Modifier and Type | Method and Description |
---|---|
XMLNode |
XMLNode.cloneObject()
Creates and returns a deep copy of this
XMLNode object. |
static XMLNode |
XMLNode.convertStringToXMLNode(java.lang.String xmlstr)
Returns an
XMLNode which is derived from a string containing XML
content. |
static XMLNode |
XMLNode.convertStringToXMLNode(java.lang.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 |
RDFAnnotationParser.createRDFAnnotation(long level)
Creates a blank RDF element suitable for use in SBML annotations.
|
static XMLNode |
RDFAnnotationParser.createRDFAnnotation(long level,
long version)
Creates a blank RDF element suitable for use in SBML annotations.
|
static XMLNode |
libsbml.deleteLayoutAnnotation(XMLNode pAnnotation)
Takes an
XMLNode and tries to find the layout annotation node and deletes it if it was found. |
static XMLNode |
libsbml.deleteLayoutIdAnnotation(XMLNode pAnnotation)
Takes an
XMLNode and tries to find the layoutId annotation node and deletes it if it was found. |
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(java.lang.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)
Returns the nth MathML
<semantics> element on this
ASTNode . |
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)
Creates an
XMLNode that represents the layoutId annotation of the species reference from the given SpeciesReference object. |
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 |
ListOfGraphicalObjects.toXML()
Creates an
XMLNode object from this. |
XMLNode |
ListOfLineEndings.toXML()
Creates an
XMLNode object from this ListOfLineEndings object. |
XMLNode |
ListOfGlobalStyles.toXML()
Creates an
XMLNode object from this ListOfGlobalStyles object. |
XMLNode |
ListOfSpeciesReferenceGlyphs.toXML()
Creates an
XMLNode object from this. |
XMLNode |
CubicBezier.toXML()
Creates an
XMLNode object from this. |
XMLNode |
GlobalRenderInformation.toXML()
Creates an
XMLNode object from this GlobalRenderInformation object. |
XMLNode |
Association.toXML()
Creates an
XMLNode object from this Association object. |
XMLNode |
GradientStop.toXML()
Creates an
XMLNode object from this GradientStop object. |
XMLNode |
ReactionGlyph.toXML()
Creates an
XMLNode object from this. |
XMLNode |
ReferenceGlyph.toXML()
Creates an
XMLNode object from this. |
XMLNode |
TextGlyph.toXML()
Creates an
XMLNode object from this. |
XMLNode |
Style.toXML()
|
XMLNode |
LocalStyle.toXML()
Creates an
XMLNode object from this LocalStyle object. |
XMLNode |
ListOfTextGlyphs.toXML()
Creates an
XMLNode object from this. |
XMLNode |
Image.toXML()
|
XMLNode |
GraphicalPrimitive1D.toXML()
Creates an
XMLNode object from this GraphicalPrimitive1D object. |
XMLNode |
ListOfCompartmentGlyphs.toXML()
Creates an
XMLNode object from this. |
XMLNode |
ListOfReactionGlyphs.toXML()
Creates an
XMLNode object from this. |
XMLNode |
ListOfCurveElements.toXML()
Creates an
XMLNode object from this ListOfCurveElements object. |
XMLNode |
SpeciesGlyph.toXML()
Creates an
XMLNode object from this. |
XMLNode |
GeneAssociation.toXML()
Creates an
XMLNode object from this. |
XMLNode |
CompartmentGlyph.toXML()
Creates an
XMLNode object from this CompartmentGlyph . |
XMLNode |
ListOfReferenceGlyphs.toXML()
Creates an
XMLNode object from this. |
XMLNode |
ListOfGradientStops.toXML()
Creates an
XMLNode object from this ListOfGradientStops object. |
XMLNode |
ListOfColorDefinitions.toXML()
Creates an
XMLNode object from this ListOfColorDefinitions object. |
XMLNode |
RenderCurve.toXML()
Creates an
XMLNode object from this RenderCurve object. |
XMLNode |
GradientBase.toXML()
|
XMLNode |
Rectangle.toXML()
Creates an
XMLNode object from this Rectangle object. |
XMLNode |
LinearGradient.toXML()
Creates an
XMLNode object from this LinearGradient object. |
XMLNode |
ListOfSpeciesGlyphs.toXML()
Creates an
XMLNode object from this. |
XMLNode |
Polygon.toXML()
|
XMLNode |
ColorDefinition.toXML()
Creates an
XMLNode object from this ColorDefinition object. |
XMLNode |
ListOfLineSegments.toXML()
Creates an
XMLNode object from this. |
