de.jstacs.data.alphabets
Class DNAAlphabet.DNAAlphabetParameterSet

java.lang.Object
  extended by de.jstacs.parameters.ParameterSet
      extended by de.jstacs.data.Alphabet.AlphabetParameterSet
          extended by de.jstacs.data.alphabets.DNAAlphabet.DNAAlphabetParameterSet
All Implemented Interfaces:
RangeIterator, Storable, Cloneable
Enclosing class:
DNAAlphabet

public static final class DNAAlphabet.DNAAlphabetParameterSet
extends Alphabet.AlphabetParameterSet

The parameter set for an DNA alphabet.

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
alternativeInstanceClass, errorMessage, parameters, parent, ranged
 
Constructor Summary
DNAAlphabet.DNAAlphabetParameterSet()
           
DNAAlphabet.DNAAlphabetParameterSet(StringBuffer representation)
           
 
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.ParameterSet
fromXML, getErrorMessage, getId, getInstance, getInstanceClass, getNumberOfParameters, getNumberOfValues, getParameterAt, getParent, hasDefaultOrIsSet, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, replaceParametersWithRangedInstance, reset, resetToFirst, setAlternativeInstanceClass, setParent, simplify, toXML, 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
Throws:
Exception

DNAAlphabet.DNAAlphabetParameterSet

public DNAAlphabet.DNAAlphabetParameterSet(StringBuffer representation)
                                    throws NonParsableException
Parameters:
representation -
Throws:
NonParsableException
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 simply creating a new ArrayList<Parameter> for the field parameters/code> and filling it with instances of subclasses of Parameter

Specified by:
loadParameters in class ParameterSet
Throws:
Exception - an Exception is thrown if the parameters could not be loaded
See Also:
ParameterSet.parameters, Parameter

getInstanceComment

public String getInstanceComment()
Description copied from class: ParameterSet
Returns a comment (a textual description) of the class that can be constructed using this ParameterSet.

Specified by:
getInstanceComment in class ParameterSet
Returns:
the comment