BNDiffSMParameter

java.lang.Object
- de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels.BNDiffSMParameter

All Implemented Interfaces:

Storable, Cloneable
```
public class BNDiffSMParameter
extends Object
implements Storable, Cloneable
```
Class for the parameters of a BayesianNetworkDiffSM. Each parameter holds its current value, the symbol and position it is responsible for and the context of the current symbol. A parameter can either be free or determined by other parameters (on the same simplex).

Author:

Jan Grau

Field Summary

Fields
Modifier and Type	Field and Description
`protected int[][]`	`context` The context of this parameter.
`protected double`	`count` The counts for this parameter.
`protected int`	`position` The position of `symbol` this parameter is responsible for.
`protected double`	`pseudoCount` The pseudocount for this parameter.
`protected byte`	`symbol` The symbol (out of some `Alphabet`) this parameter is responsible for.

Constructor Summary

Constructors
Constructor and Description
`BNDiffSMParameter(int index, byte symbol, int position, double pseudoCount, boolean free)` Creates a new `BNDiffSMParameter`, that is `BNDiffSMParameter` no `index` in the list of `BNDiffSMParameter`s of the `BayesianNetworkDiffSM` and responsible for `symbol` at position `position` and pseudo count `pseudoCount`.
`BNDiffSMParameter(int index, byte symbol, int position, int[][] context, double pseudoCount, boolean free)` Creates a new `BNDiffSMParameter`, that is `BNDiffSMParameter` no `index` in the list of `BNDiffSMParameter`s of the `BayesianNetworkDiffSM` and responsible for `symbol` at position `position` having context `context` and pseudocount `pseudoCount`.
`BNDiffSMParameter(StringBuffer representation)` The standard constructor for the interface `Storable`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addCount(double count2)` Adds `count2` to the counts of this parameter.
`BNDiffSMParameter`	`clone()`
`double`	`doesApplyFor(Sequence seq)` Indicates if the `Sequence` `seq` fulfills all requirements defined in the `context`.
`double`	`getCounts()` Returns the current counts for this parameter.
`int`	`getDepth()` Returns the depth of the tree, i.e.
`double`	`getExpValue()` Returns `Math.exp(getValue())`, which is pre-computed.
`int`	`getIndex()` Returns the index of this parameter as defined in the constructor.
`double`	`getLogPartialNormalizer()` Returns the partial derivative of the normalization constant with respect to this parameter.
`double`	`getLogT()` Returns the part of the normalization constant of parameters before this parameter in the structure of the network.
`double`	`getLogZ()` Returns the part of the normalization constant of parameters after this parameter in the structure of the network.
`int`	`getPosition()` Returns the position of the symbol this parameter is responsible for as defined in the constructor.
`double`	`getPseudoCount()` Returns the pseudocount as given in the constructor.
`double`	`getValue()` Returns the current value of this parameter.
`void`	`invalidateNormalizers()` Resets all internal normalization constants to `null`.
`boolean`	`isFree()` Indicates if this parameter is free.
`void`	`print()` Prints the counts and the value of this parameter to `System.out`.
`void`	`reset()` Resets the counts to the pseudocounts and the value to `0`.
`void`	`setValue(double value)` Sets the current value of this parameter.
`StringBuffer`	`toXML()` This method returns an XML representation as `StringBuffer` of an instance of the implementing class.

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

- Field Detail
  - symbol
```
protected byte symbol
```
    The symbol (out of some Alphabet) this parameter is responsible for.
  - position
```
protected int position
```
    The position of symbol this parameter is responsible for.
  - context
```
protected int[][] context
```
    The context of this parameter. The length context.length is equal to the number of parents, context[i] holds the information for parent no i, context[i][0] holds the position of parent i, context[i][1] ,... hold the possible configurations of parent i in the context. Normally, only context[i][1] exists, i.e. only one configuration is allowed in the context.
  - count
```
protected double count
```
    The counts for this parameter. Used for determination of plug-in parameters.
  - pseudoCount
```
protected double pseudoCount
```
    The pseudocount for this parameter. Used for determination of plug-in parameters.
- Constructor Detail
  - BNDiffSMParameter
```
public BNDiffSMParameter(int index,
                         byte symbol,
                         int position,
                         double pseudoCount,
                         boolean free)
```
    Creates a new BNDiffSMParameter, that is BNDiffSMParameter no index in the list of BNDiffSMParameters of the BayesianNetworkDiffSM and responsible for symbol at position position and pseudo count pseudoCount.
    
    Parameters:
    
    index - the index in the list of all parameters
    
    symbol - the symbol this parameter is responsible for
    
    position - the position of the symbol
    
    pseudoCount - the pseudocount
    
    free - indicates if this parameter is a free parameter
  - BNDiffSMParameter
```
public BNDiffSMParameter(int index,
                         byte symbol,
                         int position,
                         int[][] context,
                         double pseudoCount,
                         boolean free)
```
    Creates a new BNDiffSMParameter, that is BNDiffSMParameter no index in the list of BNDiffSMParameters of the BayesianNetworkDiffSM and responsible for symbol at position position having context context and pseudocount pseudoCount.
    
