org.sbml.jsbml.xml.parsers

Class MathMLStaxParser

java.lang.Object

org.sbml.jsbml.xml.parsers.MathMLStaxParser

All Implemented Interfaces:

ReadingParser

public class MathMLStaxParser
extends java.lang.Object
implements ReadingParser

A MathMLStaxParser is used to parse the MathML expressions injected into a SBML file. The name space URI of this parser is "http://www.w3.org/1998/Math/MathML". This parser is able to read and write MathML expressions (implements ReadingParser and WritingParser).

Since:

0.8

Author:

Nicolas Rodriguez

Field Summary

Fields

Modifier and Type	Field and Description
private short	indent The number of white spaces for the indent if this is to be used.
private boolean	indenting Decides whether or not the content of the MathML string should be indented.
private boolean	isFunctionDefinition
static java.lang.String	JSBML_MATH_COUNT
private boolean	lastElementWasApply
private static org.apache.log4j.Logger	logger A Logger for this class.
private static java.util.List<java.lang.String>	namespaces
private boolean	omitXMLDeclaration If true no XML declaration will be written into the MathML output, otherwise the XML version will appear at the beginning of the output.
private int	piecewiseCount integer used to count the number of piecewise elements open
private java.util.ArrayList<java.lang.Integer>	piecewiseOtherwiseCount list used to count the number of otherwise elements open related to a piecewise element.
private java.util.ArrayList<java.lang.Integer>	piecewisePieceCount list used to count the number of piece elements open related to a piecewise element.

Constructor Summary

Constructors

Constructor and Description
MathMLStaxParser()

Method Summary

Modifier and Type	Method and Description
int	getIndent() Returns the indent
boolean	getIndenting() Returns true if indenting
java.util.List<java.lang.String>	getNamespaces() Returns a List of all the namespaces that this parser is handling.
boolean	getOmitXMLDeclaration() Returns true if we need to omit the XML declaration.
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'.
private void	processMathElement(java.lang.Object contextObject) Process a MathContainer to add one to the number of math element encountered.
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.
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.
void	setIndent(int indent)
void	setIndenting(boolean indenting)
void	setOmitXMLDeclaration(boolean omitXMLDeclaration)

Methods inherited from class java.lang.Object

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

Field Detail

indent

private short indent

The number of white spaces for the indent if this is to be used.

indenting

private boolean indenting

Decides whether or not the content of the MathML string should be indented.

omitXMLDeclaration

private boolean omitXMLDeclaration

If true no XML declaration will be written into the MathML output, otherwise the XML version will appear at the beginning of the output.

logger

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

A Logger for this class.

JSBML_MATH_COUNT

public static final java.lang.String JSBML_MATH_COUNT

See Also:

Constant Field Values

lastElementWasApply

private boolean lastElementWasApply

isFunctionDefinition

private boolean isFunctionDefinition

piecewiseCount

private int piecewiseCount

integer used to count the number of piecewise elements open

piecewisePieceCount

private java.util.ArrayList<java.lang.Integer> piecewisePieceCount

list used to count the number of piece elements open related to a piecewise element.

The size of the list should be equals to piecewiseCount.

piecewiseOtherwiseCount

private java.util.ArrayList<java.lang.Integer> piecewiseOtherwiseCount

list used to count the number of otherwise elements open related to a piecewise element.

The size of the list should be equals to piecewiseCount.

namespaces

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

Constructor Detail

MathMLStaxParser

public MathMLStaxParser()

Method Detail

getIndent

public int getIndent()

Returns the indent

Returns:

the indent

getIndenting

public boolean getIndenting()

Returns true if indenting

Returns:

true if indenting

getOmitXMLDeclaration

public boolean getOmitXMLDeclaration()

Returns true if we need to omit the XML declaration.

Returns:

true if we need to omit the XML declaration.

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 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.

processMathElement

private void processMathElement(java.lang.Object contextObject)

Process a MathContainer to add one to the number of math element encountered.

Parameters:

contextObject - a MathContainer instance

setIndent

public void setIndent(int indent)

Parameters:

indent - the indent to set

setIndenting

public void setIndenting(boolean indenting)

Parameters:

indenting - the indenting to set

setOmitXMLDeclaration

public void setOmitXMLDeclaration(boolean omitXMLDeclaration)

Parameters:

omitXMLDeclaration - the omitXMLDeclaration to set

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

Returns:

a List of all the namespaces that this parser is handling