de.jstacs.data
Class AlphabetContainerParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.data.AlphabetContainerParameterSet

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

public class AlphabetContainerParameterSet
extends InstanceParameterSet

Class for the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet of an AlphabetContainer.

Author:

Jan Grau

Nested Class Summary

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, ranged

Constructor Summary

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.

AlphabetContainerParameterSet(StringBuffer representation)
The standard constructor for the interface Storable.

Method Summary

AlphabetContainerParameterSet	clone() Creates a full clone (deep copy) of this ParameterSet.
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 AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet.
boolean	isDiscrete() Indicates if all positions use DiscreteAlphabet.DiscreteAlphabetParameterSet, i.e.
boolean	isSimple() Indicates if all positions use the same Alphabet, i.e. if the corresponding AlphabetContainer is simple.
protected void	loadParameters() Loads the parameters for this ParameterSet.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

getInstance, getInstanceClass

Methods inherited from class de.jstacs.parameters.ParameterSet

fromGalaxy, getErrorMessage, getId, getIndex, getNumberOfParameters, getNumberOfValues, getParameterAt, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, replaceParametersWithRangedInstance, reset, resetToFirst, setParent, simplify, toGalaxy, valuesToString

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)

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

See Also:

AlphabetContainer.AlphabetContainerType, InstanceParameterSet.InstanceParameterSet(Class)

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

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

clone

public AlphabetContainerParameterSet clone()
                                    throws CloneNotSupportedException

Description copied from class: ParameterSet

Creates a full clone (deep copy) of this ParameterSet. As a convenience-method the user can use fillWithStandardFieldsForClone(ParameterSet) on a newly created instance of a subclass of ParameterSet to obtain a clone/copy of all standard member variables (those already defined in ParameterSet) in the passed ParameterSet. Using this method, the cloning process becomes merely three-step:

• Create a new instance of your subclass of ParameterSet, most likely with an empty constructor or the one taking just the instance class.
• Call this.fillWithStandardFieldsForClone on this instance.
• Return the instance.

This method fulfills the conventions of Object's method Object.clone().

Overrides:

clone in class ParameterSet

Returns:

a deep clone/copy of this ParameterSet

Throws:

CloneNotSupportedException

isDiscrete

public boolean isDiscrete()

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

Returns:

true if all positions are discrete, false otherwise

isSimple

public boolean isSimple()

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

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

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

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()

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

Returns:

the length

loadParameters

protected void loadParameters()
                       throws Exception

Description copied from class: ParameterSet

Loads the parameters for this ParameterSet. This is in most cases done by calling ParameterSet.initParameterList() or ParameterSet.initParameterList(int) to initialize ParameterSet.parameters and afterwards filling ParameterSet.parameters with instances of subclasses of Parameter.

Specified by:

loadParameters in class ParameterSet

Throws:

Exception - if the parameters could not be loaded

See Also:

Parameter, ParameterSet.parameters, ParameterSet.initParameterList(), ParameterSet.initParameterList(int)

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

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

Returns:

the comment of the class