Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.util |
A collection of handy utilities when working with JSBML classes,
such as classes for String manipulation or mathematical operations.
|
org.sbml.jsbml.validator.offline.constraints |
Any validation constraints related to the multi package.
|
org.sbml.jsbml.xml |
This package provides classes and methods to deal with SBML in form of XML
elements, i.e., here you can find parsers and writers for SBML and also
elements to define XML nodes to be used for notes or annotations.
|
org.sbml.jsbml.xml.parsers |
Contains classes that implement
ReadingParser
and/or WritingParser to read or write some
specific parts of an SBML file. |
org.sbml.jsbml.xml.stax |
Contains classes that use the Streaming API for XML (StAX)
to read or write an SBML file.
|
Modifier and Type | Method | Description |
---|---|---|
XMLNode |
ASTNode.addSemanticsAnnotation(XMLNode semanticsAnnotation) |
|
XMLNode |
Annotation.getAnnotationBuilder() |
Deprecated.
|
XMLNode |
Annotation.getFullAnnotation() |
|
XMLNode |
Constraint.getMessage() |
Returns the message of this
Constraint . |
XMLNode |
Annotation.getNonRDFannotation() |
Returns the
XMLNode containing annotations other than
the official RDF annotation, as defined in the SBML specifications. |
XMLNode |
AbstractSBase.getNotes() |
Returns an
XMLNode object that represent the notes of this element. |
XMLNode |
SBase.getNotes() |
Returns the
XMLNode containing the notes sub-element of
this object. |
XMLNode |
ASTNode.getSemanticsAnnotation(int n) |
Gets the nth
<semantics> annotation of this node. |
XMLNode |
Annotation.getXMLNode() |
|
XMLNode |
CVTerm.toXMLNode() |
Modifier and Type | Method | Description |
---|---|---|
java.util.List<XMLNode> |
ASTNode.getListOfSemanticsAnnotations() |
Returns the list of semantics annotations of this node.
|
Modifier and Type | Method | Description |
---|---|---|
XMLNode |
ASTNode.addSemanticsAnnotation(XMLNode semanticsAnnotation) |
|
void |
AbstractSBase.appendAnnotation(XMLNode annotation) |
|
void |
SBase.appendAnnotation(XMLNode annotation) |
Appends the given annotation to the 'annotation' subelement of this object.
|
void |
Annotation.appendNonRDFAnnotation(XMLNode annotationToAppend) |
|
void |
AbstractSBase.appendNotes(XMLNode notes) |
Appends notes to the existing notes.
|
void |
SBase.appendNotes(XMLNode notes) |
Appends 'notes' to the notes of this object.
|
static int |
AbstractSBase.getFirstElementIndex(XMLNode curNotes) |
Return the index of the first child of type 'Element' for the given
XMLNode . |
boolean |
AbstractSBase.replaceTopLevelAnnotationElement(XMLNode annotation) |
|
boolean |
SBase.replaceTopLevelAnnotationElement(XMLNode annotation) |
Replaces the top-level element of this SBML object with same name as given
annotation subelement by the given one.
|
void |
AbstractSBase.setAnnotation(XMLNode nonRDFAnnotation) |
|
void |
SBase.setAnnotation(XMLNode nonRDFAnnotation) |
Sets the non RDF part of the annotation.
