de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

Class InhConstraint

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.Constraint

de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.InhConstraint

All Implemented Interfaces:

Storable, Cloneable

Direct Known Subclasses:

InhCondProb, MEMConstraint

public abstract class InhConstraint
extends Constraint
implements Cloneable

This class is the superclass for all inhomogeneous constraints.

Author:

Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	offset This array is used to find the start indices of the conditional distributions.

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

counts, freq, usedPositions

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	InhConstraint(int[] pos, int[] alphabetLength) Creates a new InhConstraint instance.
protected	InhConstraint(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	appendAdditionalInfo(StringBuffer xml) This method appends additional information that is not stored in the base class to the StringBuffer.
InhConstraint	clone()
protected void	extractAdditionalInfo(StringBuffer xml) This method parses additional information from the StringBuffer that is not parsed in the base class.
String	getDescription(AlphabetContainer con, int i) Returns the decoded symbol for the encoded symbol i.
int	satisfiesSpecificConstraint(Sequence s, int start) This method returns the index of the specific constraint that is fulfilled by the Sequence seq beginning at position start.

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

add, add, estimate, estimateUnConditional, getCount, getFreq, getFreq, getFreqInfo, getMarginalOrder, getNumberOfSpecificConstraints, getPosition, getPositions, getXMLTag, reset, resetCounts, toString, toXML

Methods inherited from class java.lang.Object

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

Field Detail

offset

protected int[] offset

This array is used to find the start indices of the conditional distributions.

Constructor Detail

InhConstraint

protected InhConstraint(int[] pos,
                        int[] alphabetLength)

Creates a new InhConstraint instance.

Parameters:

pos - the positions

alphabetLength - the length of each alphabet (not only the used positions)

See Also:

Constraint.Constraint(int[], int)

InhConstraint

protected InhConstraint(StringBuffer xml)
                 throws NonParsableException

The standard constructor for the interface Storable. Creates a new InhConstraint instance out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the InhConstraint instance could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

Storable, Constraint.Constraint(StringBuffer)

Method Detail

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.

Specified by:

extractAdditionalInfo in class Constraint

Parameters:

xml - the StringBuffer to be parsed

Throws:

NonParsableException - if something with the parsing went wrong

clone

public InhConstraint clone()
                    throws CloneNotSupportedException

Overrides:

clone in class Constraint

Throws:

CloneNotSupportedException

satisfiesSpecificConstraint

public int satisfiesSpecificConstraint(Sequence s,
                                       int start)

Description copied from class: Constraint

This method returns the index of the specific constraint that is fulfilled by the Sequence seq beginning at position start.

Specified by:

satisfiesSpecificConstraint in class Constraint

Parameters:

s - the sequence

start - the start position

Returns:

the index of the fulfilled, specific 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.

Specified by:

appendAdditionalInfo in class Constraint

Parameters:

xml - the StringBuffer that is used for appending additional information

getDescription

public String getDescription(AlphabetContainer con,
                             int i)

Description copied from class: Constraint

Returns the decoded symbol for the encoded symbol i.

Specified by:

getDescription in class Constraint

Parameters:

con - the AlphabetContainer

i - the encoded symbol

Returns:

the decoded symbol for the encoded symbol i