public Isotope getIsotope(int massNumber) {
Iterator<Isotope> isotopeIterator = isotopes.iterator();
Isotope isotope;
while (isotopeIterator.hasNext()) {
isotope = isotopeIterator.next();
if (isotope.getMassNumber() == massNumber) {
return isotope;
}
}
return null;
}
public TreeSet<Isotope> getNaturallyOccuringIsotopes() {
TreeSet<Isotope> isotopes = new TreeSet<>();
Iterator<Isotope> isotopeIterator = this.isotopes.iterator();
Isotope isotope;
while (isotopeIterator.hasNext()) {
isotope = isotopeIterator.next();
if (isotope.getAbundance() > 0) {
isotopes.add(isotope);
}
}
return isotopes;
}
private Element(
int atomicNumber,
String name,
String symbol,
Collection<? extends Isotope> isotopes,
Group group) {
this.atomicNumber = atomicNumber;
this.name = name;
this.symbol = symbol;
this.isotopes = new TreeSet<>();
for (Isotope isotope : isotopes) {
this.isotopes.add(isotope.withElement(this));
}
this.group = group;
}
public double getMonoisotopicMass() {
if (isotopes.isEmpty()) return 0;
Iterator<Isotope> isotopeIterator = isotopes.iterator();
Isotope isotope;
Isotope mostAbundant = isotopeIterator.next();
while (isotopeIterator.hasNext()) {
isotope = isotopeIterator.next();
if (isotope.getAbundance() > mostAbundant.getAbundance()) {
mostAbundant = isotope;
}
}
return mostAbundant.getMass();
}
public double getVariance() {
double average = getAverageMass();
double difference;
double variance = 0;
double totalAbundance = 0;
Iterator<Isotope> isotopeIterator = isotopes.iterator();
Isotope isotope;
while (isotopeIterator.hasNext()) {
isotope = isotopeIterator.next();
difference = isotope.getMass() - average;
variance += difference * difference * isotope.getAbundance();
totalAbundance += isotope.getAbundance();
}
return variance / totalAbundance;
}
public double getAverageMass() {
double mass = 0;
Iterator<Isotope> isotopeIterator = isotopes.iterator();
Isotope isotope;
if (isNaturallyOccurring()) {
while (isotopeIterator.hasNext()) {
isotope = isotopeIterator.next();
mass += isotope.getMass() * isotope.getAbundance();
}
return mass;
}
while (isotopeIterator.hasNext()) {
isotope = isotopeIterator.next();
mass += isotope.getMass();
}
return mass / isotopes.size();
}