XMLNode |
Dimensions.toXML()
Creates an
XMLNode object from this. |
XMLNode |
LineEnding.toXML()
Creates an
XMLNode object from this LineEnding object. |
XMLNode |
Curve.toXML()
Creates an
XMLNode object from this. |
XMLNode |
ListOfLocalStyles.toXML()
Creates an
XMLNode object from this ListOfLocalStyles object. |
XMLNode |
GraphicalObject.toXML()
Creates an
XMLNode object from this. |
XMLNode |
Text.toXML()
Creates an
XMLNode object from this GraphicalPrimitive1D object. |
XMLNode |
GeneralGlyph.toXML()
Creates an
XMLNode object from this. |
XMLNode |
LocalRenderInformation.toXML()
Creates an
XMLNode object from this LocalRenderInformation object. |
XMLNode |
ListOfGradientDefinitions.toXML()
Creates an
XMLNode object from this ListOfGradientDefinitions object. |
XMLNode |
Ellipse.toXML()
|
XMLNode |
ListOfLocalRenderInformation.toXML()
Creates an
XMLNode object from this ListOfGradientDefinitions object. |
XMLNode |
BoundingBox.toXML()
Creates an
XMLNode object from this. |
XMLNode |
RadialGradient.toXML()
Creates an
XMLNode object from this RadialGradient object. |
XMLNode |
ListOfLayouts.toXML()
Creates an
XMLNode object from this. |
XMLNode |
ListOfGlobalRenderInformation.toXML()
Creates an
XMLNode object from this ListOfGlobalRenderInformation object. |
XMLNode |
RenderGroup.toXML()
Creates an
XMLNode object from this RenderGroup object. |
XMLNode |
Layout.toXML()
Creates an
XMLNode object from this. |
XMLNode |
SpeciesReferenceGlyph.toXML()
Creates an
XMLNode object from this. |
XMLNode |
Transformation2D.toXML()
Creates an
XMLNode object from this Transformation2D object. |
XMLNode |
LineSegment.toXML()
Creates an
XMLNode object from this. |
XMLNode |
Point.toXML(java.lang.String name)
Creates an
XMLNode object from this. |
XMLNode |
RenderCubicBezier.toXML(java.lang.String name)
Creates an
XMLNode object from this RenderCubicBezier object. |
XMLNode |
RenderPoint.toXML(java.lang.String name)
Creates an
XMLNode object from this ColorDefinition object. |
XMLNode |
SBase.toXMLNode()
Returns this element as an
XMLNode . |
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 disownedAnnotation)
|
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 java.lang.String |
XMLNode.convertXMLNodeToString(XMLNode node)
Returns a string representation of a given
XMLNode . |
static XMLNode |
libsbml.deleteLayoutAnnotation(XMLNode pAnnotation)
Takes an
XMLNode and tries to find the layout annotation node and deletes it if it was found. |
static XMLNode |
libsbml.deleteLayoutIdAnnotation(XMLNode pAnnotation)
Takes an
XMLNode and tries to find the layoutId annotation node and deletes it if it was found. |
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)
takes an annotation that has been read into the model
identifies the RDF elements
and creates a List of Layouts from the annotation
|
static ModelHistory |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation)
Parses an annotation into a
ModelHistory class instance. |
static void |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
CVTermList CVTerms) |
static void |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
CVTermList CVTerms,
java.lang.String metaId) |
static void |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
CVTermList CVTerms,
java.lang.String metaId,
XMLInputStream stream) |
static ModelHistory |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
java.lang.String metaId)
Parses an annotation into a
ModelHistory class instance. |
static ModelHistory |
RDFAnnotationParser.parseRDFAnnotation(XMLNode annotation,
java.lang.String metaId,
XMLInputStream stream)
Parses an annotation into a
ModelHistory class instance. |
static void |
libsbml.parseSpeciesReferenceAnnotation(XMLNode annotation,
SimpleSpeciesReference sr)
takes an annotation that has been read into the species reference
identifies the id elements and set the id of the species reference
|
void |
GlobalRenderInformation.parseXML(XMLNode node)
Parses the xml information in the given node and sets the attributes.
