de.jstacs.data.alphabets

Class GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet

java.lang.Object

de.jstacs.parameters.ParameterSet

de.jstacs.parameters.InstanceParameterSet<T>

de.jstacs.data.alphabets.Alphabet.AlphabetParameterSet

de.jstacs.data.alphabets.DiscreteAlphabet.DiscreteAlphabetParameterSet

de.jstacs.data.alphabets.GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet

All Implemented Interfaces:

GalaxyConvertible, Storable, Cloneable

Enclosing class:

GenericComplementableDiscreteAlphabet

public static class GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet
extends DiscreteAlphabet.DiscreteAlphabetParameterSet

This class is used as container for the parameters of a GenericComplementableDiscreteAlphabet.

Author:

Jens Keilwagen

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

Constructor Summary

Constructors

Constructor and Description
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet() This constructor creates an empty parameter set the has to be filled before it can be used to create a GenericComplementableDiscreteAlphabet.
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet(String[] alphabet, boolean caseInsensitive, int[] revComp) The main constructor.
GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet(StringBuffer representation) The standard constructor for the interface Storable.

Method Summary

Methods inherited from class de.jstacs.data.alphabets.DiscreteAlphabet.DiscreteAlphabetParameterSet

getInstanceComment

Methods inherited from class de.jstacs.data.alphabets.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, 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

GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet

public GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet()

This constructor creates an empty parameter set the has to be filled before it can be used to create a GenericComplementableDiscreteAlphabet.

GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet

public GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet(String[] alphabet,
                                                                                       boolean caseInsensitive,
                                                                                       int[] revComp)
                                                                                        throws Exception

The main constructor.

Parameters:

alphabet - the array of symbols

caseInsensitive - indicates if there will be no difference between lower case and upper case letters/symbols in the alphabet (no case sensitivity)

revComp - the array is used to provide the complementarity, revComp[i] contains the index of the complement of the i-th symbol

Throws:

Exception - if some parameter could not be set.

GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet

public GenericComplementableDiscreteAlphabet.GenericComplementableDiscreteAlphabetParameterSet(StringBuffer representation)
                                                                                        throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

Alphabet.AlphabetParameterSet#AlphabetParameterSet(StringBuffer), Storable