org.sbml.jsbml.xml.parsers

Class MathMLParser

java.lang.Object

org.sbml.jsbml.xml.parsers.MathMLParser

All Implemented Interfaces:

ReadingParser, WritingParser

Deprecated.

this class should not be used anymore, replaced by MathMLStaxParser. But we keep it in case somebody want to use Document

@Deprecated
public class MathMLParser
extends java.lang.Object
implements ReadingParser, WritingParser

A MathMLParser is used to parse the MathML expressions injected into a SBML file. This class use DOM to parse the mathML. 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

Version:

$Rev$

Author:

Marine Dumousseau, Andreas Dräger

Field Summary

Fields

Modifier and Type	Field and Description
private short	indent Deprecated. The number of white spaces for the indent if this is to be used.
private boolean	indenting Deprecated. Decides whether or not the content of the MathML string should be indented.
private boolean	omitXMLDeclaration Deprecated. 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 static java.lang.String	sbmlNS Deprecated. The SBML attribute for the additional namespace.
private static java.lang.String	sbmlUnits Deprecated. The attribute for SBML units.

Constructor Summary

Constructors

Constructor and Description
MathMLParser() Deprecated.

Method Summary

Modifier and Type	Method and Description
static boolean	checkContainsNumbersReferingToUnits(org.w3c.dom.Node node) Deprecated. Recursively checks whether the given Node contains any numbers that refer to unit declarations.
static org.w3c.dom.Document	createMathMLDocumentFor(org.w3c.dom.Node node, int sbmlLevel) Deprecated.
static java.lang.String	getDefinitionURIavogadro() Deprecated.
static java.lang.String	getDefinitionURIdelay() Deprecated.
static java.lang.String	getDefinitionURItime() Deprecated.
int	getIndent() Deprecated.
boolean	getIndenting() Deprecated.
java.util.ArrayList<java.lang.Object>	getListOfSBMLElementsToWrite(java.lang.Object sbase) Deprecated. Returns the list of children of the objectToWrite.
java.util.List<java.lang.String>	getNamespaces() Deprecated. Returns a List of all the namespaces that this parser is handling.
static java.lang.String	getNamespaceURI() Deprecated.
boolean	getOmitXMLDeclaration() Deprecated.
static java.lang.String	getSBMLNSAttribute() Deprecated.
static java.lang.String	getSBMLUnitsAttribute() Deprecated.
static java.lang.String	getXMLnamespaceSBML() Deprecated. The additional MathML name space for units to numbers.
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) Deprecated. Process the XML attribute and modify 'contextObject' in consequence.
void	processCharactersOf(java.lang.String elementName, java.lang.String characters, java.lang.Object contextObject) Deprecated. Process the text of a XML element and modify 'contextObject' in consequence.
void	processEndDocument(SBMLDocument sbmlDocument) Deprecated. Process the end of the document.
boolean	processEndElement(java.lang.String ElementName, java.lang.String prefix, boolean isNested, java.lang.Object contextObject) Deprecated. 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) Deprecated. 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) Deprecated. Process the XML element and modify 'contextObject' in consequence.
void	setIndent(int indent) Deprecated.
void	setIndenting(boolean indenting) Deprecated.
void	setOmitXMLDeclaration(boolean omitXMLDeclaration) Deprecated.
static java.lang.String	toMathML(org.w3c.dom.Document doc, boolean omitXMLDeclaration, boolean indenting, int indent) Deprecated. Write output as String.
static void	toMathML(java.io.Writer out, org.w3c.dom.Document doc, boolean omitXMLDeclaration, boolean indenting, int indent) Deprecated.
void	writeAttributes(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Deprecated. Adds the XML attributes of the sbmlElementToWrite to the attributes HashMap of the xmlObject.
void	writeCharacters(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Deprecated. Sets the characters of xmlObject depending on the sbml element to write.
void	writeElement(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Deprecated. Sets the name of xmlObject (if it is not set) to the element name of sbmlElementToWrite.
void	writeNamespaces(SBMLObjectForXML xmlObject, java.lang.Object sbmlElementToWrite) Deprecated. 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

Field Detail

sbmlNS

private static final java.lang.String sbmlNS

Deprecated.

