/**
* @param linkages
* @param atomLinkages
* @return true if atomLinkages satisfy the condition; false, otherwise.
*/
private boolean matchLinkages(List<ModificationLinkage> linkages, List<Atom[]> atomLinkages) {
int nLink = linkages.size();
if (nLink != atomLinkages.size()) {
return false;
}
for (int i = 0; i < nLink - 1; i++) {
ModificationLinkage link1 = linkages.get(i);
Atom[] atoms1 = atomLinkages.get(i);
for (int j = i + 1; j < nLink; j++) {
ModificationLinkage link2 = linkages.get(j);
Atom[] atoms2 = atomLinkages.get(j);
// check components
if (((link1.getIndexOfComponent1() == link2.getIndexOfComponent1())
!= (atoms1[0].getGroup().equals(atoms2[0].getGroup())))
|| ((link1.getIndexOfComponent1() == link2.getIndexOfComponent2())
!= (atoms1[0].getGroup().equals(atoms2[1].getGroup())))
|| ((link1.getIndexOfComponent2() == link2.getIndexOfComponent1())
!= (atoms1[1].getGroup().equals(atoms2[0].getGroup())))
|| ((link1.getIndexOfComponent2() == link2.getIndexOfComponent2())
!= (atoms1[1].getGroup().equals(atoms2[1].getGroup())))) {
return false;
}
// check atoms
String label11 = link1.getLabelOfAtomOnComponent1();
String label12 = link1.getLabelOfAtomOnComponent2();
String label21 = link2.getLabelOfAtomOnComponent1();
String label22 = link2.getLabelOfAtomOnComponent2();
if ((label11 != null && label21 != null && label11.equals(label21))
!= (atoms1[0].equals(atoms2[0]))
|| (label11 != null && label22 != null && label11.equals(label22))
!= (atoms1[0].equals(atoms2[1]))
|| (label12 != null && label21 != null && label12.equals(label21))
!= (atoms1[1].equals(atoms2[0]))
|| (label12 != null && label22 != null && label12.equals(label22))
!= (atoms1[1].equals(atoms2[1]))) {
return false;
}
}
}
return true;
}
