MEMConstraint

java.lang.Object
- de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint
- - de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhConstraint
  - - de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.MEMConstraint

All Implemented Interfaces:

Storable, Cloneable
```
public class MEMConstraint
extends InhConstraint
```
This constraint can be used for any maximum entropy model (MEM) application.

Author:

Jens Keilwagen

Field Summary
- Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhConstraint
  offset
- Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint
  counts, freq, usedPositions

Constructor Summary

Constructors
Constructor and Description
`MEMConstraint(int[] pos, int[] alphabetLength)` Creates a `MEMConstraint` as part of a (whole) model.
`MEMConstraint(int[] pos, int[] alphabetLength, int[] corrected_positions)` Creates a `MEMConstraint` as part of a model.
`MEMConstraint(StringBuffer xml)` The standard constructor for the interface `Storable`.

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`addParameters(int offset, IntList list, MEMConstraint[] constraint, double[] params, int[] start)` This method implements a heuristic to modify a constraint if a number of constraints should be delete.
`protected void`	`appendAdditionalInfo(StringBuffer xml)` This method appends additional information that is not stored in the base class to the `StringBuffer`.
`MEMConstraint`	`clone()`
`int`	`comparePosition(int offset, MEMConstraint constr)` This method computes the number of overlapping positions between the current and the given constraints.
`void`	`draw(double ess)` Draws the parameters from a Dirichlet.
`void`	`estimate(double ess)` Estimates the (smoothed) relative frequencies using the ess (equivalent sample size).
`protected void`	`extractAdditionalInfo(StringBuffer xml)` This method parses additional information from the `StringBuffer` that is not parsed in the base class.
`int`	`getCorrectedPosition(int index)` Returns the value of the corrected position `index`.
`double`	`getExpLambda(int index)` Returns the exponential value of $\lambda_{index}$ at position `index`: $\exp(\lambda_{index})$ .
`double`	`getFreq(int index)` Returns the current frequency with index `index`.
`double`	`getLambda(int index)` Returns the value of $\lambda_{index}$ .
`protected String`	`getXMLTag()` Returns the XML tag that is used for the class to en- or decode.
`void`	`multiplyExpLambdaWith(int index, double val)` Multiplies the exponential value of $\lambda_{index}$ with the factor `val`: $\exp(\lambda_{index}) \cdot val$ .
`void`	`reset()` This method resets all member variables that are in some way counters, frequencies, ...
`int`	`satisfiesSpecificConstraint(SequenceIterator sequence)` Returns the index of the constraint that is satisfied by `sequence`.
`void`	`setExpLambda(int index, double val)` Sets the exponential value of $\exp(\lambda_{index}) = val$ . (Additionally it sets the value of $\lambda_{index}$ to the logarithmic value of `val`: $\lambda_{index} = \log(val)$ .)
`void`	`setLambda(int index, double val)` Sets the value of $\lambda_{index} = val$ . (Additionally it sets the exponential value of $\lambda_{index} = val$ to the exponential value of `val`: $\exp(\lambda_{index}) = \exp(val)$ .
`String`	`toString()`

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhConstraint
getDescription, satisfiesSpecificConstraint

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint
add, add, estimateUnConditional, getCount, getFreq, getFreqInfo, getMarginalOrder, getNumberOfSpecificConstraints, getPosition, getPositions, resetCounts, toXML

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

- Constructor Detail
  - MEMConstraint
```
public MEMConstraint(int[] pos,
             int[] alphabetLength)
              throws IllegalArgumentException
```
    Creates a MEMConstraint as part of a (whole) model.
    
    Parameters:
    pos - the used positions (have to be sorted)
    alphabetLength - an array containing the length of the the alphabet for each position (of the whole model)
    
    Throws:
    
    IllegalArgumentException - if pos is not sorted
    See Also:
    Constraint.Constraint(int[], int)
  - MEMConstraint
```
public MEMConstraint(int[] pos,
             int[] alphabetLength,
             int[] corrected_positions)
              throws IllegalArgumentException
```
    Creates a MEMConstraint as part of a model.
    
    Parameters:
    pos - the used positions (have to be sorted)
    alphabetLength - an array containing the length of the the alphabet for each position (of the whole model)
    corrected_positions - an array containing the corrected positions if the maximum entropy model is decomposed into parts
    
    Throws:
    
    IllegalArgumentException - if pos is not sorted or pos.length != corrected_positions.length
    See Also:
    InhConstraint.InhConstraint(int[], int[])
  - MEMConstraint
```
public MEMConstraint(StringBuffer xml)
              throws NonParsableException
```
    The standard constructor for the interface Storable. Creates a new MEMConstraint out of its XML representation.
    
    Parameters:
    xml - the XML representation as StringBuffer
    
    Throws:
    
    NonParsableException - if the MEMConstraint could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)
    See Also:
    Storable, InhConstraint.InhConstraint(StringBuffer)
- Method Detail
  - clone
```
public MEMConstraint clone()
                    throws CloneNotSupportedException
```
    Overrides:
    
    clone in class InhConstraint
    
    Throws:
    
    CloneNotSupportedException
  - estimate
```
public void estimate(double ess)
```
    Description copied from class: Constraint
    
    Estimates the (smoothed) relative frequencies using the ess (equivalent sample size).
    