|
void |
LocalRenderInformation.parseXML(XMLNode node)
Parses the xml information in the given node and sets the attributes.
|
void |
ListOfGlobalRenderInformation.parseXML(XMLNode node)
Parses the xml information in the given node and sets the attributes.
|
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)
|
Constructor and Description |
---|
Association(XMLNode node,
FbcPkgNamespaces fbcns)
Creates a new
Association with the given FbcPkgNamespaces object,
and constructed to mimic the XMLNode: a '<gene>' node
argument will result in a
GENE_ASSOCIATION node; an
<and> node argument will result in a
AND_ASSOCIATION node; an
<or> node argument will result in a
OR_ASSOCIATION node. |
BoundingBox(XMLNode node)
Creates a new
BoundingBox from the given XMLNode |
BoundingBox(XMLNode node,
long l2version)
Creates a new
BoundingBox from the given XMLNode |
ColorDefinition(XMLNode node)
Creates a new
ColorDefinition object from the given XMLNode object. |
ColorDefinition(XMLNode node,
long l2version)
Creates a new
ColorDefinition object from the given XMLNode object. |
CompartmentGlyph(XMLNode node)
Creates a new
CompartmentGlyph from the given XMLNode |
CompartmentGlyph(XMLNode node,
long l2version)
Creates a new
CompartmentGlyph from the given XMLNode |
CubicBezier(XMLNode node)
|
CubicBezier(XMLNode node,
long l2version)
|
Curve(XMLNode node)
|
Curve(XMLNode node,
long l2version)
|
CVTerm(XMLNode node)
|
Dimensions(XMLNode node)
Creates a new
Dimensions object from the given XMLNode |
Dimensions(XMLNode node,
long l2version)
Creates a new
Dimensions object from the given XMLNode |
Ellipse(XMLNode node)
Creates a new
RadialGradient object from the given XMLNode object. |
Ellipse(XMLNode node,
long l2version)
Creates a new
RadialGradient object from the given XMLNode object. |
GeneAssociation(XMLNode node,
FbcPkgNamespaces fbcns)
|
GeneralGlyph(XMLNode node)
Creates a new
GeneralGlyph from the given XMLNode |
GeneralGlyph(XMLNode node,
long l2version)
Creates a new
GeneralGlyph from the given XMLNode |
GlobalStyle(XMLNode node)
Creates a new
GlobalStyle object from the given XMLNode object. |
GlobalStyle(XMLNode node,
long l2version)
Creates a new
GlobalStyle object from the given XMLNode object. |
GradientStop(XMLNode node)
Creates a new
GradientStop object from the given XMLNode object. |
GradientStop(XMLNode node,
long l2version)
Creates a new
GradientStop object from the given XMLNode object. |
GraphicalObject(XMLNode node)
Creates a new
GraphicalObject from the given XMLNode |
GraphicalObject(XMLNode node,
long l2version)
Creates a new
GraphicalObject from the given XMLNode |
Image(XMLNode node)
|
Image(XMLNode node,
long l2version)
|
Layout(XMLNode node)
|
Layout(XMLNode node,
long l2version)
|
LinearGradient(XMLNode node)
Creates a new
LinearGradient object from the given XMLNode object. |
LinearGradient(XMLNode node,
long l2version)
Creates a new
LinearGradient object from the given XMLNode object. |
LineEnding(XMLNode node,
long l2version)
Creates a new
LineEnding object from the given XMLNode object. |
LineSegment(XMLNode node)
Creates a new
LineSegment from the given XMLNode |
LineSegment(XMLNode node,
long l2version)
Creates a new
LineSegment from the given XMLNode |
ListOfColorDefinitions(XMLNode node)
Creates a new
ListOfColorDefinitions object from the given XMLNode object. |
ListOfCurveElements(XMLNode node)
Creates a new
ListOfCurveElements object from the given XMLNode object. |
ListOfCurveElements(XMLNode node,
