StringEditModelWithJumps.html

StringEditModelWithJumps.java

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package blog.distrib;

import java.util.*;

Subclass of StringEditModel that allows "jumps", that is, deletions of whole substrings of the original string (rather than just single characters). This is an abstract class. Subclasses must override the initJumps method to specify what jumps are allowed in a given input string, and what their probabilities are.


public abstract class StringEditModelWithJumps extends StringEditModel {

    public StringEditModelWithJumps() {
    }

    public StringEditModelWithJumps(List params) {
	super(params);
    }

    protected double getProbInternal(String input, String output) {
	arrivingJumps = new List[input.length() + 1];
	nonJumpProb = new double[input.length() + 1];
	Arrays.fill(nonJumpProb, 1.0);
	initJumps(input);

	// p[i][n] = P(at some time, scribe has written i characters and his 
        //             finger is before character n of the input)
	double[][] p = new double[output.length() + 1][input.length() + 1];

	p[0][0] = 1; // other entries automatically initialized to 0
	for (int n = 0; n <= input.length(); n++) {
	    for (int i = 0; i <= output.length(); i++) {
		// Ways of generating i characters of output (indexed 0 
		// through i-1) using input characters before position n
				
		// First way: generate i-1 characters using input before 
		// position n-1, then generate output[i-1] using input[n-1]
		if ((n > 0) && (i > 0)) {
		    p[i][n] += (p[i-1][n-1] * nonJumpProb[n-1] *
				probSubst(input, n-1, output, i-1, 
					  output.charAt(i-1)));
		}

		// Second way: generate i characters using input before 
		// position n-1, then do a deletion, skipping input[n-1]
		if (n > 0) {
		    p[i][n] += (p[i][n-1] * nonJumpProb[n-1] * 
				probDelete(input, n-1, output, i));
		}

		// Third way: generate i-1 characters using input before
		// position n, then generate output[i-1] by insertion
		if (i > 0) {
		    p[i][n] += (p[i-1][n] * nonJumpProb[n] * 
				probInsert(input, n, output, i-1, 
					   output.charAt(i-1)));
		}

		// Fourth way: generate i characters using input before 
		// position m, then do a jump from m to n
		if (arrivingJumps[n] != null) {
		    for (Iterator iter = arrivingJumps[n].iterator(); 
			 iter.hasNext(); ) {
			Jump jump = (Jump) iter.next();
			p[i][n] += (p[i][jump.origin] * jump.prob);
		    }
		}
	    }
	}

	// To generate the given output string, scribe must write it down and 
	// have his finger after the last input character, *and* decide to 
	// stop.
	return (p[output.length()][input.length()] * 
		probStop(input, input.length(), output, output.length())); 
    }

Figures out what jumps are allowed for the given input string, and calls addJump for each one.


    protected abstract void initJumps(String input);

Allows a jump from before character origin to before character dest, with probability prob. The destination must be greater than the origin. For any origin, the jump probabilities should sum to something <= 1.0; the remaining probability is distributed over non-jump moves. If you add several jumps from an origin to the same destination, the probabilities are added together.


    protected void addJump(int origin, int dest, double prob) {
	if (origin >= dest) {
	    throw new IllegalArgumentException("Origin " + origin 
					       + " greater than or equal to "
					       + "destination " + dest + ".");
	}

	nonJumpProb[origin] -= prob;
	if (nonJumpProb[origin] < 0) {
	    throw new IllegalArgumentException("Sum of jump probabilities "
					       + "from before character " 
					       + origin + " is > 1.0.");
	}
		
	if (arrivingJumps[dest] == null) {
	    arrivingJumps[dest] = new ArrayList();
	}
	arrivingJumps[dest].add(new Jump(origin, prob));
    }

    private static class Jump {
	public int origin;
	public double prob;

	public Jump(int origin, double prob) {
	    this.origin = origin;
	    this.prob = prob;
	}
    }

    private List[] arrivingJumps; // each List contains Jump objects
    private double[] nonJumpProb;
}

This file was generated on Tue Jun 08 17:53:47 PDT 2010 from file StringEditModelWithJumps.java
by the ilog.language.tools.Hilite Java tool written by Hassan Aït-Kaci