org.sbml.jsbml.xml.parsers

Class AbstractReaderWriter

java.lang.Object

org.sbml.jsbml.xml.parsers.AbstractReaderWriter

All Implemented Interfaces:

ReadingParser, WritingParser

public abstract class AbstractReaderWriter
extends java.lang.Object
implements ReadingParser, WritingParser

Contains some code shared by most of the L3 packages parsers.

Since:

1.0

Version:

$Rev$

Author:

Nicolas Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private static org.apache.log4j.Logger	logger A Logger for this class.

Constructor Summary

Constructors

Constructor and Description
AbstractReaderWriter()

Method Summary

Modifier and Type	Method and Description
protected java.lang.Object	createListOfChild(ListOf<?> listOf, java.lang.String elementName) Creates a new object instance using reflection on the listOf parent.
java.util.List<java.lang.Object>	getListOfSBMLElementsToWrite(java.lang.Object sbase) Returns the list of children of the objectToWrite.
abstract java.lang.String	getNamespaceURI() Return the namespace URI of the namespace parsed by this class.
abstract java.lang.String	getShortLabel() Returns the shortLabel of the namespace parsed by this class.
boolean	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) Process the XML attribute and modify 'contextObject' in consequence.
void	processCharactersOf(java.lang.String elementName, java.lang.String characters, java.lang.Object contextObject) Process the text of a XML element and modify 'contextObject' in consequence.
void	processEndDocument(SBMLDocument sbmlDocument) Process the end of the document.
boolean	processEndElement(java.lang.String elementName, java.lang.String prefix, boolean isNested, java.lang.Object contextObject) Process the end of the element 'elementName'.
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) Process the namespace and modify the contextObject in consequence.
abstract java.lang.Object	processStartElement(java.lang.String elementName, java.lang.String uri, java.lang.String prefix, boolean hasAttributes, boolean hasNamespaces, java.lang.Object contextObject) Process the XML element and modify 'contextObject' in consequence.
static void	processUnknownAttribute(java.lang.String attributeName, java.lang.String namespace, java.lang.String value, java.lang.String prefix, java.lang.Object contextObject) Process an unknown XML attribute.
static XMLNode	processUnknownElement(java.lang.String elementName, java.lang.String namespace, java.lang.String prefix, java.lang.Object contextObject) Process an unknown XML element.
static void	storeElementsOrder(java.lang.String elementName, java.lang.Object contextObject) Stores a list of elements as they are given.
void	writeAttributes(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Adds the XML attributes of the sbmlElementToWrite to the attributes HashMap of the xmlObject.
void	writeCharacters(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Sets the characters of xmlObject depending on the sbml element to write.
void	writeElement(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Sets the name of xmlObject (if it is not set) to the element name of sbmlElementToWrite.
void	writeNamespaces(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Sets the namespace of xmlObject (if it is not set) to the namespace of sbmlElementToWrite.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.xml.parsers.ReadingParser

getNamespaces

Methods inherited from interface org.sbml.jsbml.xml.parsers.WritingParser

getNamespaces

Field Detail

logger

private static final transient org.apache.log4j.Logger logger

A Logger for this class.

Constructor Detail

AbstractReaderWriter

public AbstractReaderWriter()

Method Detail

processAttribute

public boolean 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.

Returns:

true if the attribute was recognized and stored in the contextObject, false otherwise.

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.

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

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 abstract 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.

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.

processUnknownAttribute

public static void processUnknownAttribute(java.lang.String attributeName,
                                           java.lang.String namespace,
                                           java.lang.String value,
                                           java.lang.String prefix,
                                           java.lang.Object contextObject)

Process an unknown XML attribute. Stores it into an XMLNode. This XMLNode is put into the user object map of the contextObject, using the key JSBML.UNKNOWN_XML.

Parameters:

attributeName - the attribute name.

namespace - the attribute namespace URI.

value - the attribute value.

prefix - the attribute namespace prefix.

contextObject - the context Object.

processUnknownElement

public static XMLNode processUnknownElement(java.lang.String elementName,
                                            java.lang.String namespace,
                                            java.lang.String prefix,
                                            java.lang.Object contextObject)

Process an unknown XML element. Stores it into an XMLNode. This XMLNode is put into the user object map of the contextObject, using the key JSBML.UNKNOWN_XML.

Parameters:

elementName - the element name.

namespace - the element namespace URI.

prefix - the element namespace prefix.

contextObject - the context Object.

storeElementsOrder

public static void storeElementsOrder(java.lang.String elementName,
                                      java.lang.Object contextObject)

Stores a list of elements as they are given. This List is put into the user object map of the contextObject, using the key JSBML.CHILD_ELEMENT_NAMES.

Parameters:

elementName - the child element name

contextObject - the context object

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

createListOfChild

protected java.lang.Object createListOfChild(ListOf<?> listOf,
                                             java.lang.String elementName)

Creates a new object instance using reflection on the listOf parent.

Parameters:

listOf - the ListOf that will contain the new instance

elementName - the element name.

Returns:

a new object instance using reflection on the listOf parent or null if an error occurs when trying to instantiate the new object.

getShortLabel

public abstract java.lang.String getShortLabel()

Returns the shortLabel of the namespace parsed by this class.

Returns:

the shortLabel of the namespace parsed by this class.

getNamespaceURI

public abstract java.lang.String getNamespaceURI()

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

Returns:

the namespace URI of the namespace parsed by this class.