MultiDimensionalSequenceWrapperDiffSS

java.lang.Object
- de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore
- - de.jstacs.sequenceScores.differentiable.MultiDimensionalSequenceWrapperDiffSS

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, Storable, Cloneable
```
public class MultiDimensionalSequenceWrapperDiffSS
extends AbstractDifferentiableSequenceScore
```
This class implements a simple wrapper for multidimensional sequences. The logarithm of the score given by AbstractDifferentiableSequenceScore.getLogScoreFor(Sequence) is defined as
$\frac{1}{N}\sum_{n=0}^N \log p(\underline{x_n} | \underline{\lambda}).$

Author:

Jens Keilwagen

See Also:
MultiDimensionalSequence

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

Constructors
Constructor and Description
`MultiDimensionalSequenceWrapperDiffSS(DifferentiableSequenceScore function)` The main constructor.
`MultiDimensionalSequenceWrapperDiffSS(StringBuffer xml)` This is the constructor for `Storable`.

Method Summary

Methods
Modifier and Type	Method and Description
`MultiDimensionalSequenceWrapperDiffSS`	`clone()` Creates a clone (deep copy) of the current `DifferentiableSequenceScore` instance.
`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.
`String`	`getInstanceName()` Should return a short instance name such as iMM(0), BN(2), ...
`double`	`getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer)` 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 freeParams, 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
getAlphabetContainer, getCharacteristics, getInitialClassParam, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumberOfRecommendedStarts, getNumberOfStarts, getNumericalCharacteristics, toString

Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - MultiDimensionalSequenceWrapperDiffSS
```
public MultiDimensionalSequenceWrapperDiffSS(DifferentiableSequenceScore function)
                                      throws IllegalArgumentException,
                                             CloneNotSupportedException
```
    The main constructor.
    
    Parameters:
    function - the internally used function
    
    Throws:
    
    IllegalArgumentException - if the length is negative or does not match with AlphabetContainer.getPossibleLength()
    
    CloneNotSupportedException - if the function can not be cloned properly
  - MultiDimensionalSequenceWrapperDiffSS
```
public MultiDimensionalSequenceWrapperDiffSS(StringBuffer xml)
                                      throws NonParsableException
```
    This is the constructor for Storable. Creates a new MultiDimensionalSequenceWrapperDiffSS out of a StringBuffer .
    
    Parameters:
    xml - the XML representation as StringBuffer
    
    Throws:
    
    NonParsableException - if the XML representation could not be parsed
- Method Detail
  - 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)
  - 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
  - clone
```
public MultiDimensionalSequenceWrapperDiffSS clone()
                                            throws CloneNotSupportedException
```
    Description copied from interface: DifferentiableSequenceScore
    
    Creates a clone (deep copy) of the current DifferentiableSequenceScore instance.
    
    Specified by:
    
    clone in interface DifferentiableSequenceScore
    
    Specified by:
    
    clone in interface SequenceScore
    
    Overrides:
    
    clone in class AbstractDifferentiableSequenceScore
    
    Returns:
    the cloned instance of the current DifferentiableSequenceScore
    
    Throws:
    
    CloneNotSupportedException - if something went wrong while cloning the DifferentiableSequenceScore
  - 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)
  - 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 partialDer)
```
    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
    partialDer - 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
  - initializeFunction
```
public void initializeFunction(int index,
                      boolean freeParams,
                      DataSet[] data,
                      double[][] weights)
                        throws Exception
```
    Description copied from interface: DifferentiableSequenceScore
    
    This method creates the underlying structure of the DifferentiableSequenceScore.
    
    Parameters:
    index - the index of the class the DifferentiableSequenceScore models
    freeParams - indicates whether the (reduced) parameterization is used
    data - the data sets
    weights - the weights of the sequences in the data sets
    
    Throws:
    
    Exception - if something went wrong
  - 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
  - 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
  - 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
  - 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

Class MultiDimensionalSequenceWrapperDiffSS

Field Summary

Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore

Constructor Summary

Method Summary

Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

Methods inherited from class java.lang.Object

Constructor Detail

MultiDimensionalSequenceWrapperDiffSS

MultiDimensionalSequenceWrapperDiffSS

Method Detail

fromXML

toXML

clone

getCurrentParameterValues

getInstanceName

getLogScoreFor

getLogScoreAndPartialDerivation

getNumberOfParameters

initializeFunction

initializeFunctionRandomly

isInitialized

setParameters

toString