org.jgap.xml

Class XMLManager

java.lang.Object

org.jgap.xml.XMLManager

public class XMLManager
extends java.lang.Object

The XMLManager performs marshalling of genetic entity instances (such as Chromosomes and Genotypes) to XML representations of those entities, as well as unmarshalling. All of the methods in this class are static, so no construction is required (or allowed).

Since:

1.0

Method Summary

Modifier and Type	Method and Description
static Chromosome	getChromosomeFromDocument(Configuration a_activeConfiguration, org.w3c.dom.Document a_xmlDocument) Unmarshall a Chromosome instance from a given XML Document representation.
static Chromosome	getChromosomeFromElement(Configuration a_activeConfiguration, org.w3c.dom.Element a_xmlElement) Unmarshall a Chromosome instance from a given XML Element representation.
static Gene[]	getGenesFromElement(Configuration a_activeConfiguration, org.w3c.dom.Element a_xmlElement) Unmarshall a Chromosome instance from a given XML Element representation.
static Genotype	getGenotypeFromDocument(Configuration a_activeConfiguration, org.w3c.dom.Document a_xmlDocument) Unmarshall a Genotype instance from a given XML Document representation.
static Genotype	getGenotypeFromElement(Configuration a_activeConfiguration, org.w3c.dom.Element a_xmlElement) Unmarshall a Genotype instance from a given XML Element representation.
static org.w3c.dom.Document	readFile(java.io.File file) Reads in an XML file and returns a Document object.
static org.w3c.dom.Document	representChromosomeAsDocument(IChromosome a_subject) Deprecated. use XMLDocumentBuilder instead
static org.w3c.dom.Element	representChromosomeAsElement(IChromosome a_subject, org.w3c.dom.Document a_xmlDocument) Deprecated. use XMLDocumentBuilder instead
static org.w3c.dom.Element	representGenesAsElement(Gene[] a_geneValues, org.w3c.dom.Document a_xmlDocument) Deprecated. use XMLDocumentBuilder instead
static org.w3c.dom.Document	representGenotypeAsDocument(Genotype a_subject) Deprecated. use XMLDocumentBuilder instead
static org.w3c.dom.Element	representGenotypeAsElement(Genotype a_subject, org.w3c.dom.Document a_xmlDocument) Deprecated. use XMLDocumentBuilder instead
static void	writeFile(org.w3c.dom.Document doc, java.io.File file) Writes an XML file from a Document object.

Methods inherited from class java.lang.Object

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

Method Detail

representChromosomeAsDocument

public static org.w3c.dom.Document representChromosomeAsDocument(IChromosome a_subject)

Deprecated. use XMLDocumentBuilder instead

Marshall a Chromosome instance to an XML Document representation, including its contained Gene instances.

Parameters:

a_subject - the chromosome to represent as an XML document

Returns:

a Document object representing the given Chromosome

Since:

1.0

representGenotypeAsDocument

public static org.w3c.dom.Document representGenotypeAsDocument(Genotype a_subject)

Deprecated. use XMLDocumentBuilder instead

Marshall a Genotype to an XML Document representation, including its population of Chromosome instances.

Parameters:

a_subject - the genotype to represent as an XML document

Returns:

a Document object representing the given Genotype

Since:

1.0

representGenesAsElement

public static org.w3c.dom.Element representGenesAsElement(Gene[] a_geneValues,
                                                          org.w3c.dom.Document a_xmlDocument)

Deprecated. use XMLDocumentBuilder instead

Marshall an array of Genes to an XML Element representation.

Parameters:

a_geneValues - the genes to represent as an XML element

a_xmlDocument - a Document instance that will be used to create the Element instance. Note that the element will NOT be added to the document by this method

Returns:

an Element object representing the given genes

Since:

1.0

representChromosomeAsElement

public static org.w3c.dom.Element representChromosomeAsElement(IChromosome a_subject,
                                                               org.w3c.dom.Document a_xmlDocument)

Deprecated. use XMLDocumentBuilder instead

Marshall a Chromosome instance to an XML Element representation, including its contained Genes as sub-elements. This may be useful in scenarios where representation as an entire Document is undesirable, such as when the representation of this Chromosome is to be combined with other elements in a single Document.

Parameters:

a_subject - the chromosome to represent as an XML element

a_xmlDocument - a Document instance that will be used to create the Element instance. Note that the element will NOT be added to the document by this method

Returns:

an Element object representing the given Chromosome

Since:

1.0

representGenotypeAsElement

public static org.w3c.dom.Element representGenotypeAsElement(Genotype a_subject,
                                                             org.w3c.dom.Document a_xmlDocument)

Deprecated. use XMLDocumentBuilder instead

Marshall a Genotype instance into an XML Element representation, including its population of Chromosome instances as sub-elements. This may be useful in scenarios where representation as an entire Document is undesirable, such as when the representation of this Genotype is to be combined with other elements in a single Document.

Parameters:

a_subject - the genotype to represent as an XML element

a_xmlDocument - a Document instance that will be used to create the Element instance. Note that the element will NOT be added to the document by this method

Returns:

an Element object representing the given Genotype

Since:

1.0

getGenesFromElement

public static Gene[] getGenesFromElement(Configuration a_activeConfiguration,
                                         org.w3c.dom.Element a_xmlElement)
                                  throws ImproperXMLException,
                                         UnsupportedRepresentationException,
                                         GeneCreationException

Unmarshall a Chromosome instance from a given XML Element representation.