    Specified by:
    
    estimate in class Constraint
    
    Parameters:
    ess - the ess
  - draw
```
public void draw(double ess)
```
    Draws the parameters from a Dirichlet.
    
    Parameters:
    ess - the equivalent sample size
  - getCorrectedPosition
```
public int getCorrectedPosition(int index)
```
    Returns the value of the corrected position index.
    
    Parameters:
    index - the index of the position
    
    Returns:
    the value of the corrected position
  - getExpLambda
```
public double getExpLambda(int index)
```
    Returns the exponential value of $\lambda_{index}$ at position index: $\exp(\lambda_{index})$ .
    
    Parameters:
    index - the index
    
    Returns:
    $\exp(\lambda_{index})$
  - getLambda
```
public double getLambda(int index)
```
    Returns the value of $\lambda_{index}$ .
    
    Parameters:
    index - the index
    
    Returns:
    $\lambda_{index}$
  - multiplyExpLambdaWith
```
public void multiplyExpLambdaWith(int index,
                         double val)
```
    Multiplies the exponential value of $\lambda_{index}$ with the factor val: $\exp(\lambda_{index}) \cdot val$ .
    (Additionally it adds the logarithmic value of val to the value of $\lambda_{index}$ at position index: $\lambda_{index} + \log(val)$ .)
    
    Parameters:
    index - the index
    val - the factor/value
  - reset
```
public void reset()
```
    Description copied from class: Constraint
    
    This method resets all member variables that are in some way counters, frequencies, ...
    
    Overrides:
    
    reset in class Constraint
  - satisfiesSpecificConstraint
```
public int satisfiesSpecificConstraint(SequenceIterator sequence)
```
    Returns the index of the constraint that is satisfied by sequence.
    
    Parameters:
    sequence - the SequenceIterator
    
    Returns:
    the index of the fulfilled constraint
  - getFreq
```
public double getFreq(int index)
```
    Description copied from class: Constraint
    
    Returns the current frequency with index index.
    
    Overrides:
    
    getFreq in class Constraint
    
    Parameters:
    index - the index
    
    Returns:
    the current frequency
  - setExpLambda
```
public void setExpLambda(int index,
                double val)
```
    Sets the exponential value of $\exp(\lambda_{index}) = val$ .
    (Additionally it sets the value of $\lambda_{index}$ to the logarithmic value of val: $\lambda_{index} = \log(val)$ .)
    
    Parameters:
    index - the index
    val - the value to be set
  - setLambda
```
public void setLambda(int index,
             double val)
```
    Sets the value of $\lambda_{index} = val$ .
    (Additionally it sets the exponential value of $\lambda_{index} = val$ to the exponential value of val: $\exp(\lambda_{index}) = \exp(val)$ .
    
    Parameters:
    index - the index
    val - the value
  - toString
```
public String toString()
```
    Specified by:
    
    toString in class Constraint
  - appendAdditionalInfo
```
protected void appendAdditionalInfo(StringBuffer xml)
```
    Description copied from class: Constraint
    
    This method appends additional information that is not stored in the base class to the StringBuffer.
    
    Overrides:
    
    appendAdditionalInfo in class InhConstraint
    
    Parameters:
    xml - the StringBuffer that is used for appending additional information
  - getXMLTag
```
protected String getXMLTag()
```
    Description copied from class: Constraint
    
    Returns the XML tag that is used for the class to en- or decode.
    
    Specified by:
    
    getXMLTag in class Constraint
    
    Returns:
    the XML tag that is used for the class to en- or decode
  - extractAdditionalInfo
```
protected void extractAdditionalInfo(StringBuffer xml)
                              throws NonParsableException
```
    Description copied from class: Constraint
    
    This method parses additional information from the StringBuffer that is not parsed in the base class.
    
    Overrides:
    
    extractAdditionalInfo in class InhConstraint
    
    Parameters:
    xml - the StringBuffer to be parsed
    
    Throws:
    
    NonParsableException - if something with the parsing went wrong
  - comparePosition
```
public int comparePosition(int offset,
                  MEMConstraint constr)
```
    This method computes the number of overlapping positions between the current and the given constraints.
    
    Parameters:
    offset - the offset for the given constraint
    constr - the given constraint
    
    Returns:
    the number of matching positions
  - addParameters
```
public void addParameters(int offset,
                 IntList list,
                 MEMConstraint[] constraint,
                 double[] params,
                 int[] start)
```
    This method implements a heuristic to modify a constraint if a number of constraints should be delete.
    
    Parameters:
    offset - the offset for the constraints
    list - a list of indices of constraints that should be used in this method
    constraint - the constraints
    params - the parameters
    start - the start indices of the constraints in the paramsarray

Class MEMConstraint

Field Summary

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhConstraint

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

Constructor Summary

Method Summary

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhConstraint

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

Methods inherited from class java.lang.Object

Constructor Detail

MEMConstraint

MEMConstraint

MEMConstraint

Method Detail

clone

estimate

draw

getCorrectedPosition

getExpLambda

getLambda

multiplyExpLambdaWith

reset

satisfiesSpecificConstraint

getFreq

setExpLambda

setLambda

toString

appendAdditionalInfo

getXMLTag

extractAdditionalInfo

comparePosition

addParameters