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de.jstacs.sequenceScores.differentiable
Class UniformDiffSS

java.lang.Object
  extended by de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
      extended by de.jstacs.sequenceScores.differentiable.UniformDiffSS
All Implemented Interfaces:
DifferentiableSequenceScore, SequenceScore, Storable, Cloneable
Direct Known Subclasses:
UniformDiffSM
public class UniformDiffSS
extends AbstractDifferentiableSequenceScore

This DifferentiableSequenceScore does nothing. So it is possible to save parameters in an optimization.

Author:
Jens Keilwagen, Jan Grau

Field Summary
 
Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
alphabets, length, r
 
Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore
UNKNOWN
 
Constructor Summary
UniformDiffSS(AlphabetContainer alphabets, int length)
          This is the main constructor that creates an instance of a UniformDiffSS that models each sequence uniformly.
UniformDiffSS(StringBuffer xml)
          This is the constructor for the interface Storable.
 
Method Summary
protected  void extractFurtherInformation(StringBuffer xml)
          This method is the opposite of getFurtherInformation().
protected  void fromXML(StringBuffer xml)
          This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.
 double[] getCurrentParameterValues()
          Returns a double array of dimension DifferentiableSequenceScore.getNumberOfParameters() containing the current parameter values.
protected  StringBuffer getFurtherInformation()
          This method is used to append further information of the instance to the XML representation.
 String getInstanceName()
          Should return a short instance name such as iMM(0), BN(2), ...
 double getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList)
          Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.
 double getLogScoreFor(Sequence seq, int start)
          Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
 int getNumberOfParameters()
          Returns the number of parameters in this DifferentiableSequenceScore.
 void initializeFunction(int index, boolean meila, DataSet[] data, double[][] weights)
          This method creates the underlying structure of the DifferentiableSequenceScore.
 void initializeFunctionRandomly(boolean freeParams)
          This method initializes the DifferentiableSequenceScore randomly.
 boolean isInitialized()
          This method can be used to determine whether the instance is initialized.
 void setParameters(double[] params, int start)
          This method sets the internal parameters to the values of params between start and start + DifferentiableSequenceScore.getNumberOfParameters() - 1
 String toString(NumberFormat nf)
          This method returns a String representation of the instance.
 StringBuffer toXML()
          This method returns an XML representation as StringBuffer of an instance of the implementing class.
 
Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
clone, getAlphabetContainer, getCharacteristics, getInitialClassParam, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumberOfRecommendedStarts, getNumberOfStarts, getNumericalCharacteristics
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

UniformDiffSS

public UniformDiffSS(AlphabetContainer alphabets,
                     int length)
This is the main constructor that creates an instance of a UniformDiffSS that models each sequence uniformly.

Parameters:
alphabets - the AlphabetContainer
length - the length of the modeled sequences

UniformDiffSS

public UniformDiffSS(StringBuffer xml)
              throws NonParsableException
This is the constructor for the interface Storable. Creates a new UniformDiffSS out of its XML representation as returned by fromXML(StringBuffer).

Parameters:
xml - the XML representation as StringBuffer
Throws:
NonParsableException - if the XML representation could not be parsed
Method Detail

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

getLogScoreFor

public double getLogScoreFor(Sequence seq,
                             int start)
Description copied from interface: SequenceScore
Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.

Parameters:
seq - the Sequence
start - the start position in the Sequence
Returns:
the logarithmic score for the Sequence

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(Sequence seq,
                                              int start,
                                              IntList indices,
                                              DoubleList dList)
Description copied from interface: DifferentiableSequenceScore
Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.

