de.jstacs.data

Class AlphabetContainerParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.data.AlphabetContainer.AbstractAlphabetContainerParameterSet<AlphabetContainer>

de.jstacs.data.AlphabetContainerParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

public class AlphabetContainerParameterSet
extends AlphabetContainer.AbstractAlphabetContainerParameterSet<AlphabetContainer>

Class for the ParameterSet of an AlphabetContainer.

Author:

Jan Grau

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AlphabetContainerParameterSet.AlphabetArrayParameterSet Class for the parameters of an array of Alphabets of defined length.
static class	AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet Class for the parameter set of an array of Alphabets where each Alphabet may be used for one or more sections of positions.

Nested classes/interfaces inherited from class de.jstacs.parameters.ParameterSet

ParameterSet.ParameterList

Field Summary

Fields inherited from class de.jstacs.parameters.ParameterSet

errorMessage, parameters, parent

Constructor Summary

Constructors

Modifier	Constructor and Description
	AlphabetContainerParameterSet() Creates a new AlphabetContainerParameterSet of a complex AlphabetContainer with type AlphabetContainer.AlphabetContainerType.BOTH.
	AlphabetContainerParameterSet(Alphabet alph) Creates a new AlphabetContainerParameterSet of a simple AlphabetContainer from a single Alphabet.
	AlphabetContainerParameterSet(Alphabet[] alphabets) Creates a new AlphabetContainerParameterSet from an array of Alphabets.
	AlphabetContainerParameterSet(Alphabet[] alphabets, int[] indexes) Creates a new AlphabetContainerParameterSet from an array of Alphabets and an array of ints defining the Alphabet index i in alphabets that is used for position i.
	AlphabetContainerParameterSet(AlphabetContainer.AlphabetContainerType type, boolean simple) Creates a new AlphabetContainerParameterSet of an AlphabetContainer with AlphabetContainer.AlphabetContainerType type.
protected	AlphabetContainerParameterSet(Class<? extends AlphabetContainer> instanceClass, Alphabet... alphabets) /** Creates a new AlphabetContainerParameterSet from an array of Alphabets for a given sub-class of AlphabetContainer.
	AlphabetContainerParameterSet(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	fromXML(StringBuffer representation) Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().
String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.
String	getInstanceName() Returns the name of an instance of the class that can be constructed using this ParameterSet.
int	getPossibleLength() Returns the length of the AlphabetContainer that can be instantiated using this ParameterSet.
boolean	isDiscrete() Indicates if all positions use DiscreteAlphabet.DiscreteAlphabetParameterSet, i.e.
boolean	isSimple() Indicates if all positions use the same Alphabet, i.e.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.data.AlphabetContainer.AbstractAlphabetContainerParameterSet

clone

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getNumberOfParameters, getParameterAt, getParameterForName, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent, toGalaxy

Methods inherited from class java.lang.Object

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

Constructor Detail

AlphabetContainerParameterSet

public AlphabetContainerParameterSet(AlphabetContainer.AlphabetContainerType type,
                                     boolean simple)
                              throws Exception

Creates a new AlphabetContainerParameterSet of an AlphabetContainer with AlphabetContainer.AlphabetContainerType type. If simple is true, only a single Alphabet is expected.

Parameters:

type - the type of the alphabet(s)

simple - indicates if there shall be only a single Alphabet

Throws:

Exception - if the parameters could not be created for the given arguments

See Also:

AlphabetContainer.AlphabetContainerType, InstanceParameterSet.InstanceParameterSet(Class)

AlphabetContainerParameterSet

public AlphabetContainerParameterSet()
                              throws Exception

Creates a new AlphabetContainerParameterSet of a complex AlphabetContainer with type AlphabetContainer.AlphabetContainerType.BOTH.