The SBML attribute for the additional namespace.

See Also:

Constant Field Values

sbmlUnits

private static final java.lang.String sbmlUnits

Deprecated.

The attribute for SBML units.

See Also:

Constant Field Values

indent

private short indent

Deprecated.

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

indenting

private boolean indenting

Deprecated.

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

omitXMLDeclaration

private boolean omitXMLDeclaration

Deprecated.

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

Constructor Detail

MathMLParser

public MathMLParser()

Deprecated.

Method Detail

checkContainsNumbersReferingToUnits

public static boolean checkContainsNumbersReferingToUnits(org.w3c.dom.Node node)

Deprecated.

Recursively checks whether the given Node contains any numbers that refer to unit declarations. This check is necessary because this feature has become available in SBML Level 3 and is therefore invalid in earlier levels.

Parameters:

node - A node to be checked.

Returns:

createMathMLDocumentFor

public static org.w3c.dom.Document createMathMLDocumentFor(org.w3c.dom.Node node,
                                                           int sbmlLevel)
                                                    throws SBMLException

Deprecated.

Parameters:

node -

sbmlLevel -

Returns:

Throws:

SBMLException

getDefinitionURIavogadro

public static java.lang.String getDefinitionURIavogadro()

Deprecated.

Returns:

getDefinitionURIdelay

public static java.lang.String getDefinitionURIdelay()

Deprecated.

Returns:

getDefinitionURItime

public static java.lang.String getDefinitionURItime()

Deprecated.

Returns:

getNamespaceURI

public static java.lang.String getNamespaceURI()

Deprecated.

Returns:

the namespaceURI

getSBMLNSAttribute

public static java.lang.String getSBMLNSAttribute()

Deprecated.

Returns:

getSBMLUnitsAttribute

public static java.lang.String getSBMLUnitsAttribute()

Deprecated.

Returns:

getXMLnamespaceSBML

public static java.lang.String getXMLnamespaceSBML()

Deprecated.

The additional MathML name space for units to numbers.

Returns:

toMathML

public static java.lang.String toMathML(org.w3c.dom.Document doc,
                                        boolean omitXMLDeclaration,
                                        boolean indenting,
                                        int indent)
                                 throws java.io.IOException,
                                        SBMLException

Deprecated.

Write output as String.

Parameters:

doc -

omitXMLDeclaration -

indenting -

indent -

Returns:

Throws:

java.io.IOException

SBMLException - If illegal references to units are made for numbers and the SBML Level has been set to values before level 3.

toMathML

public static void toMathML(java.io.Writer out,
                            org.w3c.dom.Document doc,
                            boolean omitXMLDeclaration,
                            boolean indenting,
                            int indent)
                     throws java.io.IOException,
                            SBMLException

Deprecated.

Parameters:

out -

doc -

omitXMLDeclaration -

indenting -

indent -

Throws:

java.io.IOException

SBMLException

getIndent

public int getIndent()

Deprecated.

Returns:

getIndenting

public boolean getIndenting()

Deprecated.

Returns:

getListOfSBMLElementsToWrite

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

Deprecated.

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.

getOmitXMLDeclaration

public boolean getOmitXMLDeclaration()

Deprecated.

Returns:

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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.

setIndent

public void setIndent(int indent)

Deprecated.

Parameters:

indent - the indent to set

setIndenting

public void setIndenting(boolean indenting)

Deprecated.

Parameters:

indenting - the indenting to set

setOmitXMLDeclaration

public void setOmitXMLDeclaration(boolean omitXMLDeclaration)

Deprecated.

Parameters:

omitXMLDeclaration - the omitXMLDeclaration to set

writeAttributes

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

Deprecated.

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)

Deprecated.

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)

Deprecated.

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)

Deprecated.

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

getNamespaces

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

Deprecated.

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