public ExplicitSequenceMassCalc(ExplicitMods mods, SequenceMassCalc massCalcBase, IsotopeLabelType labelType)
{
_massCalcBase = massCalcBase;
_mods = new ExplicitSequenceMods
{
Mods = mods.GetModifications(labelType),
StaticBaseMods = mods.GetStaticBaseMods(labelType),
ModMasses = mods.GetModMasses(_massCalcBase.MassType, labelType),
RequiresAllCalcMods = mods.IsVariableStaticMods
};
}
public void EquivalentTest()
{
var dictHiddenIsotopeModNames = UniMod.DictHiddenIsotopeModNames;
var dictHiddenStructuralModNames = UniMod.DictHiddenStructuralModNames;
var dictIsotopeModNames = UniMod.DictIsotopeModNames;
var dictStructuralModNames = UniMod.DictStructuralModNames;
var compareDict = new SortedDictionary<string, int>();
var massCalc = new SequenceMassCalc(MassType.Monoisotopic);
foreach (var dict in new[]
{
dictStructuralModNames,
dictIsotopeModNames,
dictHiddenStructuralModNames,
dictHiddenIsotopeModNames
})
{
var unimodArray = dict.ToArray();
var actualDict = new SortedDictionary<string, int>();
int actualCount = EquivalentValues(actualDict, unimodArray);
int count, totalCount = 0;
// Check that modifications are identified with improper name.
StaticMod modToMatch;
for (int i = 0; i < unimodArray.Length; i++)
{
var original = unimodArray[i].Value;
modToMatch = (StaticMod) original.ChangeName("Test");
count = CountEquivalent(unimodArray, modToMatch, compareDict, i);
Assert.IsTrue(count >= 1);
totalCount += count;
}
Assert.AreEqual(actualCount, totalCount);
Assert.IsTrue(ArrayUtil.EqualsDeep(actualDict.ToArray(), compareDict.ToArray()));
compareDict.Clear();
totalCount = 0;
// Modify arrangement of formula.
// Should still be able to identify correct modification.
for (int i = 0; i < unimodArray.Length; i++)
{
var original = unimodArray[i].Value;
modToMatch = (StaticMod)original.ChangeName("Test");
var formula = original.Formula;
if (formula != null)
{
var dictCounts = new Dictionary<string, int>();
massCalc.ParseModCounts(formula, dictCounts);
string newFormula = GetFormula(formula, dictCounts);
modToMatch = modToMatch.ChangeFormula(newFormula);
}
count = CountEquivalent(unimodArray, modToMatch, compareDict, i);
Assert.IsTrue(count >= 1);
totalCount += count;
}
Assert.IsTrue(actualCount == totalCount);
Assert.IsTrue(ArrayUtil.EqualsDeep(actualDict.ToArray(), compareDict.ToArray()));
compareDict.Clear();
totalCount = 0;
// Add and substract 5 hydrogen atoms to test complex formulas.
for (int i = 0; i < unimodArray.Length; i++)
{
var original = unimodArray[i].Value;
var formula = original.Formula;
modToMatch = (StaticMod) original.ChangeName("Test");
if (formula != null)
{
var dictCounts = new Dictionary<string, int>();
massCalc.ParseModCounts(formula, dictCounts);
if (dictCounts.TryGetValue("H", out count))
dictCounts["H"] = count + 5;
else
dictCounts["H"] = 5;
string newFormula = GetFormula(formula, dictCounts);
if (newFormula.Contains("-"))
newFormula = newFormula + "H5";
else
newFormula = newFormula + " - H5";
modToMatch = modToMatch.ChangeFormula(newFormula);
}
count = CountEquivalent(unimodArray, modToMatch, compareDict, i);
Assert.IsTrue(count >= 1);
totalCount += count;
}
Assert.IsTrue(actualCount == totalCount);
Assert.IsTrue(ArrayUtil.EqualsDeep(actualDict.ToArray(), compareDict.ToArray()));
compareDict.Clear();
totalCount = 0;
// Change label.
for (int i = 0; i < unimodArray.Length; i++)
{
var original = unimodArray[i].Value;
var labelAtoms = original.LabelAtoms;
modToMatch = (StaticMod)original.ChangeName("Test");
if (labelAtoms != LabelAtoms.None && original.AAs != null && original.AAs.Length == 1)
{
double unexplainedMass;
string newFormula = massCalc.GetModFormula(original.AAs[0], original, out unexplainedMass);
Assert.AreEqual(0, unexplainedMass);
modToMatch = modToMatch.ChangeFormula(newFormula).ChangeLabelAtoms(LabelAtoms.None);
}
count = CountEquivalent(unimodArray, modToMatch, compareDict, i);
Assert.IsTrue(count >= 1);
totalCount += count;
}
Assert.IsTrue(actualCount == totalCount);
Assert.IsTrue(ArrayUtil.EqualsDeep(actualDict.ToArray(), compareDict.ToArray()));
// Nonexisting formulas.
foreach (StaticMod original in dict.Values)
{
modToMatch = (StaticMod)original.ChangeName("Test");
if (original.Formula != null || original.Losses != null)
modToMatch = modToMatch.ChangeFormula("H2OCl");
else if (original.LabelAtoms != LabelAtoms.None)
modToMatch = modToMatch.ChangeFormula("H2OCl").ChangeLabelAtoms(LabelAtoms.None);
count = CountEquivalent(unimodArray, modToMatch, compareDict, -1);
Assert.AreEqual(0, count);
}
compareDict.Clear();
}
}
public TypedMassCalc(IsotopeLabelType labelType, SequenceMassCalc massCalc)
{
LabelType = labelType;
MassCalc = massCalc;
}