Throws:

Exception - if the ParameterSet could not be created

See Also:

AlphabetContainerParameterSet(AlphabetContainer.AlphabetContainerType, boolean)

AlphabetContainerParameterSet

public AlphabetContainerParameterSet(StringBuffer representation)
                              throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

InstanceParameterSet.InstanceParameterSet(StringBuffer), Storable

AlphabetContainerParameterSet

public AlphabetContainerParameterSet(Alphabet alph)
                              throws Exception

Creates a new AlphabetContainerParameterSet of a simple AlphabetContainer from a single Alphabet.

Parameters:

alph - the Alphabet

Throws:

Exception - if an error occurred during the creation of the appropriate parameters

See Also:

InstanceParameterSet.InstanceParameterSet(Class)

AlphabetContainerParameterSet

public AlphabetContainerParameterSet(Alphabet[] alphabets)
                              throws Exception

Creates a new AlphabetContainerParameterSet from an array of Alphabets.

Parameters:

alphabets - the array of Alphabets

Throws:

Exception - if an error occurred during the creation of the appropriate parameters

See Also:

InstanceParameterSet.InstanceParameterSet(Class)

AlphabetContainerParameterSet

protected AlphabetContainerParameterSet(Class<? extends AlphabetContainer> instanceClass,
                                        Alphabet... alphabets)
                                 throws Exception

/** Creates a new AlphabetContainerParameterSet from an array of Alphabets for a given sub-class of AlphabetContainer.

Parameters:

instanceClass - the sub-class fo AlphabetContainer

alphabets - the alphabets

Throws:

Exception - if the parameters could not be created for the given arguments

AlphabetContainerParameterSet

public AlphabetContainerParameterSet(Alphabet[] alphabets,
                                     int[] indexes)
                              throws Exception

Creates a new AlphabetContainerParameterSet from an array of Alphabets and an array of ints defining the Alphabet index i in alphabets that is used for position i.

Parameters:

alphabets - the Alphabets

indexes - the indexes

Throws:

Exception - if an error occurred during the creation of the appropriate parameters

See Also:

InstanceParameterSet.InstanceParameterSet(Class)

Method Detail

isDiscrete

public boolean isDiscrete()

Indicates if all positions use DiscreteAlphabet.DiscreteAlphabetParameterSet, i.e. if all Alphabets of the corresponding AlphabetContainer are discrete.

Specified by:

isDiscrete in class AlphabetContainer.AbstractAlphabetContainerParameterSet<AlphabetContainer>

Returns:

true if all positions are discrete, false otherwise

See Also:

AlphabetContainer.isDiscrete()

isSimple

public boolean isSimple()

Description copied from class: AlphabetContainer.AbstractAlphabetContainerParameterSet

Indicates if all positions use the same Alphabet, i.e. if the corresponding AlphabetContainer is simple.

Specified by:

isSimple in class AlphabetContainer.AbstractAlphabetContainerParameterSet<AlphabetContainer>

Returns:

true if all positions use the same Alphabet, false otherwise

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

Overrides:

toXML in class InstanceParameterSet<AlphabetContainer>

Returns:

the XML representation

fromXML

protected void fromXML(StringBuffer representation)
                throws NonParsableException

Description copied from class: ParameterSet

Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().

Overrides:

fromXML in class InstanceParameterSet<AlphabetContainer>

Parameters:

representation - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

See Also:

ParameterSet.toXML()

getPossibleLength

public int getPossibleLength()

Description copied from class: AlphabetContainer.AbstractAlphabetContainerParameterSet

Returns the length of the AlphabetContainer that can be instantiated using this ParameterSet.

Specified by:

getPossibleLength in class AlphabetContainer.AbstractAlphabetContainerParameterSet<AlphabetContainer>

Returns:

the length

See Also:

AlphabetContainer.getPossibleLength()

getInstanceName

public String getInstanceName()

Description copied from class: InstanceParameterSet

Returns the name of an instance of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceName in class InstanceParameterSet<AlphabetContainer>

Returns:

the name of the class

getInstanceComment

public String getInstanceComment()

Description copied from class: InstanceParameterSet

Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:

getInstanceComment in class InstanceParameterSet<AlphabetContainer>

Returns:

the comment of the class