Modifier and Type | Method and Description |
---|---|
XMLNode |
XMLNode.cloneObject()
Creates and returns a deep copy of this
XMLNode . |
static XMLNode |
XMLNode.convertStringToXMLNode(String xmlstr)
Returns an
XMLNode which is derived from a string containing XML
content. |
static XMLNode |
XMLNode.convertStringToXMLNode(String xmlstr,
XMLNamespaces xmlns)
Returns an
XMLNode which is derived from a string containing XML
content. |
static XMLNode |
RDFAnnotationParser.createAnnotation()
Creates a blank annotation and returns its root
XMLNode object. |
static XMLNode |
RDFAnnotationParser.createCVTerms(SBase obj)
Takes a list of
CVTerm objects and creates a the RDF 'Description'
element. |
static XMLNode |
RDFAnnotationParser.createRDFAnnotation()
Creates a blank RDF element suitable for use in SBML annotations.
|
static XMLNode |
libsbml.deleteLayoutAnnotation(XMLNode pAnnotation) |
static XMLNode |
libsbml.deleteLayoutIdAnnotation(XMLNode pAnnotation) |
static XMLNode |
RDFAnnotationParser.deleteRDFAnnotation(XMLNode annotation)
Deletes any SBML MIRIAM RDF annotation found in the given
XMLNode
tree and returns
any remaining annotation content. |
static XMLNode |
RDFAnnotationParser.deleteRDFCVTermAnnotation(XMLNode annotation)
|
static XMLNode |
RDFAnnotationParser.deleteRDFHistoryAnnotation(XMLNode annotation)
Deletes any SBML MIRIAM RDF 'History' annotation found in the given
XMLNode tree and returns
any remaining annotation content. |
XMLNode |
SBase.getAnnotation()
Returns the content of the 'annotation' subelement of this object as
a tree of
XMLNode objects. |
XMLNode |
XMLNode.getChild(long n)
Returns the
n th child of this XMLNode . |
XMLNode |
XMLNode.getChild(String name)
Returns the first child of this
XMLNode with the corresponding name. |
XMLNode |
Constraint.getMessage()
Get the message, if any, associated with this
Constraint |
XMLNode |
SBase.getNotes()
Returns the content of the 'notes' subelement of this object as
a tree of
XMLNode objects. |
XMLNode |
ASTNode.getSemanticsAnnotation(long n)
Get the nth semantic annotation of this node.
|
XMLNode |
XMLNode.insertChild(long n,
XMLNode node)
Inserts a copy of the given node as the
n th child of this
XMLNode . |
static XMLNode |
RDFAnnotationParser.parseCVTerms(SBase obj)
Takes a list of
CVTerm objects and creates a complete SBML annotation
around it. |
static XMLNode |
libsbml.parseLayoutId(SimpleSpeciesReference sr) |
static XMLNode |
libsbml.parseLayouts(Model pModel) |
static XMLNode |
RDFAnnotationParser.parseModelHistory(SBase obj)
Reads the model history and cvTerms stored in
obj and creates the
XML structure for an SBML annotation representing that metadata if
there is a model history stored in obj . |
static XMLNode |
RDFAnnotationParser.parseOnlyModelHistory(SBase obj)
Reads the model history stored in
obj and creates the
XML structure for an SBML annotation representing that history. |
XMLNode |
XMLNode.removeChild(long n)
Removes the
n th child of this XMLNode and returns the
removed node. |
XMLNode |
Association.toXML() |
XMLNode |
Layout.toXML() |
XMLNode |
Curve.toXML() |
XMLNode |
ListOfLayouts.toXML() |
XMLNode |
ListOfGraphicalObjects.toXML() |
XMLNode |
ListOfReactionGlyphs.toXML() |
XMLNode |
ReactionGlyph.toXML() |
XMLNode |
ListOfCompartmentGlyphs.toXML() |
XMLNode |
ListOfLineSegments.toXML() |
XMLNode |
TextGlyph.toXML() |
XMLNode |
GeneAssociation.toXML() |
XMLNode |
CubicBezier.toXML() |
XMLNode |
SpeciesGlyph.toXML() |
XMLNode |
GraphicalObject.toXML() |
XMLNode |
BoundingBox.toXML() |
XMLNode |
ReferenceGlyph.toXML() |
XMLNode |
Dimensions.toXML() |
XMLNode |
SpeciesReferenceGlyph.toXML() |
XMLNode |
GeneralGlyph.toXML() |
XMLNode |
ListOfReferenceGlyphs.toXML() |
XMLNode |
LineSegment.toXML() |
XMLNode |
ListOfSpeciesGlyphs.toXML() |
XMLNode |
ListOfTextGlyphs.toXML() |
XMLNode |
ListOfSpeciesReferenceGlyphs.toXML() |
XMLNode |
CompartmentGlyph.toXML() |
XMLNode |
Point.toXML(String name) |
Modifier and Type | Method and Description |
---|---|
int |
XMLNode.addChild(XMLNode node)
Adds a copy of
node as a child of this XMLNode . |
int |
ASTNode.addSemanticsAnnotation(XMLNode sAnnotation)
|
int |
SBase.appendAnnotation(XMLNode annotation)
Appends the given
annotation to the 'annotation' subelement of this
object. |
int |
SpeciesReference.appendAnnotation(XMLNode annotation)
Appends annotation content to any existing content in the 'annotation'
subelement of this object.
