/// <summary>
/// Compares a peptide document with a small molecule document which is presumed to be
/// derived from the peptide document via RefinementSettings.ConvertToSmallMolecules()
/// </summary>
public static void ConvertedSmallMoleculeDocumentIsSimilar(SrmDocument document, SrmDocument converted)
{
// Are both versions valid?
Serializable(converted);
Serializable(document);
var convertedMoleculeGroupsIterator = converted.MoleculeGroups.GetEnumerator();
foreach (var peptideGroupDocNode in document.MoleculeGroups)
{
convertedMoleculeGroupsIterator.MoveNext();
var convertedMoleculeGroupDocNode = convertedMoleculeGroupsIterator.Current;
var convertedMoleculesIterator = convertedMoleculeGroupDocNode.Molecules.GetEnumerator();
foreach (var mol in peptideGroupDocNode.Molecules)
{
convertedMoleculesIterator.MoveNext();
var convertedMol = convertedMoleculesIterator.Current;
if (convertedMol.Note != null)
{
Assert.AreEqual(mol.Note ?? string.Empty, convertedMol.Note.Replace(RefinementSettings.TestingConvertedFromProteomic, string.Empty));
}
else
{
Assert.AreEqual(mol.CustomIon.InvariantName, SrmDocument.TestingNonProteomicMoleculeName); // This was the magic test molecule
}
Assert.AreEqual(mol.SourceKey, convertedMol.SourceKey);
Assert.AreEqual(mol.Rank, convertedMol.Rank);
Assert.AreEqual(mol.Results, convertedMol.Results);
Assert.AreEqual(mol.ExplicitRetentionTime, convertedMol.ExplicitRetentionTime);
Assert.AreEqual(mol.BestResult, convertedMol.BestResult);
var convertedTransitionGroupIterator = convertedMol.TransitionGroups.GetEnumerator();
foreach (var transitionGroupDocNode in mol.TransitionGroups)
{
convertedTransitionGroupIterator.MoveNext();
var convertedTransitionGroupDocNode = convertedTransitionGroupIterator.Current;
Assert.AreEqual(transitionGroupDocNode.TransitionGroup.PrecursorCharge, convertedTransitionGroupDocNode.TransitionGroup.PrecursorCharge);
Assert.AreEqual(transitionGroupDocNode.TransitionGroup.LabelType, convertedTransitionGroupDocNode.TransitionGroup.LabelType);
Assert.AreEqual(transitionGroupDocNode.PrecursorMz, convertedTransitionGroupDocNode.PrecursorMz, SequenceMassCalc.MassTolerance, "transitiongroup as small molecule");
Assert.AreEqual(transitionGroupDocNode.IsotopeDist, convertedTransitionGroupDocNode.IsotopeDist);
// Remove any library info, since for the moment at least small molecules don't support this and it won't roundtrip
var resultsNew = RefinementSettings.RemoveTransitionGroupChromInfoLibraryInfo(transitionGroupDocNode);
Assert.AreEqual(resultsNew, convertedTransitionGroupDocNode.Results, transitionGroupDocNode + " vs " + convertedTransitionGroupDocNode);
Assert.AreEqual(transitionGroupDocNode.TransitionGroup.PrecursorCharge, convertedTransitionGroupDocNode.TransitionGroup.PrecursorCharge);
Assert.AreEqual(transitionGroupDocNode.TransitionGroup.LabelType, convertedTransitionGroupDocNode.TransitionGroup.LabelType);
var convertedTransitionIterator = convertedTransitionGroupDocNode.Transitions.GetEnumerator();
foreach (var transition in transitionGroupDocNode.Transitions)
{
convertedTransitionIterator.MoveNext();
var convertedTransition = convertedTransitionIterator.Current;
Assert.AreEqual(transition.Mz, convertedTransition.Mz, SequenceMassCalc.MassTolerance, "transition as small molecule");
Assert.AreEqual(transition.IsotopeDistInfo, convertedTransition.IsotopeDistInfo);
Assert.AreEqual(transition.Results, convertedTransition.Results);
}
Assert.IsFalse(convertedTransitionIterator.MoveNext());
}
Assert.IsFalse(convertedTransitionGroupIterator == null || convertedTransitionGroupIterator.MoveNext());
}
Assert.IsFalse(convertedMoleculesIterator.MoveNext());
}
Assert.IsFalse(convertedMoleculeGroupsIterator.MoveNext());
}
