public void IgnoreMultipleTags()
{
var modificationLookup = new CompositeModificationLookup(new[]
{
new IgnoreKeyModificationLookup(ProFormaKey.Mass),
new IgnoreKeyModificationLookup(ProFormaKey.Info)
});
var term = new ProFormaTerm("SEQVENCE", tags: new List <ProFormaTag>
{
new ProFormaTag(3, new[] { new ProFormaDescriptor(ProFormaKey.Mass, "14.05") }),
new ProFormaTag(5, new[] { new ProFormaDescriptor(ProFormaKey.Info, "not important") })
});;
var proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNull(proteoform.LocalizedModifications);
term = new ProFormaTerm("SEQVENCE", tags: new List <ProFormaTag>
{
new ProFormaTag(3, new[]
{
new ProFormaDescriptor(ProFormaKey.Mass, "14.05"),
new ProFormaDescriptor(ProFormaKey.Info, "not important")
})
});
proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNull(proteoform.LocalizedModifications);
}
public void MultipleDefaultLookups()
{
var lookup = new CompositeModificationLookup(new[] { _psiModLookup, _unimodLookup });
var mod_psi = lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, "3-hydroxy-L-proline"));
Assert.IsNotNull(mod_psi);
var mod_uni = lookup.GetModification(new ProFormaDescriptor(ProFormaKey.Name, "Trimethyl"));
Assert.IsNotNull(mod_uni);
}
public void MultipleModsOneSite()
{
var modificationLookup = new CompositeModificationLookup(new IProteoformModificationLookup[]
{
new IgnoreKeyModificationLookup(ProFormaKey.Mass),
new IgnoreKeyModificationLookup(ProFormaKey.Info),
new BrnoModificationLookup(_elementProvider),
_residLookup
});
// Modifications have same chemical formula ... OK
var term = new ProFormaTerm("SEQVKENCE", tags: new List <ProFormaTag>
{
new ProFormaTag(4, new[]
{
this.CreateBrnoDescriptor("ph"),
new ProFormaDescriptor(ProFormaKey.Identifier, ProFormaEvidenceType.Resid, "AA0038")
})
});
var proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNotNull(proteoform.LocalizedModifications);
Assert.AreEqual(1, proteoform.LocalizedModifications.Count);
Assert.AreEqual(4, ((IProteoformLocalizedModification)proteoform.LocalizedModifications.Single()).ZeroBasedStartIndex);
// Modifications have different chemical formulas ... throw!
term = new ProFormaTerm("SEQVKENCE", tags: new List <ProFormaTag>
{
new ProFormaTag(4, new[]
{
this.CreateBrnoDescriptor("me1"),
this.CreateBrnoDescriptor("ac")
})
});
Assert.Throws <ProteoformGroupCreateException>(() => _factory.CreateProteoformGroup(term, modificationLookup));
// What about different mods at different indexes?
term = new ProFormaTerm("SEQVKENCE", tags: new List <ProFormaTag>
{
new ProFormaTag(4, new[]
{
this.CreateBrnoDescriptor("ac")
}),
new ProFormaTag(7, new[]
{
this.CreateBrnoDescriptor("me1"),
})
});
proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNotNull(proteoform.LocalizedModifications);
Assert.AreEqual(2, proteoform.LocalizedModifications.Count);
// What about descriptors that don't have chemical formulas?
term = new ProFormaTerm("SEQVKENCE", tags: new List <ProFormaTag>
{
new ProFormaTag(7, new[]
{
this.CreateBrnoDescriptor("me1"),
new ProFormaDescriptor(ProFormaKey.Info, "hello!")
})
});
proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNotNull(proteoform.LocalizedModifications);
Assert.AreEqual(1, proteoform.LocalizedModifications.Count);
Assert.AreEqual(7, ((IProteoformLocalizedModification)proteoform.LocalizedModifications.Single()).ZeroBasedStartIndex);
// Multiple N terminal mods.
term = new ProFormaTerm("SEQVKENCE", null,
new[]
{
this.CreateBrnoDescriptor("ph"),
new ProFormaDescriptor(ProFormaKey.Identifier, ProFormaEvidenceType.Resid, "AA0038")
}, null, null
);
proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNull(proteoform.LocalizedModifications);
Assert.IsNotNull(proteoform.NTerminalModification);
term = new ProFormaTerm("SEQVKENCE", null,
new[]
{
this.CreateBrnoDescriptor("me1"),
this.CreateBrnoDescriptor("ac")
}, null, null
);
Assert.Throws <ProteoformGroupCreateException>(() => _factory.CreateProteoformGroup(term, modificationLookup));
// Multiple C terminal mods.
term = new ProFormaTerm("SEQVKENCE", null, null,
new[]
{
this.CreateBrnoDescriptor("ph"),
new ProFormaDescriptor(ProFormaKey.Identifier, ProFormaEvidenceType.Resid, "AA0038")
}, null
);
proteoform = _factory.CreateProteoformGroup(term, modificationLookup);
Assert.IsNull(proteoform.LocalizedModifications);
Assert.IsNotNull(proteoform.CTerminalModification);
term = new ProFormaTerm("SEQVKENCE", null, null,
new[]
{
this.CreateBrnoDescriptor("me1"),
this.CreateBrnoDescriptor("ac")
}, null
);
Assert.Throws <ProteoformGroupCreateException>(() => _factory.CreateProteoformGroup(term, modificationLookup));
}