private void FindById(IProteoformModificationLookup lookup, ProFormaKey key, ProFormaEvidenceType evidenceType,
int correctId, string extraPrefix)
{
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{extraPrefix}{correctId}")));
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{correctId}")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, "-1")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{extraPrefix}0")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, $"{extraPrefix}2200")));
}
private void FindByName(IProteoformModificationLookup lookup, ProFormaEvidenceType evidenceType,
bool isDefault, string correctName)
{
if (isDefault)
{
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.None, correctName)));
}
Assert.IsNotNull(lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, evidenceType, correctName)));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.None, "Something")));
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, evidenceType, "Something")));
}
public void InvalidIntegerHandling()
{
var descriptor = new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.Unimod, "abc");
// I want this to return true and then throw an exception later.
// This gives me an opportunity to give a meaningful error (and not just return false)
// In this case, it is also obvious that the Unimod handler was intended, so an attempt to create
// a modification should be made.
Assert.True(_unimodLookup.CanHandleDescriptor(descriptor));
Assert.Throws <ProteoformModificationLookupException>(() => _unimodLookup.GetModification(descriptor));
}
public void FormulaLookup()
{
string formulaString = "C2H2O";
ProFormaDescriptor proFormaDescriptor = new ProFormaDescriptor(ProFormaKey.Formula, formulaString);
ChemicalFormula chemicalFormula = new ChemicalFormula(new IEntityCardinality <IElement>[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement("C"), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement("H"), 2),
new EntityCardinality <IElement>(_elementProvider.GetElement("O"), 1),
});
var proteoformModification = _formulaLookup.GetModification(proFormaDescriptor);
Assert.IsInstanceOf(typeof(IHasChemicalFormula), proteoformModification);
var formulaMod = (IHasChemicalFormula)proteoformModification;
Assert.AreEqual(chemicalFormula, formulaMod.GetChemicalFormula());
}
private IProteoformMassDelta?GetModification(IList <ProFormaDescriptor>?descriptors, IProteoformModificationLookup modificationLookup,
string multipleModsErrorMessage)
{
IProteoformMassDelta?modification = null;
if (descriptors != null && descriptors.Count > 0)
{
if (modificationLookup == null)
{
throw new ProteoformGroupCreateException("Cannot lookup tag because lookup wasn't provided.");
}
foreach (var descriptor in descriptors)
{
IProteoformMassDelta?mod = null;
if (modificationLookup.CanHandleDescriptor(descriptor))
{
mod = modificationLookup.GetModification(descriptor);
}
else
{
throw new ProteoformGroupCreateException($"Couldn't handle descriptor {descriptor}.");
}
if (modification == null)
{
modification = mod;
}
else if (mod != null)
{
if (mod is IHasChemicalFormula form1 &&
modification is IHasChemicalFormula form2 &&
!form1.GetChemicalFormula().Equals(form2.GetChemicalFormula()))
{
throw new ProteoformGroupCreateException(multipleModsErrorMessage);
}
}
}
}
return(modification);
}
private IProteoformMassDelta?GetModification(IProFormaDescriptor?descriptor, IProteoformModificationLookup modificationLookup)
{
IProteoformMassDelta?modification = null;
if (descriptor != null)
{
if (modificationLookup == null)
{
throw new ProteoformGroupCreateException("Cannot lookup tag because lookup wasn't provided.");
}
if (modificationLookup.CanHandleDescriptor(descriptor))
{
return(modificationLookup.GetModification(descriptor));
}
throw new ProteoformGroupCreateException($"Couldn't handle descriptor {descriptor}.");
}
return(modification);
}
public void PsiModIsotope()
{
var parser = new PsiModOboParser();
PsiModTerm[] modifications = parser.Parse(PsiModOboParserTest.GetFilePath()).ToArray();
PsiModTerm psiMod402 = modifications.Single(x => x.Id == "MOD:00402");
IProteoformModificationLookup psiModLookup = PsiModModificationLookup.CreateFromModifications(new[] { psiMod402 },
_elementProvider);
this.FindById(psiModLookup, ProFormaKey.Identifier, ProFormaEvidenceType.PsiMod, 402, "MOD:");
var mod = psiModLookup.GetModification(new ProFormaDescriptor(ProFormaKey.Identifier,
ProFormaEvidenceType.PsiMod, "MOD:00402"));
ChemicalFormula chemicalFormula = new ChemicalFormula(
new IEntityCardinality <IElement>[]
{
new EntityCardinality <IElement>(_elementProvider.GetElement("C"), 22),
new EntityCardinality <IElement>(_elementProvider.GetElement("H", 1), 30),
new EntityCardinality <IElement>(_elementProvider.GetElement("H", 2), 8),
new EntityCardinality <IElement>(_elementProvider.GetElement("N"), 4),
new EntityCardinality <IElement>(_elementProvider.GetElement("O"), 6),
new EntityCardinality <IElement>(_elementProvider.GetElement("S"), 1),
});
Assert.IsInstanceOf(typeof(IHasChemicalFormula), mod);
var formulaMod = (IHasChemicalFormula)mod;
Assert.IsTrue(chemicalFormula.Equals(formulaMod.GetChemicalFormula()));
Assert.IsInstanceOf(typeof(IIdentifiable), mod);
var idMod = (IIdentifiable)mod;
Assert.AreEqual("MOD:00402", idMod.Id);
Assert.AreEqual("Gygi ICAT(TM) d8 modified cysteine", idMod.Name);
}
private void InvalidIdHandling(string id, IProteoformModificationLookup lookup, ProFormaKey key,
ProFormaEvidenceType evidenceType = ProFormaEvidenceType.None)
{
Assert.Throws <ProteoformModificationLookupException>(
() => lookup.GetModification(new ProFormaDescriptor(key, evidenceType, id)));
}
