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## de.jstacs.models.discrete.homogeneous.parameters
Class HomMMParameterSet

    java.lang.Object
      de.jstacs.parameters.ParameterSet
          de.jstacs.parameters.InstanceParameterSet
              de.jstacs.parameters.SequenceScoringParameterSet
                  de.jstacs.models.discrete.DGMParameterSet
                      de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet
                          de.jstacs.models.discrete.homogeneous.parameters.HomMMParameterSet

All Implemented Interfaces:
  GalaxyConvertible, RangeIterator, Storable, Cloneable

    public class HomMMParameterSet

extends HomogeneousModelParameterSet

This class implements a container for all parameters of a homogeneous Markov model.

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.SequenceScoringParameterSet
`alphabet, length`

Fields inherited from class de.jstacs.parameters.ParameterSet
`errorMessage, parameters, parent, ranged`

Constructor Summary
`HomMMParameterSet()` An empty constructor.
`HomMMParameterSet(AlphabetContainer alphabet, double ess, String description, byte order)` Creates a new `HomMMParameterSet` with `AlphabetContainer`, ess (equivalent sample size), description and order of the homogeneous Markov model.
`HomMMParameterSet(StringBuffer s)` 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`.

Methods inherited from class de.jstacs.models.discrete.homogeneous.parameters.HomogeneousModelParameterSet
`hasDefaultOrIsSet, loadParameters`

Methods inherited from class de.jstacs.models.discrete.DGMParameterSet
`clone, getInstanceName, setEss`

Methods inherited from class de.jstacs.parameters.SequenceScoringParameterSet
`equals, fromXML, getAlphabetContainer, getLength, getNumberOfParameters, getParameterAt, replaceParametersWithRangedInstance, reset, toXML`

Methods inherited from class de.jstacs.parameters.InstanceParameterSet
`getInstance, getInstanceClass`

Methods inherited from class de.jstacs.parameters.ParameterSet
`fromGalaxy, getErrorMessage, getId, getIndex, getNumberOfValues, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, resetToFirst, setParent, simplify, toGalaxy, valuesToString`

Methods inherited from class java.lang.Object
`finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

### HomMMParameterSet

    public HomMMParameterSet(StringBuffer s)
                      throws NonParsableException

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

  Parameters:
    `s` - the XML representation as `StringBuffer`
  Throws:
    `NonParsableException` - if the `HomMMParameterSet` could not be reconstructed out of the XML representation (the `StringBuffer` could not be parsed)
  See Also:
    `Storable`, `HomogeneousModelParameterSet.HomogeneousModelParameterSet(StringBuffer)`

### HomMMParameterSet

    public HomMMParameterSet()

  An empty constructor. Creates a new `HomMMParameterSet`.

### HomMMParameterSet

    public HomMMParameterSet(AlphabetContainer alphabet,
                             double ess,
                             String description,
                             byte order)
                      throws Exception

  Creates a new `HomMMParameterSet` with `AlphabetContainer`, ess (equivalent sample size), description and order of the homogeneous Markov model.

  Parameters:
    `alphabet` - the `AlphabetContainer`
    `ess` - the ess (equivalent sample size)
    `description` - the description
    `order` - the order of the Markov model
  Throws:
    `Exception` - if something went wrong
  See Also:
    `HomogeneousModelParameterSet.HomogeneousModelParameterSet(Class, AlphabetContainer, double, String, byte)`

Method Detail

### 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

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