org.sbml.jsbml.xml.parsers

Class LayoutParser

java.lang.Object

org.sbml.jsbml.xml.parsers.LayoutParser

All Implemented Interfaces:

PackageParser, ReadingParser, WritingParser

Parses the SBML level 2 layout extension package elements and attributes. The namespaceURI URI of this parser is "http://projects.eml.org/bcb/sbml/level2". This parser is able to read and write elements of the layout package (implements ReadingParser and WritingParser).

Since:

1.0

Version:

$Rev: 1830 $

Author:

Nicolas Rodriguez, Sebastian Frölich, Andreas Dräger

Field Detail

logger

private org.apache.log4j.Logger logger

namespaceURI

private static final java.lang.String namespaceURI

The namespace URI of this parser.

See Also:

Constant Field Values

groupList

private LayoutParser.LayoutList groupList

The layoutList enum which represents the name of the list this parser is currently reading.

log4jLogger

private org.apache.log4j.Logger log4jLogger

Log4j logger

sbmlLayoutElements

private java.util.HashMap<java.lang.String,java.lang.Class<? extends java.lang.Object>> sbmlLayoutElements

This map contains all the relationships XML element name <=> matching java class.

Constructor Detail

LayoutParser

public LayoutParser()

Method Detail

getNamespaceURI

public static java.lang.String getNamespaceURI()

Returns:

the namespaceURI of this parser.

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

Parameters:

sbase - the SBase component to write.

Returns:

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

writeAttributes

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

Description copied from interface: WritingParser

Adds the XML attributes of the sbmlElementToWrite to the attributes HashMap of the xmlObject.

Specified by:

writeAttributes in interface WritingParser

Parameters:

xmlObject - contains the XML information about sbmlElement.

sbmlElementToWrite - the SBase component to write

writeCharacters

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

Description copied from interface: WritingParser

Sets the characters of xmlObject depending on the sbml element to write.

Specified by:

writeCharacters in interface WritingParser

Parameters:

xmlObject - contains the XML information about sbmlElement.

sbmlElementToWrite - the SBase component to write

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

Parameters:

xmlObject - contains the XML information about sbmlElement.

sbmlElementToWrite - the SBase component to write

writeNamespaces

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

Description copied from interface: WritingParser

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

Specified by:

writeNamespaces in interface WritingParser

Parameters:

xmlObject - contains the XML information about sbmlElement.

sbmlElementToWrite - the SBase component to write

processAttribute

public void processAttribute(java.lang.String elementName,
                    java.lang.String attributeName,
                    java.lang.String value,
                    java.lang.String uri,
                    java.lang.String prefix,
                    boolean isLastAttribute,
                    java.lang.Object contextObject)

Description copied from interface: ReadingParser

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

For example, if the contextObject is an instance of Reaction and the attributeName is 'fast', this method will set the 'fast' variable of the 'contextObject' to 'value'. Then it will return the modified Reaction instance.

Specified by:

processAttribute in interface ReadingParser

Parameters:

elementName - the localName of the XML element.

attributeName - the attribute localName of the XML element.

value - the value of the XML attribute.

prefix - the attribute prefix

isLastAttribute - boolean value to know if this attribute is the last attribute of the XML element.

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

processCharactersOf

public void processCharactersOf(java.lang.String elementName,
                       java.lang.String characters,
                       java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the text of a XML element and modify 'contextObject' in consequence.

For example, if the contextObject is an instance of Creator and the elementName is 'Family', this method will set the familyName of the 'contextObject' to the text value. Then it will return the changed Creator instance.

Specified by:

processCharactersOf in interface ReadingParser

Parameters:

elementName - the localName of the XML element.

characters - the text of this XML element.

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

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

Parameters:

sbmlDocument - the final initialized SBMLDocument instance.

processNamespace

public void processNamespace(java.lang.String elementName,
                    java.lang.String URI,
                    java.lang.String prefix,
                    java.lang.String localName,
                    boolean hasAttributes,
                    boolean isLastNamespace,
                    java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the namespace and modify the contextObject in consequence.

For example, if the contextObject is an instance of SBMLDocument, the namespaces will be stored in the SBMLNamespaces HashMap of this SBMLDocument.

Specified by:

processNamespace in interface ReadingParser

Parameters:

elementName - the localName of the XML element.

URI - the URI of the namespace

prefix - the prefix of the namespace.

localName - the localName of the namespace.

hasAttributes - boolean value to know if there are attributes after the namespace declarations.

isLastNamespace - boolean value to know if this namespace is the last namespace of this element.

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

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

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.

setNamespace

private void setNamespace(SBase sbase,
                java.lang.String namespace)

Parameters:

sbase -

namespace -

processEndElement

public boolean processEndElement(java.lang.String elementName,
                        java.lang.String prefix,
                        boolean isNested,
                        java.lang.Object contextObject)

Description copied from interface: ReadingParser

Process the end of the element 'elementName'. Modify or not the contextObject.

Specified by:

processEndElement in interface ReadingParser

Parameters:

elementName - the localName of the XML element.

prefix - the prefix of the XML element.

isNested - boolean value to know if the XML element is a nested element.

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

Returns:

true to remove the contextObject from the stack, if false is returned the contextObject will stay on top of the stack

setLevelAndVersionFor

private void setLevelAndVersionFor(java.lang.Object newContextObject,
                         SBase parent)

Sets level and version properties of the new object according to the value in the model.

Parameters:

newContextObject -

parent -

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

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.

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.

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.

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.