/**
* Checks if each next {@link ILigand} is different from the previous one according to the {@link
* CIPLigandRule}. It assumes that the input is sorted based on that rule.
*
* @param ligands array of {@link ILigand} to check
* @return true, if all ligands are different
*/
@TestMethod("testCheckIfAllLigandsAreDifferent,testCheckIfAllLigandsAreDifferent_False")
public static boolean checkIfAllLigandsAreDifferent(ILigand[] ligands) {
for (int i = 0; i < (ligands.length - 1); i++) {
if (cipRule.compare(ligands[i], ligands[i + 1]) == 0) return false;
}
return true;
}
/**
* Obtain the permutation parity (-1,0,+1) to put the ligands in descending order (highest first).
* A parity of 0 indicates two or more ligands were equivalent.
*
* @param ligands the ligands to sort
* @return parity, odd (-1), even (+1) or none (0)
*/
private static int permParity(final ILigand[] ligands) {
// count the number of swaps made by insertion sort - if duplicates
// are fount the parity is 0
int swaps = 0;
for (int j = 1, hi = ligands.length; j < hi; j++) {
ILigand ligand = ligands[j];
int i = j - 1;
int cmp = 0;
while ((i >= 0) && (cmp = cipRule.compare(ligand, ligands[i])) > 0) {
ligands[i + 1] = ligands[i--];
swaps++;
}
if (cmp == 0) // identical entries
return 0;
ligands[i + 1] = ligand;
}
// odd (-1) or even (+1)
return (swaps & 0x1) == 0x1 ? -1 : +1;
}