import java.util.*;

// T J Finney, 2001
// Not to be sold without my permission.

class Scribe {

	// static methods
	
	// copy MS
	// acc = prob. of making an accurate copy (per unit)
	// If not accurate, scribe will insert existing reading or novel reading.
	// Prob. of adding novel reading is 1 / s^n, where s is number of states
	// and n is a suitable exponent. E.g., for n = 2,
	// s     1     2     3     4     5
	// p     1.00  0.25  0.11  0.07  0.04
	// Thanks to J R Adair for this idea.
	public static MS copy (MS source, double acc) {
		MS target = new MS (source.getAncestry());
		int num = MS.getSize();
		for (int i = 0; i < num; i++) {
			if (Stats.trial(acc)) {
				// accurate: transfer source reading
				target.setUnit(i, source.getUnit(i));
			} else {
				// inaccurate: insert different reading
				// calculate probability of novel reading
				double nov = Math.pow((double) MS.howManyStates(i), -1.5);
				if (Stats.trial(nov)) {
					// create novel reading
					target.setUnit(i, MS.addState(i));
				} else {
					// create novel reading if no others
					if (MS.howManyStates(i) == 1) {
						MS.addState(i);
					}
					// select existing reading besides current one
					int current = source.getUnit(i);
					int existing = current;
					while (current == existing) {
						existing = MS.getState(i);
					}
					target.setUnit(i, existing);
				}
			}
		}
		return target;
	}
	
	// correct MS
	public static void correct (MS ms, MS source) {
		// get prob. of correcting difference
		double corr = Stats.getRand();
		int num = MS.getSize();
		for (int i = 0; i < num; i++) {
			if (Stats.trial(corr)) {
				ms.setUnit(i, source.getUnit(i));
			}
		}
	}
	
	// main: test
	public static void main (String [] args) {
		
		MS.initStates();
		
		MS ms1 = MS.makeArchetype();
		MS[] ms = new MS[10];
		System.out.println("copy() ten times");
		ms[0] = ms1;
		ms[0].print();
		for (int i = 1; i < 10; i++) {
			ms[i] = Scribe.copy(ms[i - 1], 0.5);
			ms[i].print();
		}
		
		System.out.println("correct()");
		for (int i = 0; i < 10; i++) {
			Scribe.correct(ms[i], ms1);
			ms[i].print();
		}
	}
}