|
void |
Constraint.setMessage(XMLNode message) |
Sets the message of this
Constraint to 'message'. |
void |
Annotation.setNonRDFAnnotation(XMLNode nonRDFAnnotation) |
Sets the value of the non RDF annotations
|
void |
AbstractSBase.setNotes(XMLNode notes) |
|
void |
SBase.setNotes(XMLNode notesXMLNode) |
Sets the
XMLNode containing the notes sub-element of
this object. |
void |
Annotation.setXMLNode(XMLNode nonRDFannotation) |
Constructor | Description |
---|---|
Annotation(XMLNode annotation) |
|
CVTerm(XMLNode miriam) |
Modifier and Type | Method | Description |
---|---|---|
XMLNode |
SampledField.getData() |
Returns the value of data
|
Modifier and Type | Method | Description |
---|---|---|
void |
SampledField.setData(XMLNode data) |
Sets the value of data
|
Modifier and Type | Method | Description |
---|---|---|
static java.lang.String |
SBMLtools.toXML(XMLNode xml) |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
SBaseConstraints.checkHtmlBodyContent(ValidationContext ctx,
SBase sb,
XMLNode topLevelNode) |
Checks that each sub elements of the given
XMLNode are allowed inside a body element. |
static boolean |
SBaseConstraints.checkHtmlHeadContent(ValidationContext ctx,
SBase sb,
XMLNode topLevelNode) |
Checks that each sub elements of the given
XMLNode are allowed inside a head element. |
Modifier and Type | Method | Description |
---|---|---|
XMLNode |
XMLNode.clone() |
|
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. |
XMLNode |
XMLNode.getChild(int childIndex) |
Returns the child
XMLNode at index childIndex. |
XMLNode |
XMLNode.getChildAt(int childIndex) |
|
XMLNode |
XMLNode.getChildElement(java.lang.String elementName,
java.lang.String elementURI) |
Gets the first direct child element of this
XMLNode with the given local name and namespace. |
XMLNode |
XMLNode.insertChild(int n,
XMLNode node) |
Inserts a node as the
n th child of this
XMLNode . |
XMLNode |
XMLNode.removeChild(int n) |
Removes the
n th child of this XMLNode and returns the
removed node. |
Modifier and Type | Method | Description |
---|---|---|
java.util.List<XMLNode> |
XMLNode.getChildElements(java.lang.String elementName,
java.lang.String elementURI) |
Gets all the direct children of this
XMLNode with the given local
name and namespace. |
Modifier and Type | Method | Description |
---|---|---|
int |
XMLNode.addChild(XMLNode node) |
Adds a child to this
XMLNode . |
static java.lang.String |
XMLNode.convertXMLNodeToString(XMLNode node) |
Returns a string representation of a given
XMLNode . |
int |
XMLNode.indexOf(XMLNode searched) |
Searches for first occurrence of the given XMLNode among the immediate children of this
XMLNode and returns the index with which that child could be accessed e.g.
|
XMLNode |
XMLNode.insertChild(int n,
XMLNode node) |
Inserts a node as the
n th child of this
XMLNode . |
boolean |
XMLNode.removeChild(XMLNode xmlNode) |
Removes the first occurrence of the specified element from this list.
|
Constructor | Description |
---|---|
XMLNode(XMLNode orig) |
Creates a copy of this
XMLNode . |
Modifier and Type | Method | Description |
---|---|---|
static XMLNode |
AbstractReaderWriter.processUnknownElement(java.lang.String elementName,
java.lang.String namespace,
java.lang.String prefix,
java.lang.Object contextObject) |
Process an unknown XML element.
|
XMLNode |
AnnotationWriter.writeAnnotation(SBase contextObject,
XMLNode xmlNode) |
|
XMLNode |
SBMLRDFAnnotationParser.writeAnnotation(SBase contextObject,
XMLNode xmlNode) |
Modifier and Type | Method | Description |
---|---|---|
int |
SBMLRDFAnnotationParser.getNumberOfNonEmptyChildElement(XMLNode xmlNode) |
Returns the number of child XMLNode, excluding text XMLNode that
contains only spaces.
|
static java.lang.String |
XMLNodeWriter.toXML(XMLNode xmlNode) |
|
void |
XMLNodeWriter.write(XMLNode xmlNode) |
|
XMLNode |
AnnotationWriter.writeAnnotation(SBase contextObject,
XMLNode xmlNode) |
|
XMLNode |
SBMLRDFAnnotationParser.writeAnnotation(SBase contextObject,
XMLNode xmlNode) |
Modifier and Type | Method | Description |
---|---|---|
XMLNode |
SBMLReader.readNotes(java.lang.String notesXHTML) |
|
XMLNode |
SBMLReader.readNotes(java.lang.String notesXHTML,
TreeNodeChangeListener listener) |
Reads a notes XML
String into an XMLNode . |