Saving and loading a model

//create a Sample for each class from the input data, using the DNA alphabet
Sample[] data = new Sample[2];
data[0] = new DNASample( args[0] );

//the length of our input sequences
int length = data[0].getElementLength();

data[1] = new Sample( new DNASample( args[1] ), length );
 
//create a new PWM
BayesianNetworkModel pwm = new BayesianNetworkModel( new BayesianNetworkModelParameterSet(
		//the alphabet and the length of the model:
		data[0].getAlphabetContainer(), length, 
		//the equivalent sample size to compute hyper-parameters
		4, 
		//some identifier for the model
		"my PWM", 
		//we want a PWM, which is an inhomogeneous Markov model (IMM) of order 0
		ModelType.IMM, (byte) 0, 
		//we want to estimate the MAP-parameters
		LearningType.ML_OR_MAP ) );
 
//create a new classifier
ModelBasedClassifier classifier = new ModelBasedClassifier( pwm, pwm );
 
//train the classifier
classifier.train( data );
 
//create the XML-representation of the classifier
StringBuffer buf = classifier.toXML();
 
//write it to disk
FileManager.writeFile( new File(home+"myClassifier.xml"), buf );
 
//read XML-representation from disk
StringBuffer buf2 = FileManager.readFile( new File(home+"myClassifier.xml") );
 
//create new classifier from read StringBuffer containing XML-code
ModelBasedClassifier loaded = new ModelBasedClassifier(buf2);