public void remove(Atom atom) {
SimpleIterator<Atom> it = newIterator();
for (it.moveToBeginning(); !it.isAtEnd() && it.getElement() != atom; it.next()) {}
if (!it.isAtEnd()) {
it.remove();
}
}
/**
* @param atom
* @return true if atom belongs to this solution
*/
public boolean contains(Atom atom) {
boolean contain = false;
SimpleIterator<Atom> it = newIterator();
while (!it.isAtEnd()) {
if (it.getElement().equals(atom)) {
contain = true;
break;
}
it.next();
}
return contain;
}
/**
* Compares two molecules modulo associativity and commutativity, and takes into account
* multiplicities
*
* @param molecule
* @return true if this molecule is the same to the molecule given
*/
public boolean equals(Molecule molecule) {
SimpleIterator<Atom> it1 = newIterator();
SimpleIterator<Atom> it2 = molecule.newIterator();
// following array records already checked atoms (because of multiplicities
// > 1)
boolean[] checked = new boolean[molecule.size()];
for (int i = 0; i < checked.length; i++) {
checked[i] = false;
}
boolean equals;
int j;
if (size() != molecule.size()) {
equals = false;
} else {
it1.moveToBeginning();
equals = true;
while (!it1.isAtEnd() && equals) {
it2.moveToBeginning();
j = 0;
while (!it2.isAtEnd() && (checked[j] || !it2.getElement().equals(it1.getElement()))) {
it2.next();
j++;
}
if (it2.isAtEnd()) {
// it1.getElement() not found in molecule (taking multiplicities into
// account)
equals = false;
} else {
checked[j] = true;
}
it1.next();
}
}
return equals;
}
// public class Molecule extends SimpleLinkedList<Atom> {
public String toString() {
SimpleIterator<Atom> it = newIterator();
String s = "";
while (!it.isAtEnd()) {
s = s + it.getElement();
if (it.hasNext()) {
s = s + ",";
}
it.next();
}
if (s.length() == 0) {
s = ""; // empty molecule
}
return s;
}