de.jstacs.data
Class AlphabetContainerParameterSet.AlphabetArrayParameterSet

java.lang.Object
  extended by de.jstacs.parameters.ParameterSet
      extended by de.jstacs.parameters.ExpandableParameterSet
          extended by de.jstacs.parameters.ArrayParameterSet
              extended by de.jstacs.data.AlphabetContainerParameterSet.AlphabetArrayParameterSet
All Implemented Interfaces:
GalaxyConvertible, Storable, Cloneable
Enclosing class:
AlphabetContainerParameterSet

public static class AlphabetContainerParameterSet.AlphabetArrayParameterSet
extends ArrayParameterSet

Class for the parameters of an array of Alphabets of defined length.

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.ExpandableParameterSet
commentTemplate, nameTemplate, template
 
Fields inherited from class de.jstacs.parameters.ParameterSet
errorMessage, parameters, parent
 
Constructor Summary
AlphabetContainerParameterSet.AlphabetArrayParameterSet()
          Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet with type AlphabetContainer.AlphabetContainerType.BOTH.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets, AlphabetContainer.AlphabetContainerType type)
          Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of Alphabets and the information about the type of the Alphabets.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type)
          Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information about the type of the Alphabets, e.g.
AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
          The standard constructor for the interface Storable .
 
Method Summary
 AlphabetContainerParameterSet.AlphabetArrayParameterSet clone()
          Creates a full clone (deep copy) of this ParameterSet.
 void fromXML(StringBuffer representation)
          Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().
 String getInstanceComment()
          Returns a descriptive comment on this AlphabetContainerParameterSet.AlphabetArrayParameterSet.
 String getInstanceName()
          Returns a descriptive name for this AlphabetContainerParameterSet.AlphabetArrayParameterSet .
 StringBuffer toXML()
          This method returns an XML representation as StringBuffer of an instance of the implementing class.
 
Methods inherited from class de.jstacs.parameters.ArrayParameterSet
getNumberOfParameters, getParameterAt, hasDefaultOrIsSet
 
Methods inherited from class de.jstacs.parameters.ExpandableParameterSet
addParameterToSet, fromGalaxy, parameterRemovable, removeParameterFromSet, replaceContentWith, toGalaxy
 
Methods inherited from class de.jstacs.parameters.ParameterSet
getAllParameterNames, getComment, getComment, getErrorMessage, getIndex, getName, getName, getParameterForName, getParent, initParameterList, initParameterList, isAtomic, isComparable, parametersLoaded, reset, setParent
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet(AlphabetContainer.AlphabetContainerType type)
                                                        throws Exception
Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from the information about the type of the Alphabets, e.g. if the array shall contain only the parameters for discrete Alphabet s.

Parameters:
type - the type of the Alphabet(s)
Throws:
Exception - if the AlphabetContainerParameterSet.AlphabetArrayParameterSet could not be created
See Also:
ArrayParameterSet.ArrayParameterSet(ParameterSet, String, String)

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet()
                                                        throws Exception
Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet with type AlphabetContainer.AlphabetContainerType.BOTH.

Throws:
Exception - if the AlphabetContainerParameterSet.AlphabetArrayParameterSet could not be created

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet(StringBuffer representation)
                                                        throws NonParsableException
The standard constructor for the interface Storable . Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet out of its XML representation.

Parameters:
representation - the XML representation as StringBuffer
Throws:
NonParsableException - if the AlphabetContainerParameterSet.AlphabetArrayParameterSet could not be reconstructed out of the XML representation (the StringBuffer representation could not be parsed)
See Also:
ArrayParameterSet.ArrayParameterSet(StringBuffer), Storable

AlphabetContainerParameterSet.AlphabetArrayParameterSet

public AlphabetContainerParameterSet.AlphabetArrayParameterSet(Alphabet[] alphabets,
                                                               AlphabetContainer.AlphabetContainerType type)
                                                        throws Exception
Creates a new AlphabetContainerParameterSet.AlphabetArrayParameterSet from an array of Alphabets and the information about the type of the Alphabets.

Parameters:
alphabets - the Alphabets
type - the type of the AlphabetContainer
Throws:
Exception - if the AlphabetContainerParameterSet.AlphabetArrayParameterSet could not be created
Method Detail

clone

public AlphabetContainerParameterSet.AlphabetArrayParameterSet clone()
                                                              throws CloneNotSupportedException
Description copied from class: ParameterSet
Creates a full clone (deep copy) of this ParameterSet. As a convenience-method the user can use fillWithStandardFieldsForClone(ParameterSet) on a newly created instance of a subclass of ParameterSet to obtain a clone/copy of all standard member variables (those already defined in ParameterSet) in the passed ParameterSet. Using this method, the cloning process becomes merely three-step:
This method fulfills the conventions of Object's method Object.clone().

Overrides:
clone in class ExpandableParameterSet
Returns:
a deep clone/copy of this ParameterSet
Throws:
CloneNotSupportedException

toXML

public StringBuffer toXML()
Description copied from interface: Storable
This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:
toXML in interface Storable
Overrides:
toXML in class ArrayParameterSet
Returns:
the XML representation

fromXML

public void fromXML(StringBuffer representation)
             throws NonParsableException
Description copied from class: ParameterSet
Parses the instance fields of a ParameterSet from the XML representation as returned by ParameterSet.toXML().

Overrides:
fromXML in class ArrayParameterSet
Parameters:
representation - the XML representation as StringBuffer
Throws:
NonParsableException - if the XML code could not be parsed
See Also:
ParameterSet.toXML()

getInstanceName

public String getInstanceName()
Returns a descriptive name for this AlphabetContainerParameterSet.AlphabetArrayParameterSet .

Returns:
the descriptive name

getInstanceComment

public String getInstanceComment()
Returns a descriptive comment on this AlphabetContainerParameterSet.AlphabetArrayParameterSet.

Returns:
the descriptive comment