public void TestClone_Isotopes()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
IIsotope carb = builder.NewIsotope("C");
IIsotope flu = builder.NewIsotope("F");
IIsotope h1 = builder.NewIsotope("H");
mfRange.AddIsotope(carb, 0, 5);
mfRange.AddIsotope(flu, 2, 8);
mfRange.AddIsotope(h1, 4, 10);
Assert.AreEqual(3, mfRange.Count);
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(carb));
Assert.AreEqual(2, mfRange.GetIsotopeCountMin(flu));
Assert.AreEqual(4, mfRange.GetIsotopeCountMin(h1));
Assert.AreEqual(5, mfRange.GetIsotopeCountMax(carb));
Assert.AreEqual(8, mfRange.GetIsotopeCountMax(flu));
Assert.AreEqual(10, mfRange.GetIsotopeCountMax(h1));
object clone = mfRange.Clone();
Assert.IsTrue(clone is MolecularFormulaRange);
Assert.AreEqual(mfRange.Count, ((MolecularFormulaRange)clone).Count);
Assert.AreEqual(3, ((MolecularFormulaRange)clone).Count);
Assert.AreEqual(3, ((MolecularFormulaRange)clone).Count);
Assert.AreEqual(0, ((MolecularFormulaRange)clone).GetIsotopeCountMin(carb));
Assert.AreEqual(2, ((MolecularFormulaRange)clone).GetIsotopeCountMin(flu));
Assert.AreEqual(4, ((MolecularFormulaRange)clone).GetIsotopeCountMin(h1));
Assert.AreEqual(5, ((MolecularFormulaRange)clone).GetIsotopeCountMax(carb));
Assert.AreEqual(8, ((MolecularFormulaRange)clone).GetIsotopeCountMax(flu));
Assert.AreEqual(10, ((MolecularFormulaRange)clone).GetIsotopeCountMax(h1));
}
public void TestGetIsotopeCountMin_IIsotope4()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
IIsotope carb1 = builder.NewIsotope("C");
IIsotope h1 = builder.NewIsotope("H");
IIsotope carb2 = builder.NewIsotope("C");
carb2.Abundance = 13.0876689;
IIsotope h2 = builder.NewIsotope("H");
h2.Abundance = 2.0968768;
mfRange.AddIsotope(carb1, 0, 10);
mfRange.AddIsotope(h1, 0, 10);
mfRange.AddIsotope(carb2, 5, 10);
mfRange.AddIsotope(h2, 5, 10);
Assert.AreEqual(4, mfRange.Count);
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(carb1));
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(h1));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(carb2));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(h2));
}
public void TestGetIsotopeCountMin_IIsotope()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
IIsotope carb = builder.NewIsotope("C");
IIsotope h1 = builder.NewIsotope("H");
IIsotope flu = builder.NewIsotope("F");
mfRange.AddIsotope(carb, 0, 10);
mfRange.AddIsotope(h1, 0, 10);
Assert.AreEqual(2, mfRange.Count);
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(carb));
Assert.AreEqual(0, mfRange.GetIsotopeCountMin(h1));
Assert.AreEqual(-1, mfRange.GetIsotopeCountMin(flu));
}
public void TestRemoveAllIsotopes()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
IIsotope carb = builder.NewIsotope("C");
IIsotope flu = builder.NewIsotope("F");
IIsotope h1 = builder.NewIsotope("H");
mfRange.AddIsotope(carb, 0, 10);
mfRange.AddIsotope(flu, 0, 10);
mfRange.AddIsotope(h1, 0, 10);
// remove the Fluorine
mfRange.Clear();
Assert.AreEqual(0, mfRange.Count);
Assert.AreEqual(-1, mfRange.GetIsotopeCountMin(carb));
Assert.AreEqual(-1, mfRange.GetIsotopeCountMin(h1));
Assert.AreEqual(-1, mfRange.GetIsotopeCountMin(flu));
}
public void TestGetIsotopeCountMin_IIsotope3()
{
MolecularFormulaRange mfRange = new MolecularFormulaRange();
IIsotope carb1 = builder.NewIsotope("C");
IIsotope h1 = builder.NewIsotope("H");
IIsotope carb2 = builder.NewIsotope("C");
IIsotope h2 = builder.NewIsotope("H");
mfRange.AddIsotope(carb1, 0, 10);
mfRange.AddIsotope(h1, 0, 10);
mfRange.AddIsotope(carb2, 5, 10);
mfRange.AddIsotope(h2, 5, 10);
Assert.AreEqual(2, mfRange.Count);
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(carb1));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(h1));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(carb2));
Assert.AreEqual(5, mfRange.GetIsotopeCountMin(h2));
}
/// <summary>
/// Initiate the MolecularFormulaGenerator.
