de.jstacs.data
Class AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

java.lang.Object
  de.jstacs.parameters.ParameterSet
      de.jstacs.parameters.ExpandableParameterSet
          de.jstacs.data.AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

All Implemented Interfaces:

RangeIterator, Storable, Cloneable

Enclosing class:

AlphabetContainerParameterSet

public static class AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
extends ExpandableParameterSet

Class for the parameters of an array of Alphabets where each alphabet may be used for one or more sections of positions.

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, ranged

Constructor Summary

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[] alphabets, int[] indexes)
Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an array of Alphabets, an array of indexes that define the index of the Alphabet in alphabets belonging to that position in indexes and a parameter if the alphabets may be discrete only.

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType type)
Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of discrete or continuous alphabets.

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation)
Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from its XML representation.

Method Summary

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet	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 ParameterSet.
String	getInstanceName() Returns a descriptive name for this ParameterSet.
boolean	hasDefaultOrIsSet() Returns true if all parameters in this ParameterSet are either set by the user or have default values.
protected void	loadParameters() Loads the parameters for this ParameterSet.
static LinkedList<Integer>	parseSections(String sections) Parses the sections as defined in sections to a list of Integers.
StringBuffer	toXML() This method returns an XML-representation of an instance of the implementing class.

Methods inherited from class de.jstacs.parameters.ExpandableParameterSet

addParameterToSet, parameterRemovable, removeParameterFromSet, replaceContentWith, replaceParametersWithRangedInstance

Methods inherited from class de.jstacs.parameters.ParameterSet

getErrorMessage, getId, getNumberOfParameters, getNumberOfValues, getParameterAt, getParent, initParameterList, initParameterList, isAtomic, isRanged, makeRanged, next, parametersLoaded, propagateId, recieveId, reset, resetToFirst, setParent, simplify, valuesToString

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

public AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType type)
                                                                 throws Exception

Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of discrete or continuous alphabets.

Parameters:

type - the type of the alphabet(s)

Throws:

Exception - is thrown if the Parameters could not be created

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

public AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[] alphabets,
                                                                        int[] indexes)
                                                                 throws Exception

Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an array of Alphabets, an array of indexes that define the index of the Alphabet in alphabets belonging to that position in indexes and a parameter if the alphabets may be discrete only.

Parameters:

alphabets - the alphabets

indexes - the indexes

Throws:

Exception - is thrown if the Parameters could not be created

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

public AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation)
                                                                 throws NonParsableException

Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from its XML representation.

Parameters:

representation - the XML representation

Throws:

NonParsableException - is thrown if representation could not be parsed

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 ExpandableParameterSet

Throws:

Exception - an Exception is thrown if the parameters could not be loaded

See Also:

ParameterSet.parameters, Parameter

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML-representation of an instance of the implementing class.

Specified by:

toXML in interface Storable

Overrides:

toXML in class ExpandableParameterSet

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 ExpandableParameterSet

Parameters:

representation - the XML-representation

Throws:

NonParsableException - is thrown if the XML-code could not be parsed

hasDefaultOrIsSet

public boolean hasDefaultOrIsSet()

Description copied from class: ParameterSet

Returns true if all parameters in this ParameterSet are either set by the user or have default values. If any additional constraints are required on your parameters you should either specify some ParameterValidator on these parameters or implement these constraints by overriding this method in your implementation of ParameterSet. It is recommended to specify a useful remark which constraint failed in the member-variable errorMessage, which will be displayed to the user. In the overriding method super.hasDefaultOrIsSet() should be called prior to checking specific constraints.

Overrides:

hasDefaultOrIsSet in class ParameterSet

Returns:

true if all parameters have some allowed value set

parseSections

public static LinkedList<Integer> parseSections(String sections)
                                         throws Exception

Parses the sections as defined in sections to a list of Integers. Sections may be defined as ranges (e.g. "3-6"), as lists (e.g. "3,4,5,6"), or as combinations of both (e.g. ("3-5,6").

Parameters:

sections - the sections

Returns:

the list of positions

Throws:

Exception - is thrown if sections could not be parsed, contains a position more than once or contains positions that are out of range

clone

public AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet 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:

• Create a new instance of your subclass of ParameterSet>, most likely with an empty constructor or the one taking just the instance-class
• call this.fillWithStandardFieldsForClone on this instance
• return the instance

This method fulfills the conventions of Object's method Object.clone()

Overrides:

clone in class ExpandableParameterSet

Returns:

a deep clone of this ParameterSet

Throws:

CloneNotSupportedException

getInstanceName

public String getInstanceName()

Returns a descriptive name for this ParameterSet.

Returns:

the name

getInstanceComment

public String getInstanceComment()

Returns a descriptive comment on this ParameterSet.

Returns:

the comment