Implementation of a homogeneous Markov model of order 0 based on AbstractModel

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import java.util.Arrays;

import de.jstacs.NonParsableException;
import de.jstacs.NotTrainedException;
import de.jstacs.models.AbstractModel;
import de.jstacs.results.NumericalResult;
import de.jstacs.results.NumericalResultSet;

public class HomogeneousMarkovModel extends AbstractModel {

	private double[] logProbs;//array for the parameters, i.e. the probabilities for each symbol
	private boolean isTrained;//stores if the model has been trained

	public HomogeneousMarkovModel( AlphabetContainer alphabets ) throws Exception {
		super( alphabets, 0 ); //we have a homogeneous Model, hence the length is set to 0
		//a homogeneous Model can only handle simple alphabets
		if(! (alphabets.isSimple() && alphabets.isDiscrete()) ){
			throw new Exception("Only simple and discrete alphabets allowed");
		//initialize parameter array
		this.logProbs = new double[(int) alphabets.getAlphabetLengthAt( 0 )];
		isTrained = false; //we have not trained the model, yet

	public HomogeneousMarkovModel( StringBuffer stringBuff ) throws NonParsableException { 
            super( stringBuff ); 

	protected void fromXML( StringBuffer xml ) throws NonParsableException {
		//extract our XML-code
		xml = XMLParser.extractForTag( xml, "homogeneousMarkovModel" );
		//extract all the variables using XMLParser
		alphabets = (AlphabetContainer) XMLParser.extractStorableForTag( xml, "alphabets" );
		length = XMLParser.extractIntForTag( xml, "length" );
		logProbs = XMLParser.extractDoubleArrayForTag( xml, "logProbs" );
		isTrained = XMLParser.extractBooleanForTag( xml, "isTrained" );

	public StringBuffer toXML() {
		StringBuffer buf = new StringBuffer();
		//pack all the variables using XMLParser
		XMLParser.appendStorableWithTags( buf, alphabets, "alphabets" );
		XMLParser.appendIntWithTags( buf, length, "length" );
		XMLParser.appendDoubleArrayWithTags( buf, logProbs, "logProbs" );
		XMLParser.appendBooleanWithTags( buf, isTrained, "isTrained" );
		//add our own tag
		XMLParser.addTags( buf, "homogeneousMarkovModel" );
		return buf;

	public String getInstanceName() { 
            return "Homogeneous Markov model of order 0"; 

	public double getLogPriorTerm() throws Exception { 
            //we use ML-estimation, hence no prior term
            return 0; 

	public NumericalResultSet getNumericalCharacteristics() throws Exception {
		//we do not have much to tell here
		return new NumericalResultSet(new NumericalResult("Number of parameters","The number of parameters this model uses",logProbs.length));

	public double getLogProbFor( Sequence sequence, int startpos, int endpos ) throws NotTrainedException, Exception {
		double seqLogProb = 0.0;
		//compute the log-probability of the sequence between startpos and endpos (inclusive)
		//as sum of the single symbol log-probabilities
		for(int i=startpos;i<=endpos;i++){
			//directly access the array by the numerical representation of the symbols
			seqLogProb += logProbs[sequence.discreteVal( i )];
		return seqLogProb;
	public double getProbFor( Sequence sequence, int startpos, int endpos ) throws NotTrainedException, Exception {
		return Math.exp( getLogProbFor(sequence, startpos, endpos) );

	public boolean isTrained() { 
            return isTrained; 

	public void train( Sample data, double[] weights ) throws Exception {
		//reset the parameter array
		Arrays.fill( logProbs, 0.0 );
		//default sequence weight
		double w = 1;
		//for each sequence in the data set
		for(int i=0;i<data.getNumberOfElements();i++){
			//retrieve sequence
			Sequence seq = data.getElementAt( i );
			//if we do have any weights, use them
			if(weights != null){
				w = weights[i];
			//for each position in the sequence
			for(int j=0;j<seq.getLength();j++){
				//count symbols, weighted by weights
				logProbs[ seq.discreteVal( j ) ] += w;
		//compute normalization
		double norm = 0.0;
		for(int i=0;i<logProbs.length;i++){ norm += logProbs[i]; }
		//normalize probs to obtain proper probabilities
		for(int i=0;i<logProbs.length;i++){ logProbs[i] = Math.log( logProbs[i]/norm ); }
		//now the model is trained
		isTrained = true;