// ## operation getMatchedFunctionalGroup(LinkedList)
public LinkedList getMatchedFunctionalGroup(LinkedList p_reactants) {
// #[ operation getMatchedFunctionalGroup(LinkedList)
LinkedList fgCollection = new LinkedList();
boolean found = false;
Iterator r_iter = p_reactants.iterator();
while (r_iter.hasNext()) {
found = false;
Object o = r_iter.next();
ChemGraph cg = null;
if (o instanceof Species) cg = ((Species) r_iter.next()).getChemGraph();
else cg = (ChemGraph) o;
Iterator t_iter = reactantTree.iterator();
while (t_iter.hasNext()) {
HierarchyTree t = (HierarchyTree) t_iter.next();
Stack s = t.findMatchedPath(cg);
if (s != null && !s.isEmpty()) {
found = true;
fgCollection.add(s);
}
}
if (!found) {
// System.out.println("can't find matched path: " + cg.toString());
// System.exit(0);
return null;
}
}
return fgCollection;
// #]
}
// Constructors
// ## operation StructureTemplate(Matchable,Matchable)
public StructureTemplate(Matchable p_reactant1, Matchable p_reactant2) {
{
reactantTree = new ArrayList();
}
// #[ operation StructureTemplate(Matchable,Matchable)
reactants.add(p_reactant1);
if (p_reactant2 != null) reactants.add(p_reactant2);
// #]
}
// ## operation getAllowedFunctionalGroupAt(int)
public Matchable getAllowedFunctionalGroupAt(int p_index) {
// #[ operation getAllowedFunctionalGroupAt(int)
Matchable t = (Matchable) (reactants.get(p_index - 1));
if (t == null) return null;
return t;
// #]
}
// ## operation generateReverse(ReactionAdjList)
public StructureTemplate generateReverse(ReactionAdjList p_reactionAdjList) {
// #[ operation generateReverse(ReactionAdjList)
int r_num = getReactantNumber();
Matchable r1 = getAllowedFunctionalGroupAt(1);
LinkedList reactant = new LinkedList();
reactant.add(r1);
if (r_num == 2) {
Matchable r2 = getAllowedFunctionalGroupAt(2);
reactant.add(r2);
}
LinkedList reverse = p_reactionAdjList.reactFunctionalGroup(reactant);
StructureTemplate reverseRT = new StructureTemplate(reverse);
reverseRT.reactantTree = this.reactantTree;
return reverseRT;
// #]
}
// ## operation StructureTemplate(Matchable)
public StructureTemplate(Matchable p_reactant) {
{
reactantTree = new ArrayList();
}
// #[ operation StructureTemplate(Matchable)
reactants.add(p_reactant);
// #]
}
// ## operation setReactant(int,LinkedHashSet)
public void setReactant(int p_position, LinkedHashSet p_reactantFGSet) {
// #[ operation setReactant(int,LinkedHashSet)
reactants.add(p_position, p_reactantFGSet);
// #]
}
// ## operation getReactants()
public Iterator getReactants() {
// #[ operation getReactants()
Iterator iter = reactants.iterator();
return iter;
// #]
}
// ## operation getReactantNumber()
public int getReactantNumber() {
// #[ operation getReactantNumber()
return reactants.size();
// #]
}