public void TestNullArguments()
{
ChemicalFormula formulaA = new ChemicalFormula("CO");
IHasChemicalFormula ok = null;
Assert.AreEqual("item", Assert.Throws <ArgumentNullException>(() => { formulaA.Add(ok); }).ParamName);
ChemicalFormula ok2 = null;
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.Add(ok2); }).ParamName);
Assert.AreEqual("other", Assert.Throws <ArgumentNullException>(() => { new ChemicalFormula(ok2); }).ParamName);
Element ok3 = null;
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.AddPrincipalIsotopesOf(ok3, 0); }).ParamName);
Assert.AreEqual("item", Assert.Throws <ArgumentNullException>(() => { formulaA.Remove(ok); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.Remove(ok2); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.IsSubsetOf(ok2); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { formulaA.IsSupersetOf(ok2); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.CountWithIsotopes(ok3); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { formulaA.CountSpecificIsotopes(ok3, 0); }).ParamName);
Assert.IsFalse(formulaA.Equals(ok2));
IEnumerable <IHasChemicalFormula> ok4 = null;
Assert.AreEqual("formulas", Assert.Throws <ArgumentNullException>(() => { ChemicalFormula.Combine(ok4); }).ParamName);
Assert.AreEqual("element", Assert.Throws <ArgumentNullException>(() => { PeriodicTable.Add(ok3); }).ParamName);
Assert.AreEqual("formula", Assert.Throws <ArgumentNullException>(() => { new IsotopicDistribution(ok2); }).ParamName);
IHasMass ok5 = null;
Assert.AreEqual("objectWithMass", Assert.Throws <ArgumentNullException>(() => { ok5.ToMZ(0); }).ParamName);
var ok7 = new PhysicalObjectWithChemicalFormula("C");
}
protected AminoAcidPolymer(AminoAcidPolymer aminoAcidPolymer, int firstResidue, int length, bool includeModifications)
{
Length = length;
residues = new Residue[length];
bool isNterm = firstResidue == 0;
bool isCterm = length + firstResidue == aminoAcidPolymer.Length;
_nTerminus = isNterm ? aminoAcidPolymer.NTerminus : new ChemicalFormulaTerminus(ChemicalFormula.ParseFormula("H"));
_cTerminus = isCterm ? aminoAcidPolymer.CTerminus : new ChemicalFormulaTerminus(ChemicalFormula.ParseFormula("OH"));
double monoMass = _nTerminus.MonoisotopicMass + _cTerminus.MonoisotopicMass;
Residue[] otherAminoAcids = aminoAcidPolymer.residues;
if (includeModifications && aminoAcidPolymer.ContainsModifications())
{
_modifications = new IHasMass[length + 2];
for (int i = 0; i < length; i++)
{
var aa = otherAminoAcids[i + firstResidue];
residues[i] = aa;
monoMass += aa.MonoisotopicMass;
IHasMass mod = aminoAcidPolymer._modifications[i + firstResidue + 1];
if (mod == null)
{
continue;
}
_modifications[i + 1] = mod;
monoMass += mod.MonoisotopicMass;
}
}
else
{
for (int i = 0, j = firstResidue; i < length; i++, j++)
{
var aa = otherAminoAcids[j];
residues[i] = aa;
monoMass += aa.MonoisotopicMass;
}
}
MonoisotopicMass = monoMass;
if (includeModifications)
{
if (isNterm)
{
NTerminusModification = aminoAcidPolymer.NTerminusModification;
}
if (isCterm)
{
CTerminusModification = aminoAcidPolymer.CTerminusModification;
}
}
}
/// <summary>
/// Remove a chemical formula containing object from this chemical formula
/// </summary>
/// <param name="item">The object that contains a chemical formula</param>
public void Remove(IHasChemicalFormula item)
{
if (item == null)
{
throw new ArgumentNullException("item", "Cannot remove null item from formula");
}
Remove(item.ThisChemicalFormula);
}
/// <summary>
/// Add a chemical formula containing object to this chemical formula
/// </summary>
/// <param name="item">The object that contains a chemical formula</param>
public void Add(IHasChemicalFormula item)
{
if (item == null)
{
throw new ArgumentNullException("item", "Cannot add null item to formula");
}
Add(item.ThisChemicalFormula);
}
protected AminoAcidPolymer(string sequence, IHasChemicalFormula nTerm, IHasChemicalFormula cTerm)
{
MonoisotopicMass = 0;
Length = sequence.Length;
residues = new Residue[Length];
NTerminus = nTerm;
CTerminus = cTerm;
ParseSequence(sequence);
}
private void ReplaceTerminus(ref IHasChemicalFormula terminus, IHasChemicalFormula value)
{
if (terminus != null)
{
MonoisotopicMass -= terminus.MonoisotopicMass;
}
terminus = value;
if (value != null)
{
MonoisotopicMass += value.MonoisotopicMass;
}
}
/// <summary>
/// Gets the chemical formula of this amino acid polymer.