    Parameters:
    
    index - the index in the list of all parameters
    
    symbol - the symbol this parameter is responsible for
    
    position - the position of the symbol
    
    context - the context of this parameter
    
    pseudoCount - the pseudocount
    
    free - indicates if this parameter is a free parameter
  - BNDiffSMParameter
```
public BNDiffSMParameter(StringBuffer representation)
                  throws NonParsableException
```
    The standard constructor for the interface Storable. Re-creates a parameter from its XML-representation as returned by the method toXML().
    
    Parameters:
    
    representation - the XML code as StringBuffer
    
    Throws:
    
    NonParsableException - if the StringBuffer representation could not be parsed
- Method Detail
  - clone
```
public BNDiffSMParameter clone()
                        throws CloneNotSupportedException
```
    Overrides:
    
    clone in class Object
    
    Throws:
    
    CloneNotSupportedException
  - getPseudoCount
```
public double getPseudoCount()
```
    Returns the pseudocount as given in the constructor.
    
    Returns:
    
    the pseudocount
    
    See Also:
    
    BNDiffSMParameter(int, byte, int, double, boolean), BNDiffSMParameter(int, byte, int, int[][], double, boolean)
  - reset
```
public void reset()
```
    Resets the counts to the pseudocounts and the value to 0.
  - getDepth
```
public int getDepth()
```
    Returns the depth of the tree, i.e. the number of parents of this parameter.
    
    Returns:
    
    the depth of the tree
  - print
```
public void print()
```
    Prints the counts and the value of this parameter to System.out.
  - doesApplyFor
```
public double doesApplyFor(Sequence seq)
```
    Indicates if the Sequence seq fulfills all requirements defined in the context.
    
    Parameters:
    
    seq - the sequence
    
    Returns:
    
    true if this parameter is responsible for seq, false otherwise
  - getValue
```
public double getValue()
```
    Returns the current value of this parameter.
    
    Returns:
    
    the current value
  - setValue
```
public void setValue(double value)
```
    Sets the current value of this parameter.
    
    Parameters:
    
    value - the new value to be set
  - getExpValue
```
public double getExpValue()
```
    Returns Math.exp(getValue()), which is pre-computed.
    
    Returns:
    
    the exponential value of this parameter
  - toXML
```
public StringBuffer toXML()
```
    Description copied from interface: Storable
    
    This method returns an XML representation as StringBuffer of an instance of the implementing class.
    
    Specified by:
    
    toXML in interface Storable
    
    Returns:
    
    the XML representation
  - invalidateNormalizers
```
public void invalidateNormalizers()
```
    Resets all internal normalization constants to null.
  - getLogPartialNormalizer
```
public double getLogPartialNormalizer()
                               throws Exception
```
    Returns the partial derivative of the normalization constant with respect to this parameter.
    
    Returns:
    
    the partial derivative
    
    Throws:
    
    Exception - if no normalization constants have been pre-computed
  - getCounts
```
public double getCounts()
```
    Returns the current counts for this parameter.
    
    Returns:
    
    the current counts
  - addCount
```
public void addCount(double count2)
```
    Adds count2 to the counts of this parameter.
    
    Parameters:
    
    count2 - the counts to be added
  - isFree
```
public boolean isFree()
```
    Indicates if this parameter is free.
    
    Returns:
    
    true if the parameter is free, false otherwise
  - getPosition
```
public int getPosition()
```
    Returns the position of the symbol this parameter is responsible for as defined in the constructor.
    
    Returns:
    
    the position of this parameter this parameter is responsible for
    
    See Also:
    
    BNDiffSMParameter(int, byte, int, double, boolean), BNDiffSMParameter(int, byte, int, int[][], double, boolean)
  - getIndex
```
public int getIndex()
```
    Returns the index of this parameter as defined in the constructor.
    
    Returns:
    
    the index of this parameter in the list of all parameters
    
    See Also:
    
    BNDiffSMParameter(int, byte, int, double, boolean), BNDiffSMParameter(int, byte, int, int[][], double, boolean)
  - getLogZ
```
public double getLogZ()
```
    Returns the part of the normalization constant of parameters after this parameter in the structure of the network.
    
    Returns:
    
    the normalization constant
  - getLogT
```
public double getLogT()
```
    Returns the part of the normalization constant of parameters before this parameter in the structure of the network.
    
    Returns:
    
    the normalization constant

Class BNDiffSMParameter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

symbol

position

context

count

pseudoCount

Constructor Detail

BNDiffSMParameter

BNDiffSMParameter

BNDiffSMParameter

Method Detail

clone

getPseudoCount

reset

getDepth

print

doesApplyFor

getValue

setValue

getExpValue

toXML

invalidateNormalizers

getLogPartialNormalizer

getCounts

addCount

isFree

getPosition

getIndex

getLogZ

getLogT