/** Sets up all parameters with target Graph target */
public MoleculeParameters(Molecule target) {
// automatically set initial individuals size range
int vertices = target.getVerticesSize();
verticesInterval.set(Math.max(2, vertices / 2), vertices * 2);
cyclesInterval.set(0, target.getNumberOfCycles() * 2);
// insure that all possible vertex and edge types are in initial population in roughly equal
// quantities
java.util.Hashtable elements = new java.util.Hashtable();
for (VertexIterator v = target.getVertexIterator(); v.more(); v.next()) {
String s = v.vertex().toString();
if (!elements.containsKey(s)) {
elements.put(s, s);
try {
provider.add((Vertex) v.vertex().clone());
} catch (CloneNotSupportedException e) {
Error.fatal("can't clone vertex: " + e);
}
}
}
for (EdgeIterator e = target.getEdgeIterator(); e.more(); e.next()) {
String s = e.edge().toString();
if (!elements.containsKey(s)) {
elements.put(s, s);
try {
provider.add((Edge) e.edge().clone());
} catch (CloneNotSupportedException ee) {
Error.fatal("can't clone edge: " + ee);
}
}
}
setParameters(target);
}
private static void buildAtomicNumberTable() {
elementHashtable = new Hashtable(223); // 223 is a nice prime number
if (elementAr == null) {
System.out.println("Error! elementAr has not been initialized!");
Error.fatal("Element: elementAr has not been initialized!");
}
for (int i = 0; i < symbolAr.length; i++) {
elementHashtable.put(symbolAr[i], new Element(i));
}
}