/// </summary>
/// <param name="minMass">Lower boundary of the target mass range</param>
/// <param name="maxMass">Upper boundary of the target mass range</param>
/// <param name="mfRange">A range of elemental compositions defining the search space</param>
/// <exception cref="ArgumentOutOfRangeException">In case some of the isotopes in mfRange has undefined exact mass or in case illegal parameters are provided (e.g., negative mass values or empty MolecularFormulaRange)</exception>
/// <seealso cref="MolecularFormulaRange"/>
internal RoundRobinFormulaGenerator(IChemObjectBuilder builder,
double minMass, double maxMass,
MolecularFormulaRange mfRange)
{
this.builder = builder;
var isotopes = new List <IIsotope>(mfRange.GetIsotopes().Count());
foreach (IIsotope iso in mfRange.GetIsotopes())
{
if (mfRange.GetIsotopeCountMin(iso) >= 0 && mfRange.GetIsotopeCountMax(iso) > 0)
{
isotopes.Add(iso);
}
}
this.decomposer = DecomposerFactory.Instance.GetDecomposerFor(isotopes.ToArray()).DecomposeIterator(minMass, maxMass, mfRange);
this.done = false;
this.mfRange = mfRange;
}
/// <summary>
/// Returns an iterator over all decompositons of this mass range
/// </summary>
/// <param name="from">lowest mass to decompose</param>
/// <param name="to">(inclusive) largest mass to decompose</param>
/// <param name="boundaries">defines lowerbounds and upperbounds for the number of elements</param>
internal DecompIterator DecomposeIterator(double from, double to, MolecularFormulaRange boundaries)
{
Init();
if (to < 0d || from < 0d)
{
throw new ArgumentException("Expect positive mass for decomposition: [" + from + ", " + to + "]");
}
if (to < from)
{
throw new ArgumentException("Negative range given: [" + from + ", " + to + "]");
}
int[] minValues = new int[weights.Count];
int[] boundsarray = new int[weights.Count];
double cfrom = from, cto = to;
Arrays.Fill(boundsarray, int.MaxValue);
if (boundaries != null)
{
for (int i = 0; i < boundsarray.Length; i++)
{
IIsotope el = weights[i].GetOwner();
int max = boundaries.GetIsotopeCountMax(el);
int min = boundaries.GetIsotopeCountMin(el);
if (min >= 0 || max >= 0)
{
boundsarray[i] = max - min;
minValues[i] = min;
if (minValues[i] > 0)
{
double reduceWeightBy = weights[i].GetMass() * min;
cfrom -= reduceWeightBy;
cto -= reduceWeightBy;
}
}
}
}
int[] minmax = new int[2];
IntegerBound(cfrom, cto, minmax);
int deviation = minmax[1] - minmax[0];
//calculate the required ERTs
if ((1 << (ERTs.Length - 1)) <= deviation)
{
CalcERT(deviation);
}
{
int[][][] ERTs = this.ERTs;
//take ERT with required deviation
int[][] currentERT;
if (deviation == 0)
{
currentERT = ERTs[0];
}
else
{
currentERT = ERTs[32 - Ints.NumberOfLeadingZeros(deviation)];
}
return(new DecompIterator(currentERT, minmax[0], minmax[1], from, to, minValues, boundsarray, weights));
}
}
/// <summary>
/// Initiate the MolecularFormulaGenerator.
/// </summary>
/// <param name="minMass">Lower boundary of the target mass range</param>
/// <param name="maxMass">Upper boundary of the target mass range</param>
/// <param name="mfRange">A range of elemental compositions defining the search space</param>
/// <exception cref="ArgumentOutOfRangeException">In case some of the isotopes in mfRange has undefined exact mass or in case illegal parameters are provided (e.g., negative mass values or empty MolecularFormulaRange)</exception>
/// <seealso cref="MolecularFormulaRange"/>
public FullEnumerationFormulaGenerator(IChemObjectBuilder builder,
double minMass, double maxMass,
MolecularFormulaRange mfRange)
{
Trace.TraceInformation("Initiate MolecularFormulaGenerator, mass range " + minMass + "-" + maxMass);
// Check parameter values
if (minMass < 0.0)
{
throw (new ArgumentOutOfRangeException(nameof(minMass), "The minimum and maximum mass values must be >=0"));
}
if (maxMass < 0.0)
{
throw (new ArgumentOutOfRangeException(nameof(maxMass), "The minimum and maximum mass values must be >=0"));
}
if ((minMass > maxMass))
{
throw (new ArgumentException("Minimum mass must be <= maximum mass"));
}
if ((mfRange == null) || (mfRange.GetIsotopes().Count() == 0))
{
throw (new ArgumentException("The MolecularFormulaRange parameter must be non-null and must contain at least one isotope"));
}
// Save the parameters
this.builder = builder;
this.minMass = minMass;
this.maxMass = maxMass;
// Sort the elements by mass in ascending order. That speeds up
// the search.
var isotopesSet = new SortedSet <IIsotope>(
new IIsotopeSorterByMass());
foreach (IIsotope isotope in mfRange.GetIsotopes())
{
// Check if exact mass of each isotope is set
if (isotope.ExactMass == null)
{
throw new ArgumentException($"The exact mass value of isotope {isotope} is not set");
}
isotopesSet.Add(isotope);
}
isotopes = isotopesSet.ToArray();
// Save the element counts from the provided MolecularFormulaRange
minCounts = new int[isotopes.Length];
maxCounts = new int[isotopes.Length];
for (int i = 0; i < isotopes.Length; i++)
{
minCounts[i] = mfRange.GetIsotopeCountMin(isotopes[i]);
maxCounts[i] = mfRange.GetIsotopeCountMax(isotopes[i]);
// Update the maximum count according to the mass limit
int maxCountAccordingToMass = (int)Math.Floor(maxMass
/ isotopes[i].ExactMass.Value);
if (maxCounts[i] > maxCountAccordingToMass)
{
maxCounts[i] = maxCountAccordingToMass;
}
}
// Set the current counters to minimal values, initially
currentCounts = Arrays.CopyOf(minCounts, minCounts.Length);
}