de.jstacs.sequenceScores.statisticalModels.trainable

Class UniformTrainSM

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

de.jstacs.sequenceScores.statisticalModels.trainable.UniformTrainSM

All Implemented Interfaces:

SequenceScore, StatisticalModel, TrainableStatisticalModel, Storable, Cloneable

public class UniformTrainSM
extends AbstractTrainableStatisticalModel

This class represents a uniform model. Sometimes it's also called uninformed model. It can be used if nothing is known about a statistical process.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

alphabets, length

Constructor Summary

Constructors

Constructor and Description
UniformTrainSM(AlphabetContainer alphabet) Creates a new UniformTrainSM using a given AlphabetContainer.
UniformTrainSM(StringBuffer stringBuff) The standard constructor for the interface Storable.

Method Summary

Methods

Modifier and Type	Method and Description
UniformTrainSM	clone() Follows the conventions of Object's clone()-method.
DataSet	emitDataSet(int n, int... lengths) This method returns a DataSet object containing artificial sequence(s).
void	fromXML(StringBuffer representation) This method should only be used by the constructor that works on a StringBuffer.
String	getInstanceName() Should return a short instance name such as iMM(0), BN(2), ...
double	getLogPriorTerm() Returns a value that is proportional to the log of the prior.
double	getLogProbFor(Sequence sequence, int startpos, int endpos) Returns the logarithm of the probability of (a part of) the given sequence given the model.
byte	getMaximalMarkovOrder() This method returns the maximal used Markov order, if possible.
NumericalResultSet	getNumericalCharacteristics() Returns the subset of numerical values that are also returned by SequenceScore.getCharacteristics().
boolean	isInitialized() Returns true if the model is trained, false otherwise.
String	toString(NumberFormat nf) Returns the String "".
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.
void	train(DataSet data, double[] weights) Deprecated.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.AbstractTrainableStatisticalModel

check, getAlphabetContainer, getCharacteristics, getLength, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, toString, train

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

UniformTrainSM

public UniformTrainSM(AlphabetContainer alphabet)

Creates a new UniformTrainSM using a given AlphabetContainer.

Parameters:

alphabet - the alphabets used in the model

UniformTrainSM

public UniformTrainSM(StringBuffer stringBuff)
               throws NonParsableException

The standard constructor for the interface Storable. Creates a new UniformTrainSM out of a StringBuffer.

Parameters:

stringBuff - the StringBuffer to be parsed

Throws:

NonParsableException - if the StringBuffer is not parsable

Method Detail

clone

public UniformTrainSM clone()
                     throws CloneNotSupportedException

Description copied from class: AbstractTrainableStatisticalModel

Follows the conventions of Object's clone()-method.

Specified by:

clone in interface SequenceScore

Specified by:

clone in interface TrainableStatisticalModel

Overrides:

clone in class AbstractTrainableStatisticalModel

Returns:

an object, that is a copy of the current AbstractTrainableStatisticalModel (the member-AlphabetContainer isn't deeply cloned since it is assumed to be immutable). The type of the returned object is defined by the class X directly inherited from AbstractTrainableStatisticalModel. Hence X's clone()-method should work as:
1. Object o = (X)super.clone();
2. all additional member variables of o defined by X that are not of simple data-types like int, double, ... have to be deeply copied
3. return o

Throws:

CloneNotSupportedException - if something went wrong while cloning

getLogProbFor

public double getLogProbFor(Sequence sequence,
                   int startpos,
                   int endpos)
                     throws IllegalArgumentException,
                            WrongAlphabetException

Description copied from interface: StatisticalModel

Returns the logarithm of the probability of (a part of) the given sequence given the model. If at least one random variable is continuous the value of density function is returned.

It extends the possibility given by the method StatisticalModel.getLogProbFor(Sequence, int) by the fact, that the model could be e.g. homogeneous and therefore the length of the sequences, whose probability should be returned, is not fixed. Additionally, the end position of the part of the given sequence is given and the probability of the part from position startpos to endpos (inclusive) should be returned.
The length and the alphabets define the type of data that can be modeled and therefore both has to be checked.

