/** Overhang scars helper * */
private ArrayList<String> assignScarsHelper(RNode parent, ArrayList<RNode> children) {
ArrayList<String> scars = new ArrayList<String>();
// Loop through each one of the children to assign rule-instructed overhangs... enumerated
// numbers currently
for (int i = 0; i < children.size(); i++) {
RNode child = children.get(i);
if (i > 0) {
if (child.getLOverhang().isEmpty()) {
scars.add("_");
}
scars.add("BB");
}
// Make recursive call
if (child.getStage() > 0) {
// Remove the current parent from the list
ArrayList<RNode> grandChildren = new ArrayList<RNode>();
grandChildren.addAll(child.getNeighbors());
if (grandChildren.contains(parent)) {
grandChildren.remove(parent);
}
ArrayList<String> childScars = assignScarsHelper(child, grandChildren);
scars.addAll(childScars);
} else {
ArrayList<String> childScars = new ArrayList<String>();
if (child.getComposition().size() > 1) {
if (!child.getScars().isEmpty()) {
childScars.addAll(child.getScars());
} else {
for (int j = 0; j < child.getComposition().size() - 1; j++) {
childScars.add("_");
}
child.setScars(childScars);
}
}
scars.addAll(childScars);
}
}
// Keep scars for re-used parts with scars
if (!scars.isEmpty()) {
parent.setScars(scars);
return scars;
} else {
return parent.getScars();
}
}
