@Override
protected Align clone() {
Align a = new Align();
a.indexInAlignment = indexInAlignment;
a.hit_index = hit_index;
a.query_index = query_index;
return a;
}
@Override
public Align next() {
if (curr.indexInAlignment >= owner().getAlignLength()) {
throw new IllegalStateException();
}
Align ret = curr.clone();
char ch = curr.getHitChar();
char cq = curr.getQueryChar();
if (ch != '-' && ch != ' ') {
curr.hit_index += hitShift();
}
if (cq != '-' && cq != ' ') {
curr.query_index++;
}
++curr.indexInAlignment;
return ret;
}
MyIterator() {
curr = new Align();
curr.query_index = owner().getQueryFrom1();
curr.hit_index = owner().getHitFrom1();
curr.indexInAlignment = 0;
}
