if (!HasFile)
{
throw new IOException(Resources.FileIterator_WriteTransition_Unexpected_failure_writing_transitions);
}
exporter.WriteTransition(_writer, seq, peptide, group, groupPrimary, transition, step);
// If not full-scan, count transtions
if (!_isPrecursorLimited)
{
TransitionCount++;
}
// Otherwise, count precursors
else if (!ReferenceEquals(_nodeGroupLast, group))
{
TransitionCount++;
_nodeGroupLast = group;
}
}
private static void VerifyExportRoundTrip(AbstractMassListExporter exporter, SrmDocument docFasta)
{
var docImport = AssertEx.RoundTripTransitionList(exporter);
int countProteinTermTran, countProteinTerm;
VerifyMultiLabelContent(docFasta, docImport, out countProteinTerm, out countProteinTermTran);
}
public void WriteRequiredTransitions(AbstractMassListExporter exporter, RequiredPeptideSet requiredPeptides)
{
foreach (var requiredPeptide in requiredPeptides.Peptides)
{
var seq = requiredPeptide.PeptideGroupNode;
var peptide = requiredPeptide.PeptideNode;
foreach (var group in peptide.TransitionGroups)
{
foreach (var transition in group.Transitions)
{
WriteTransition(exporter, seq, peptide, group, null, transition, 0);
}
}
}
}
public static SrmDocument RoundTripTransitionList(AbstractMassListExporter exporter)
{
exporter.Export(null);
// Reverse the output lines and import into a new document
var docExport = exporter.Document;
var docImport = new SrmDocument(docExport.Settings);
string transitionList = exporter.MemoryOutput.Values.ToArray()[0].ToString();
IdentityPath pathAdded;
var inputs = new MassListInputs(DuplicateAndReverseLines(transitionList, exporter.HasHeaders),
CultureInfo.InvariantCulture, TextUtil.SEPARATOR_CSV);
docImport = docImport.ImportMassList(inputs, IdentityPath.ROOT, out pathAdded);
IsDocumentState(docImport, 1,
docExport.MoleculeGroupCount,
docExport.MoleculeCount,
docExport.MoleculeTransitionGroupCount,
docExport.MoleculeTransitionCount);
return(docImport);
}
private static void VerifyExportRoundTrip(AbstractMassListExporter exporter, SrmDocument docFasta)
{
var docImport = AssertEx.RoundTripTransitionList(exporter);
int countProteinTermTran, countProteinTerm;
VerifyMultiLabelContent(docFasta, docImport, out countProteinTerm, out countProteinTermTran);
}
