org.sbml.jsbml.xml.parsers

Class L3LayoutParser

java.lang.Object

org.sbml.jsbml.xml.parsers.AbstractReaderWriter

org.sbml.jsbml.xml.parsers.L3LayoutParser

All Implemented Interfaces:

PackageParser, ReadingParser, WritingParser

This class is used to parse the layout extension package elements and attributes. The namespaceURI URI of this parser is "http://www.sbml.org/sbml/level3/version1/layout/version1". This parser is able to read and write elements of the layout package (implements ReadingParser and WritingParser).

Since:

1.0

Version:

$Rev: 1639 $

Author:

Nicolas Rodriguez

Field Detail

logger

private org.apache.log4j.Logger logger

namespaces

private static final java.util.List<java.lang.String> namespaces

Constructor Detail

L3LayoutParser

public L3LayoutParser()

Method Detail

getNamespaceURI

public java.lang.String getNamespaceURI()

Description copied from class: AbstractReaderWriter

Return the namespace URI of the namespace parsed by this class.

Specified by:

getNamespaceURI in class AbstractReaderWriter

Returns:

the namespace URI of the namespace parsed by this class.

getShortLabel

public java.lang.String getShortLabel()

Description copied from class: AbstractReaderWriter

Returns the shortLabel of the namespace parsed by this class.

Specified by:

getShortLabel in class AbstractReaderWriter

Returns:

the shortLabel of the namespace parsed by this class.

getListOfSBMLElementsToWrite

public java.util.List<java.lang.Object> getListOfSBMLElementsToWrite(java.lang.Object sbase)

Description copied from interface: WritingParser

Returns the list of children of the objectToWrite.

Specified by:

getListOfSBMLElementsToWrite in interface WritingParser

Overrides:

getListOfSBMLElementsToWrite in class AbstractReaderWriter

Parameters:

sbase - the SBase component to write.

Returns:

the list of components that 'SBase' contains. Represents the list of subNodes of this SBase component.

processStartElement

public java.lang.Object processStartElement(java.lang.String elementName,
                                   java.lang.String uri,
                                   java.lang.String prefix,
                                   boolean hasAttributes,
                                   boolean hasNamespaces,
                                   java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the XML element and modify 'contextObject' in consequence.

For example, if the contextObject is an instance of Event and the elementName is 'trigger', this method will create a new Trigger instance and will set the trigger instance of the 'contextObject' to the new Trigger. Then the method will return the new Trigger instance which is the new environment.

Specified by:

processStartElement in interface ReadingParser

Specified by:

processStartElement in class AbstractReaderWriter

Parameters:

elementName - the localName of the XML element to process

prefix - the prefix of the XML element to process

hasAttributes - boolean value to know if this XML element has attributes.

hasNamespaces - boolean value to know if this XML element contains namespace declarations.

contextObject - the object to set or modify depending on the identity of the current XML element. This object represents the context of the XML element in the SBMLDocument.

Returns:

a new contextObject which represents the environment of the next node/subnode in the SBMLDocument. If null is returned, the contextObject will not change.

processEndDocument

public void processEndDocument(SBMLDocument sbmlDocument)

Description copied from interface: ReadingParser

Process the end of the document. Do the necessary changes in the SBMLDocument. For example, check if all the annotations are valid, etc.

Specified by:

processEndDocument in interface ReadingParser

Overrides:

processEndDocument in class AbstractReaderWriter

Parameters:

sbmlDocument - the final initialized SBMLDocument instance.

writeElement

public void writeElement(SBMLObjectForXML xmlObject,
                java.lang.Object sbmlElementToWrite)

Description copied from interface: WritingParser

Sets the name of xmlObject (if it is not set) to the element name of sbmlElementToWrite.

Specified by:

writeElement in interface WritingParser

Overrides:

writeElement in class AbstractReaderWriter

Parameters:

xmlObject - contains the XML information about sbmlElement.

sbmlElementToWrite - the SBase component to write

getNamespaces

public java.util.List<java.lang.String> getNamespaces()

Description copied from interface: ReadingParser

Returns a List of all the namespaces that this parser is handling.

Specified by:

getNamespaces in interface ReadingParser

Specified by:

getNamespaces in interface WritingParser

Returns:

a List of all the namespaces that this parser is handling

getPackageNamespaces

public java.util.List<java.lang.String> getPackageNamespaces()

Description copied from interface: PackageParser

Returns a List of all the valid namespaces for the package.

Specified by:

getPackageNamespaces in interface PackageParser

Returns:

a List of all the valid namespaces for the package.

getNamespaceFor

public java.lang.String getNamespaceFor(int level,
                               int version,
                               int packageVersion)

Description copied from interface: PackageParser

Gets the namespace for this package that correspond to the given SBML level, version and the package version.

Returns null if the combined level, version and packageVersion is invalid or not known from the package parser implementation.

Specified by:

getNamespaceFor in interface PackageParser

Parameters:

level - - the SBML level

version - - the SBML version

packageVersion - - the package version

Returns:

the namespace for this package that correspond to the given SBML level and version and the package version or null if nothing valid is found.

getPackageName

public java.lang.String getPackageName()

Description copied from interface: PackageParser

Returns the short name of this package.

Specified by:

getPackageName in interface PackageParser

Returns:

the short name of this package.

isRequired

public boolean isRequired()

Description copied from interface: PackageParser

Returns the value of the required attribute for this package.

Specified by:

isRequired in interface PackageParser

Returns:

the value of the required attribute for this package.

createPluginFor

public SBasePlugin createPluginFor(SBase sbase)

Description copied from interface: PackageParser

Creates a new SBasePlugin for the given SBase and add it to the SBasePlugin map of the SBase.

Specified by:

createPluginFor in interface PackageParser

Parameters:

sbase - - the sbase for which you want to create an SBasePlugin

Returns:

a new SBasePlugin corresponding to the given SBase.