de.jstacs.data.alphabets
Class DNAAlphabet.DNAAlphabetParameterSet

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

All Implemented Interfaces:

GalaxyConvertible, RangeIterator, Storable, Cloneable

Enclosing class:

DNAAlphabet

public static final class DNAAlphabet.DNAAlphabetParameterSet
extends DiscreteAlphabet.DiscreteAlphabetParameterSet

The parameter set for a DNAAlphabet.

Author:

Jan Grau, 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, ranged

Constructor Summary

DNAAlphabet.DNAAlphabetParameterSet()
Creates a new DNAAlphabet.DNAAlphabetParameterSet.

DNAAlphabet.DNAAlphabetParameterSet(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

DNAAlphabet.DNAAlphabetParameterSet

public DNAAlphabet.DNAAlphabetParameterSet()
                                    throws Exception

Creates a new DNAAlphabet.DNAAlphabetParameterSet.

Throws:

Exception - if an error occurred

See Also:

Alphabet.AlphabetParameterSet#AlphabetParameterSet(Class)

DNAAlphabet.DNAAlphabetParameterSet

public DNAAlphabet.DNAAlphabetParameterSet(StringBuffer representation)
                                    throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

Alphabet.AlphabetParameterSet#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.

Overrides:

loadParameters in class DiscreteAlphabet.DiscreteAlphabetParameterSet

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.

Overrides:

getInstanceComment in class DiscreteAlphabet.DiscreteAlphabetParameterSet

Returns:

the comment of the class