long l2version)
Creates a new
ListOfCurveElements object from the given XMLNode object. |
ListOfGlobalStyles(XMLNode node)
Creates a new
ListOfGlobalStyles object from the given XMLNode object. |
ListOfGradientDefinitions(XMLNode node)
Creates a new
ListOfGradientDefinitions object from the given XMLNode object. |
ListOfGradientDefinitions(XMLNode node,
long l2version)
Creates a new
ListOfGradientDefinitions object from the given XMLNode object. |
ListOfGradientStops(XMLNode node)
Creates a new
ListOfGradientStops object from the given XMLNode object. |
ListOfGradientStops(XMLNode node,
long l2version)
Creates a new
ListOfGradientStops object from the given XMLNode object. |
ListOfLineEndings(XMLNode node)
Creates a new
ListOfLineEndings object from the given XMLNode object. |
ListOfLineEndings(XMLNode node,
long l2version)
Creates a new
ListOfLineEndings object from the given XMLNode object. |
ListOfLocalStyles(XMLNode node)
Creates a new
ListOfLocalStyles object from the given XMLNode object. |
LocalStyle(XMLNode node)
Creates a new
LocalStyle object from the given XMLNode object. |
LocalStyle(XMLNode node,
long l2version)
Creates a new
LocalStyle object from the given XMLNode object. |
ModelCreator(XMLNode creator)
Creates a new
ModelCreator from an XMLNode . |
Point(XMLNode node)
|
Point(XMLNode node,
long l2version)
|
Polygon(XMLNode node)
|
Polygon(XMLNode node,
long l2version)
|
RadialGradient(XMLNode node,
long l2version)
Creates a new
RadialGradient object from the given XMLNode object. |
ReactionGlyph(XMLNode node)
Creates a new
ReactionGlyph from the given XMLNode |
ReactionGlyph(XMLNode node,
long l2version)
Creates a new
ReactionGlyph from the given XMLNode |
Rectangle(XMLNode node)
Creates a new Rectangle object from the given
XMLNode object. |
Rectangle(XMLNode node,
long l2version)
Creates a new Rectangle object from the given
XMLNode object. |
ReferenceGlyph(XMLNode node)
Creates a new
ReferenceGlyph from the given XMLNode |
ReferenceGlyph(XMLNode node,
long l2version)
Creates a new
ReferenceGlyph from the given XMLNode |
RenderCubicBezier(XMLNode node)
Creates a new
RenderCubicBezier object from the given XMLNode object. |
RenderCubicBezier(XMLNode node,
long l2version)
Creates a new
RenderCubicBezier object from the given XMLNode object. |
RenderCurve(XMLNode node)
Creates a new
RenderCurve object from the given XMLNode object. |
RenderCurve(XMLNode node,
long l2version)
Creates a new
RenderCurve object from the given XMLNode object. |
RenderGroup(XMLNode group)
Creates a new
RenderGroup object from the given XMLNode object. |
RenderGroup(XMLNode group,
long l2version)
Creates a new
RenderGroup object from the given XMLNode object. |
RenderPoint(XMLNode node)
Creates a new
RenderPoint object from the given XMLNode object. |
RenderPoint(XMLNode node,
long l2version)
Creates a new
RenderPoint object from the given XMLNode object. |
SpeciesGlyph(XMLNode node)
Creates a new
SpeciesGlyph from the given XMLNode |
SpeciesGlyph(XMLNode node,
long l2version)
Creates a new
SpeciesGlyph from the given XMLNode |
SpeciesReferenceGlyph(XMLNode node)
Creates a new
SpeciesReferenceGlyph from the given XMLNode |
SpeciesReferenceGlyph(XMLNode node,
long l2version)
Creates a new
SpeciesReferenceGlyph from the given XMLNode |
Text(XMLNode node)
|
Text(XMLNode node,
long l2version)
|
TextGlyph(XMLNode node)
|
TextGlyph(XMLNode node,
long l2version)
|
XMLNode(XMLNode orig)
Copy constructor; creates a copy of this
XMLNode . |