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:

GalaxyConvertible, Storable, Cloneable

Enclosing class:

AlphabetContainerParameterSet

public static class AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet
extends ExpandableParameterSet

Class for the parameter set 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

Constructor Summary

Constructors

Constructor and Description
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet() Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of discrete and continuous Alphabets.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(Alphabet[] alphabets, int[] indexes) Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet from an array of Alphabets and an array of indexes that define the index of the Alphabet in alphabets belonging to that position in indexes.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType type) Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of discrete or continuous Alphabets.
AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation) The standard constructor for the interface Storable .

Method Summary

Methods

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

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, getNumberOfParameters, getParameterAt, 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.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 - if the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet could not be created

See Also:

ExpandableParameterSet.ExpandableParameterSet(ParameterSet, String, String)

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

public AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet()
                                                                 throws Exception

Creates a new AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet for a set of discrete and continuous Alphabets.

Throws:

Exception - if the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet 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 and an array of indexes that define the index of the Alphabet in alphabets belonging to that position in indexes.

Parameters:

alphabets - the array of Alphabets

indexes - the array of indexes of the Alphabets belonging to the positions

Throws:

Exception - if the AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet could not be created

See Also:

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(AlphabetContainer.AlphabetContainerType)

AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet

public AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet(StringBuffer representation)
                                                                 throws NonParsableException

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

Parameters:

representation - the XML representation as StringBuffer

Throws:

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

See Also:

ExpandableParameterSet.ExpandableParameterSet(StringBuffer), Storable

Method Detail

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 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 as StringBuffer

Throws:

NonParsableException - if the XML code could not be parsed

See Also:

ParameterSet.toXML()

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.ParameterSet.hasDefaultOrIsSet() should be called prior to checking specific constraints.

Overrides:

hasDefaultOrIsSet in class ParameterSet

Returns:

true if all parameters have some allowed value set, false otherwise

parseSections

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

Parses the sections as defined in sections to a LinkedList 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 LinkedList of positions

Throws:

Exception - 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/copy of this ParameterSet

Throws:

CloneNotSupportedException

getInstanceName

public String getInstanceName()

Returns a descriptive name for this AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet.

Returns:

the descriptive name

getInstanceComment

public String getInstanceComment()

Returns a descriptive comment on this AlphabetContainerParameterSet.SectionDefinedAlphabetParameterSet.

Returns:

the descriptive comment