Parameters:

a_activeConfiguration - current Configuration object

a_xmlElement - the XML Element representation of the Chromosome

Returns:

a new Chromosome instance setup with the data from the XML Element representation

Throws:

ImproperXMLException - if the given Element is improperly structured or missing data

UnsupportedRepresentationException - if the actively configured Gene implementation does not support the string representation of the alleles used in the given XML document

GeneCreationException - if there is a problem creating or populating a Gene instance

Since:

1.0

getChromosomeFromElement

public static Chromosome getChromosomeFromElement(Configuration a_activeConfiguration,
                                                  org.w3c.dom.Element a_xmlElement)
                                           throws ImproperXMLException,
                                                  InvalidConfigurationException,
                                                  UnsupportedRepresentationException,
                                                  GeneCreationException

Unmarshall a Chromosome instance from a given XML Element representation.

Parameters:

a_activeConfiguration - the current active Configuration object that is to be used during construction of the Chromosome

a_xmlElement - the XML Element representation of the Chromosome

Returns:

a new Chromosome instance setup with the data from the XML Element representation

Throws:

ImproperXMLException - if the given Element is improperly structured or missing data

InvalidConfigurationException - if the given Configuration is in an inconsistent state

UnsupportedRepresentationException - if the actively configured Gene implementation does not support the string representation of the alleles used in the given XML document

GeneCreationException - if there is a problem creating or populating a Gene instance

Since:

1.0

getGenotypeFromElement

public static Genotype getGenotypeFromElement(Configuration a_activeConfiguration,
                                              org.w3c.dom.Element a_xmlElement)
                                       throws ImproperXMLException,
                                              InvalidConfigurationException,
                                              UnsupportedRepresentationException,
                                              GeneCreationException

Unmarshall a Genotype instance from a given XML Element representation. Its population of Chromosomes will be unmarshalled from the Chromosome sub-elements.

Parameters:

a_activeConfiguration - the current active Configuration object that is to be used during construction of the Genotype and Chromosome instances

a_xmlElement - the XML Element representation of the Genotype

Returns:

a new Genotype instance, complete with a population of Chromosomes, setup with the data from the XML Element representation

Throws:

ImproperXMLException - if the given Element is improperly structured or missing data

InvalidConfigurationException - if the given Configuration is in an inconsistent state

UnsupportedRepresentationException - if the actively configured Gene implementation does not support the string representation of the alleles used in the given XML document

GeneCreationException - if there is a problem creating or populating a Gene instance

Since:

1.0

getGenotypeFromDocument

public static Genotype getGenotypeFromDocument(Configuration a_activeConfiguration,
                                               org.w3c.dom.Document a_xmlDocument)
                                        throws ImproperXMLException,
                                               InvalidConfigurationException,
                                               UnsupportedRepresentationException,
                                               GeneCreationException

Unmarshall a Genotype instance from a given XML Document representation. Its population of Chromosomes will be unmarshalled from the Chromosome sub-elements.

Parameters:

a_activeConfiguration - the current active Configuration object that is to be used during construction of the Genotype and Chromosome instances

a_xmlDocument - the XML Document representation of the Genotype

Returns:

A new Genotype instance, complete with a population of Chromosomes, setup with the data from the XML Document representation

Throws:

ImproperXMLException - if the given Document is improperly structured or missing data

InvalidConfigurationException - if the given Configuration is in an inconsistent state

UnsupportedRepresentationException - if the actively configured Gene implementation does not support the string representation of the alleles used in the given XML document

GeneCreationException - if there is a problem creating or populating a Gene instance

Since:

1.0

getChromosomeFromDocument

public static Chromosome getChromosomeFromDocument(Configuration a_activeConfiguration,
                                                   org.w3c.dom.Document a_xmlDocument)
                                            throws ImproperXMLException,
                                                   InvalidConfigurationException,
                                                   UnsupportedRepresentationException,
                                                   GeneCreationException

Unmarshall a Chromosome instance from a given XML Document representation. Its genes will be unmarshalled from the gene sub-elements.

Parameters:

a_activeConfiguration - the current active Configuration object that is to be used during construction of the Chromosome instances

a_xmlDocument - the XML Document representation of the Chromosome

Returns:

a new Chromosome instance setup with the data from the XML Document representation

Throws:

ImproperXMLException - if the given Document is improperly structured or missing data

InvalidConfigurationException - if the given Configuration is in an inconsistent state

UnsupportedRepresentationException - if the actively configured Gene implementation does not support the string representation of the alleles used in the given XML document

GeneCreationException - if there is a problem creating or populating a Gene instance

Since:

1.0

readFile

public static org.w3c.dom.Document readFile(java.io.File file)
                                     throws java.io.IOException,
                                            org.xml.sax.SAXException

Reads in an XML file and returns a Document object.

Parameters:

file - the file to be read in

Returns:

Document

Throws:

java.io.IOException

SAXException

Since:

2.0

writeFile

public static void writeFile(org.w3c.dom.Document doc,
                             java.io.File file)
                      throws java.io.IOException

Writes an XML file from a Document object.

Parameters:

doc - the Document object to be written to file

file - the file to be written

Throws:

java.io.IOException

Since:

2.0