Parameters:

sequence - the given sequence

startpos - the start position within the given sequence

endpos - the last position to be taken into account

Returns:

the logarithm of the probability or the value of the density function of (the part of) the given sequence given the model

Throws:

IllegalArgumentException

WrongAlphabetException

isInitialized

public boolean isInitialized()

Returns true if the model is trained, false otherwise.

Returns:

true if the model is trained, false otherwise

fromXML

public void fromXML(StringBuffer representation)
             throws NonParsableException

Description copied from class: AbstractTrainableStatisticalModel

This method should only be used by the constructor that works on a StringBuffer. It is the counter part of Storable.toXML().

Specified by:

fromXML in class AbstractTrainableStatisticalModel

Parameters:

representation - the XML representation of the model

Throws:

NonParsableException - if the StringBuffer is not parsable or the representation is conflicting

See Also:

AbstractTrainableStatisticalModel.AbstractTrainableStatisticalModel(StringBuffer)

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Returns:

the XML representation

toString

public String toString(NumberFormat nf)

Returns the String "".

Parameters:

nf - the NumberFormat for the String representation of parameters or probabilities

Returns:

a String representation of the instance

train

@Deprecated
public void train(DataSet data,
                    double[] weights)
           throws IOException

Deprecated.

Description copied from interface: TrainableStatisticalModel

Trains the TrainableStatisticalModel object given the data as DataSet using the specified weights. The weight at position i belongs to the element at position i. So the array weight should have the number of sequences in the data set as dimension. (Optionally it is possible to use weight == null if all weights have the value one.)
This method should work non-incrementally. That means the result of the following series: train(data1); train(data2) should be a fully trained model over data2 and not over data1+data2. All parameters of the model were given by the call of the constructor.

Parameters:

data - the given sequences as DataSet

weights - the weights of the elements, each weight should be non-negative

Throws:

IOException

See Also:

DataSet.getElementAt(int), DataSet.ElementEnumerator

emitDataSet

public DataSet emitDataSet(int n,
                  int... lengths)
                    throws Exception

Description copied from interface: StatisticalModel

This method returns a DataSet object containing artificial sequence(s).

There are two different possibilities to create a data set for a model with length 0 (homogeneous models).

1. emitDataSet( int n, int l ) should return a data set with n sequences of length l.
2. emitDataSet( int n, int[] l ) should return a data set with n sequences which have a sequence length corresponding to the entry in the given array l.

There are two different possibilities to create a data set for a model with length greater than 0 (inhomogeneous models).
emitDataSet( int n ) and emitDataSet( int n, null ) should return a data set with n sequences of length of the model ( SequenceScore.getLength()).

The standard implementation throws an Exception.

Specified by:

emitDataSet in interface StatisticalModel

Overrides:

emitDataSet in class AbstractTrainableStatisticalModel

Parameters:

n - the number of sequences that should be contained in the returned data set

lengths - the length of the sequences for a homogeneous model; for an inhomogeneous model this parameter should be null or an array of size 0.

Returns:

a DataSet containing the artificial sequence(s)

Throws:

Exception - if the emission did not succeed

NotTrainedException - if the model is not trained yet

See Also:

DataSet

getLogPriorTerm

public double getLogPriorTerm()
                       throws Exception

Description copied from interface: StatisticalModel

Returns a value that is proportional to the log of the prior. For maximum likelihood (ML) 0 should be returned.

Returns:

a value that is proportional to the log of the prior

Throws:

Exception - if something went wrong

getMaximalMarkovOrder

public byte getMaximalMarkovOrder()
                           throws UnsupportedOperationException

Description copied from interface: StatisticalModel

This method returns the maximal used Markov order, if possible.

Specified by:

getMaximalMarkovOrder in interface StatisticalModel

Overrides:

getMaximalMarkovOrder in class AbstractTrainableStatisticalModel

Returns:

maximal used Markov order

Throws:

UnsupportedOperationException - if the model can't give a proper answer

getNumericalCharacteristics

public NumericalResultSet getNumericalCharacteristics()
                                               throws Exception

Description copied from interface: SequenceScore

Returns the subset of numerical values that are also returned by SequenceScore.getCharacteristics().

Returns:

the numerical characteristics of the current instance

Throws:

Exception - if some of the characteristics could not be defined

getInstanceName

public String getInstanceName()

Description copied from interface: SequenceScore

Should return a short instance name such as iMM(0), BN(2), ...

Returns:

a short instance name