public void DescriptorHandling()
{
this.DescriptorHandling(_unimodLookup, ProFormaEvidenceType.Unimod, true);
this.DescriptorHandling(_residLookup, ProFormaEvidenceType.Resid, false);
this.DescriptorHandling(_psiModLookup, ProFormaEvidenceType.PsiMod, true);
this.DescriptorHandling(_uniProtModLookup, ProFormaEvidenceType.UniProt, false);
Assert.IsTrue(_formulaLookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Formula, "Anything")));
}
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));
}
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 void DescriptorHandling(IProteoformModificationLookup lookup, ProFormaEvidenceType key, bool isDefault)
{
// If the key is a specific mod type, always handle
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, "Anything")));
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, "")));
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, null)));
// If using modification name, must have no ending or end in proper ending
Assert.IsTrue(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, key, "Something")));
Assert.IsFalse(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, "Something")));
Assert.IsFalse(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, ProFormaEvidenceType.Brno, "Something")));
// This is malformed and must be interpreted as a mod "name" ... will fail when looking up modification
//Assert.AreEqual(lookup.CanHandleDescriptor(new ProFormaDescriptor(ProFormaKey.Name, $"Something [{key}]")), isDefault);
}
private IProteoformMassDelta?GetModification(IProFormaDescriptor?descriptor, IProteoformModificationLookup modificationLookup)
{
IProteoformMassDelta?modification = null;
if (descriptor != null)
{
if (modificationLookup == null)
{
throw new ProteoformGroupCreateException("Cannot lookup tag because lookup wasn't provided.");
}
if (modificationLookup.CanHandleDescriptor(descriptor))
{
return(modificationLookup.GetModification(descriptor));
}
throw new ProteoformGroupCreateException($"Couldn't handle descriptor {descriptor}.");
}
return(modification);
}