de.jstacs.data.alphabets
Class DiscreteAlphabet.DiscreteAlphabetParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.InstanceParameterSet
          de.jstacs.data.Alphabet.AlphabetParameterSet
              de.jstacs.data.alphabets.DiscreteAlphabet.DiscreteAlphabetParameterSet

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

Direct Known Subclasses:

DNAAlphabet.DNAAlphabetParameterSet, GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet

Enclosing class:

DiscreteAlphabet

public static class DiscreteAlphabet.DiscreteAlphabetParameterSet
extends Alphabet.AlphabetParameterSet

Class for the ParameterSet of a DiscreteAlphabet.

Author:

Jan Grau

Nested Class Summary

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

	DiscreteAlphabet.DiscreteAlphabetParameterSet() Creates a new DiscreteAlphabet.DiscreteAlphabetParameterSet with empty values.
	DiscreteAlphabet.DiscreteAlphabetParameterSet(char[] alphabet, boolean caseInsensitive) Creates a new DiscreteAlphabet.DiscreteAlphabetParameterSet from an alphabet of symbols given as a char array.
protected	DiscreteAlphabet.DiscreteAlphabetParameterSet(Class<? extends DiscreteAlphabet> clazz) This constructor should only be used for parameter sets that are intended to created subclasses of DiscreteAlphabet.
	DiscreteAlphabet.DiscreteAlphabetParameterSet(String[] alphabet, boolean caseInsensitive) Creates a new DiscreteAlphabet.DiscreteAlphabetParameterSet from an alphabet given as a String array.
	DiscreteAlphabet.DiscreteAlphabetParameterSet(StringBuffer representation) The standard constructor for the interface Storable .

Method Summary

String	getInstanceComment() Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.
protected void	loadParameters() Loads the parameters for this ParameterSet.

Methods inherited from class de.jstacs.data.Alphabet.AlphabetParameterSet

clone, getInstanceName

Methods inherited from class de.jstacs.parameters.InstanceParameterSet

fromXML, getInstance, getInstanceClass, toXML

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

DiscreteAlphabet.DiscreteAlphabetParameterSet

protected DiscreteAlphabet.DiscreteAlphabetParameterSet(Class<? extends DiscreteAlphabet> clazz)

This constructor should only be used for parameter sets that are intended to created subclasses of DiscreteAlphabet.

Parameters:

clazz - the class the should be created with this parameter set

DiscreteAlphabet.DiscreteAlphabetParameterSet

public DiscreteAlphabet.DiscreteAlphabetParameterSet()

Creates a new DiscreteAlphabet.DiscreteAlphabetParameterSet with empty values.

See Also:

Alphabet.AlphabetParameterSet.Alphabet.AlphabetParameterSet(Class)

DiscreteAlphabet.DiscreteAlphabetParameterSet

public DiscreteAlphabet.DiscreteAlphabetParameterSet(String[] alphabet,
                                                     boolean caseInsensitive)
                                              throws Exception

Creates a new DiscreteAlphabet.DiscreteAlphabetParameterSet from an alphabet given as a String array.

Parameters:

alphabet - the alphabet as String array

caseInsensitive - indicates if the DiscreteAlphabet shall be case insensitive

Throws:

Exception - if the parameter set could not be created

See Also:

DiscreteAlphabet.DiscreteAlphabetParameterSet()

DiscreteAlphabet.DiscreteAlphabetParameterSet

public DiscreteAlphabet.DiscreteAlphabetParameterSet(char[] alphabet,
                                                     boolean caseInsensitive)
                                              throws Exception

Creates a new DiscreteAlphabet.DiscreteAlphabetParameterSet from an alphabet of symbols given as a char array.

Parameters:

alphabet - the array of symbols

caseInsensitive - indicates if the DiscreteAlphabet shall be case insensitive

Throws:

Exception - if the parameter set could not be created

See Also:

DiscreteAlphabet.DiscreteAlphabetParameterSet()

DiscreteAlphabet.DiscreteAlphabetParameterSet

public DiscreteAlphabet.DiscreteAlphabetParameterSet(StringBuffer representation)
                                              throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

Alphabet.AlphabetParameterSet.Alphabet.AlphabetParameterSet(StringBuffer), Storable

Method Detail

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)

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