|
int |
Model.appendAnnotation(XMLNode annotation)
Appends annotation content to any existing content in the 'annotation'
subelement of this object.
|
int |
SBase.appendNotes(XMLNode notes)
Appends the given
notes to the 'notes' subelement of this object. |
static String |
XMLNode.convertXMLNodeToString(XMLNode node)
Returns a string representation of a given
XMLNode . |
static XMLNode |
libsbml.deleteLayoutAnnotation(XMLNode pAnnotation) |
static XMLNode |
libsbml.deleteLayoutIdAnnotation(XMLNode pAnnotation) |
static XMLNode |
RDFAnnotationParser.deleteRDFAnnotation(XMLNode annotation)
Deletes any SBML MIRIAM RDF annotation found in the given
XMLNode
tree and returns
any remaining annotation content. |
static XMLNode |
RDFAnnotationParser.deleteRDFCVTermAnnotation(XMLNode annotation)
|
static XMLNode |
RDFAnnotationParser.deleteRDFHistoryAnnotation(XMLNode annotation)
Deletes any SBML MIRIAM RDF 'History' annotation found in the given
XMLNode tree and returns
any remaining annotation content. |
static boolean |
SyntaxChecker.hasExpectedXHTMLSyntax(XMLNode xhtml)
|
static boolean |
SyntaxChecker.hasExpectedXHTMLSyntax(XMLNode xhtml,
SBMLNamespaces sbmlns)
|
XMLNode |
XMLNode.insertChild(long n,
XMLNode node)
Inserts a copy of the given node as the
n th child of this
XMLNode . |
static void |
libsbml.parseLayoutAnnotation(XMLNode annotation,
ListOfLayouts layouts) |
static ModelHistory |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation)
Parses an annotation into a
ModelHistory class instance. |
static void |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
CVTermList CVTerms) |
static ModelHistory |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
String metaId)
Parses an annotation into a
ModelHistory class instance. |
static ModelHistory |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
String metaId,
XMLInputStream stream)
Parses an annotation into a
ModelHistory class instance. |
static void |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
org.sbml.libsbml.SWIGTYPE_p_List CVTerms,
String metaId)
|
static void |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
org.sbml.libsbml.SWIGTYPE_p_List CVTerms,
String metaId,
XMLInputStream stream)
|
static void |
libsbml.parseSpeciesReferenceAnnotation(XMLNode annotation,
SimpleSpeciesReference sr) |
int |
SBase.replaceTopLevelAnnotationElement(XMLNode annotation)
Replaces the given top-level element within the 'annotation'
subelement of this SBML object and with the annotation element supplied.
|
int |
SBase.setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object.
|
int |
SpeciesReference.setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object to a
copy of
annotation . |
int |
Model.setAnnotation(XMLNode annotation)
Sets the value of the 'annotation' subelement of this SBML object to a
copy of
annotation . |
int |
Constraint.setMessage(XMLNode xhtml)
Sets the message of this
Constraint . |
int |
SBase.setNotes(XMLNode notes)
Sets the value of the 'notes' subelement of this SBML object.
|
boolean |
XMLNode.xmlEquals(XMLNode other)
|
boolean |
XMLNode.xmlEquals(XMLNode other,
boolean ignoreURI)
|