/// </summary>
/// <returns></returns>
public ChemicalFormula GetChemicalFormula()
{
var formula = new ChemicalFormula();
// Handle Modifications
if (ContainsModifications())
{
for (int i = 0; i < Length + 2; i++)
{
if (_modifications[i] == null)
{
continue;
}
IHasChemicalFormula chemMod = _modifications[i] as IHasChemicalFormula;
if (chemMod == null)
{
throw new MzLibException("Modification " + _modifications[i] + " does not have a chemical formula!");
}
formula.Add(chemMod.ThisChemicalFormula);
}
}
// Handle N-Terminus
formula.Add(NTerminus.ThisChemicalFormula);
// Handle C-Terminus
formula.Add(CTerminus.ThisChemicalFormula);
// Handle Amino Acid Residues
for (int i = 0; i < Length; i++)
{
formula.Add(residues[i].ThisChemicalFormula);
}
return(formula);
}
public IEnumerable <Fragment> Fragment(FragmentTypes types, int minIndex, int maxIndex, bool calculateChemicalFormula)
{
foreach (FragmentTypes type in types.GetIndividualFragmentTypes())
{
bool isChemicalFormula = calculateChemicalFormula;
ChemicalFormula capFormula = type.GetIonCap();
bool isCTerminal = type.GetTerminus() == Terminus.C;
double monoMass = capFormula.MonoisotopicMass;
ChemicalFormula formula = new ChemicalFormula(capFormula);
IHasChemicalFormula terminus = isCTerminal ? CTerminus : NTerminus;
monoMass += terminus.MonoisotopicMass;
if (isChemicalFormula)
{
formula.Add(terminus);
}
bool first = true;
bool hasMod = _modifications != null;
for (int i = 0; i <= maxIndex; i++)
{
int aaIndex = isCTerminal ? Length - i : i - 1;
// Handle the terminus mods first in a special case
IHasMass mod;
if (first)
{
first = false;
if (hasMod)
{
mod = _modifications[aaIndex + 1];
if (mod != null)
{
monoMass += mod.MonoisotopicMass;
if (isChemicalFormula)
{
if (mod is IHasChemicalFormula modFormula)
{
formula.Add(modFormula);
}
else
{
isChemicalFormula = false;
}
}
}
}
continue;
}
monoMass += residues[aaIndex].MonoisotopicMass;
formula.Add(residues[aaIndex]);
if (hasMod)
{
mod = _modifications[aaIndex + 1];
if (mod != null)
{
monoMass += mod.MonoisotopicMass;
if (isChemicalFormula)
{
if (mod is IHasChemicalFormula modFormula)
{
formula.Add(modFormula);
}
else
{
isChemicalFormula = false;
}
}
}
}
if (i < minIndex)
{
continue;
}
if (isChemicalFormula)
{
yield return(new ChemicalFormulaFragment(type, i, formula, this));
}
else
{
yield return(new Fragment(type, i, monoMass, this));
}
}
}
}
/// <summary>
/// Remove a chemical formula containing object from this chemical formula
/// </summary>
/// <param name="item">The object that contains a chemical formula</param>
public void Remove(IHasChemicalFormula item)
{
Remove(item.ThisChemicalFormula);
}
/// <summary>
/// Add a chemical formula containing object to this chemical formula
/// </summary>
/// <param name="item">The object that contains a chemical formula</param>
public void Add(IHasChemicalFormula item)
{
Add(item.ThisChemicalFormula);
}
