de.jstacs.motifDiscovery.history

Class RestrictedRepeatHistory

java.lang.Object

de.jstacs.motifDiscovery.history.RestrictedRepeatHistory

All Implemented Interfaces:

History, Storable, Cloneable

public class RestrictedRepeatHistory
extends Object
implements History

This class implements a history that allows operations (i.e. a pair of int), that are not a priorily forbidden and that are done before less than a specified threshold. This enables the user for instance to allow each operation exactly once. Furthermore, this class has a switch that allows to forbid an operation for which the reverse operation has been performed in the last step.

If shrink operations are allowed by the user then a shrink operation is allow anytime. This helps to keep the motif short.

Author:

Jens Keilwagen

Constructor Summary

Constructors

Constructor and Description
RestrictedRepeatHistory() This constructor creates an instance that allows to shift, shrink, and expand the motif, to do the reverse operation, and to do each operation at most once.
RestrictedRepeatHistory(boolean allowReverse) This constructor creates an instance that allows to shift, shrink, and expand the motif, and allows to do each operation at most once.
RestrictedRepeatHistory(boolean allowShift, boolean allowShrink, boolean allowExpand) This constructor creates an instance that allows to do each operation at most once.
RestrictedRepeatHistory(boolean allowShift, boolean allowShrink, boolean allowExpand, boolean allowReverse, int threshold) This constructor creates an instance with user specified allowed operations and threshold.
RestrictedRepeatHistory(int threshold) This constructor creates an instance that allows to shift shrink and expand the motif.
RestrictedRepeatHistory(StringBuffer xml) This is the constructor for the interface Storable.

Method Summary

Methods

Modifier and Type	Method and Description
void	clear() This method clears the history, i.e.
RestrictedRepeatHistory	clone() This method returns a deep copy of the instance
boolean	operationAllowed(int... op) Returns true if the specified operation is allowed, i.e.
void	operationPerfomed(int... op) This method puts an operation to the history.
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

Constructor Detail

RestrictedRepeatHistory

public RestrictedRepeatHistory()

This constructor creates an instance that allows to shift, shrink, and expand the motif, to do the reverse operation, and to do each operation at most once.

RestrictedRepeatHistory

public RestrictedRepeatHistory(boolean allowReverse)

This constructor creates an instance that allows to shift, shrink, and expand the motif, and allows to do each operation at most once.

Parameters:

allowReverse - whether it is allowed to do the reverse operation as next operation or not

RestrictedRepeatHistory

public RestrictedRepeatHistory(int threshold)

This constructor creates an instance that allows to shift shrink and expand the motif.

Parameters:

threshold - the number of times each operation can be done

Throws:

IllegalArgumentException - if the threshold is below 1

RestrictedRepeatHistory

public RestrictedRepeatHistory(boolean allowShift,
                       boolean allowShrink,
                       boolean allowExpand)

This constructor creates an instance that allows to do each operation at most once.

Parameters:

allowShift - whether it is allowed to shift the motif

allowShrink - whether it is allowed to shrink the motif

allowExpand - whether it is allowed to expand the motif

RestrictedRepeatHistory

public RestrictedRepeatHistory(boolean allowShift,
                       boolean allowShrink,
                       boolean allowExpand,
                       boolean allowReverse,
                       int threshold)
                        throws IllegalArgumentException

This constructor creates an instance with user specified allowed operations and threshold.

Parameters:

allowShift - whether it is allowed to shift the motif

allowShrink - whether it is allowed to shrink the motif

allowExpand - whether it is allowed to expand the motif

allowReverse - whether it is allowed to do the reverse operation as next operation or not

threshold - the number of times each operation can be done

Throws:

IllegalArgumentException - if the threshold is below 1

RestrictedRepeatHistory

public RestrictedRepeatHistory(StringBuffer xml)
                        throws NonParsableException

This is the constructor for the interface Storable.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

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

clone

public RestrictedRepeatHistory clone()
                              throws CloneNotSupportedException

Description copied from interface: History

This method returns a deep copy of the instance

Specified by:

clone in interface History

Overrides:

clone in class Object

Returns:

a deep copy

Throws:

CloneNotSupportedException - if not possible

See Also:

Cloneable, Object.clone()

clear

public void clear()

Description copied from interface: History

This method clears the history, i.e. it removes all operations from the history.

Specified by:

clear in interface History

operationAllowed

public boolean operationAllowed(int... op)

Description copied from interface: History

Returns true if the specified operation is allowed, i.e. it does not conflict with any operation from the history.

Specified by:

operationAllowed in interface History

Parameters:

op - the operation to be tested

Returns:

true if the specified operation is allowed

operationPerfomed

public void operationPerfomed(int... op)

Description copied from interface: History

This method puts an operation to the history.

Specified by:

operationPerfomed in interface History

Parameters:

op - the performed operation