Parameters:
seq - the Sequence
start - the start position in the Sequence
indices - an IntList of indices, after method invocation the list should contain the indices i where $\frac{\partial \log score(seq)}{\partial \lambda_i}$ is not zero
dList - a DoubleList of partial derivations, after method invocation the list should contain the corresponding $\frac{\partial \log score(seq)}{\partial \lambda_i}$ that are not zero
Returns:
the logarithmic score for the Sequence

getNumberOfParameters

public int getNumberOfParameters()
Description copied from interface: DifferentiableSequenceScore
Returns the number of parameters in this DifferentiableSequenceScore. If the number of parameters is not known yet, the method returns DifferentiableSequenceScore.UNKNOWN.

Returns:
the number of parameters in this DifferentiableSequenceScore
See Also:
DifferentiableSequenceScore.UNKNOWN

setParameters

public void setParameters(double[] params,
                          int start)
Description copied from interface: DifferentiableSequenceScore
This method sets the internal parameters to the values of params between start and start + DifferentiableSequenceScore.getNumberOfParameters() - 1

Parameters:
params - the new parameters
start - the start index in params

getFurtherInformation

protected StringBuffer getFurtherInformation()
This method is used to append further information of the instance to the XML representation. This method is designed to allow subclasses to add information to the XML representation.

Returns:
the further information as XML code in a StringBuffer
See Also:
extractFurtherInformation(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

extractFurtherInformation

protected void extractFurtherInformation(StringBuffer xml)
                                  throws NonParsableException
This method is the opposite of getFurtherInformation(). It extracts further information of the instance from a XML representation.

Parameters:
xml - the StringBuffer containing the information to be extracted as XML code
Throws:
NonParsableException - if the StringBuffer could not be parsed
See Also:
getFurtherInformation()

fromXML

protected void fromXML(StringBuffer xml)
                throws NonParsableException
Description copied from class: AbstractDifferentiableSequenceScore
This method is called in the constructor for the Storable interface to create a scoring function from a StringBuffer.

Specified by:
fromXML in class AbstractDifferentiableSequenceScore
Parameters:
xml - the XML representation as StringBuffer
Throws:
NonParsableException - if the StringBuffer could not be parsed
See Also:
AbstractDifferentiableSequenceScore.AbstractDifferentiableSequenceScore(StringBuffer)

toString

public String toString(NumberFormat nf)
Description copied from interface: SequenceScore
This method returns a String representation of the instance.

Parameters:
nf - the NumberFormat for the String representation of parameters or probabilities
Returns:
a String representation of the instance

getCurrentParameterValues

public double[] getCurrentParameterValues()
                                   throws Exception
Description copied from interface: DifferentiableSequenceScore
Returns a double array of dimension DifferentiableSequenceScore.getNumberOfParameters() containing the current parameter values. If one likes to use these parameters to start an optimization it is highly recommended to invoke DifferentiableSequenceScore.initializeFunction(int, boolean, DataSet[], double[][]) before. After an optimization this method can be used to get the current parameter values.

Returns:
the current parameter values
Throws:
Exception - if no parameters exist (yet)

isInitialized

public boolean isInitialized()
Description copied from interface: SequenceScore
This method can be used to determine whether the instance is initialized. If the instance is initialized you should be able to invoke SequenceScore.getLogScoreFor(Sequence).

Returns:
true if the instance is initialized, false otherwise

initializeFunctionRandomly

public void initializeFunctionRandomly(boolean freeParams)
                                throws Exception
Description copied from interface: DifferentiableSequenceScore
This method initializes the DifferentiableSequenceScore randomly. It has to create the underlying structure of the DifferentiableSequenceScore.

Parameters:
freeParams - indicates whether the (reduced) parameterization is used
Throws:
Exception - if something went wrong

initializeFunction

public void initializeFunction(int index,
                               boolean meila,
                               DataSet[] data,
                               double[][] weights)
Description copied from interface: DifferentiableSequenceScore
This method creates the underlying structure of the DifferentiableSequenceScore.

Parameters:
index - the index of the class the DifferentiableSequenceScore models
meila - indicates whether the (reduced) parameterization is used
data - the data sets
weights - the weights of the sequences in the data sets
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