org.sbml.jsbml
public class AlgebraicRule extends Rule
| Modifier and Type | Field and Description |
|---|---|
private static long |
serialVersionUID
Generated serial version identifier.
|
ignoredExtensions, ignoredXMLElements, lvlistOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS| Constructor and Description |
|---|
AlgebraicRule()
Creates an AlgebraicRule instance.
|
AlgebraicRule(AlgebraicRule ar)
Creates an AlgebraicRule instance from a given
AlgebraicRule
instance. |
AlgebraicRule(ASTNode math,
int level,
int version)
Creates an AlgebraicRule instance from math, level and version.
|
AlgebraicRule(int level,
int version)
Creates an AlgebraicRule instance from level and version.
|
| Modifier and Type | Method and Description |
|---|---|
AlgebraicRule |
clone()
Creates a deep copy of this object, i.e., a new
SBase with the same properties
like this one. |
Variable |
getDerivedVariable()
Provides a convenient way to obtain the variable whose amount
is determined by this rule.
|
boolean |
isCompartmentVolume()
(SBML Level 1 only) Predicate returning true or false depending on
whether this Rule is an CompartmentVolumeRule.
|
boolean |
isParameter()
(SBML Level 1 only) Predicate returning true or false depending on
whether this Rule is an ParameterRule.
|
boolean |
isSpeciesConcentration()
(SBML Level 1 only) Predicate returning
true or false depending on
whether this Rule is an SpeciesConcentrationRule. |
getParent, isAlgebraic, isAssignment, isRatecontainsUndeclaredUnits, getAllowsChildren, getChildAt, getChildCount, getDerivedUnitDefinition, getDerivedUnits, getFormula, getMath, getMathMLString, isSetMath, readAttribute, setFormula, setMath, toString, unsetFormula, unsetMath, writeXMLAttributesaddCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setLevelAndVersion, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTermaddAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySetfinalize, getClass, notify, notifyAll, wait, wait, waitaddCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTermaddAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySetprivate static final long serialVersionUID
public AlgebraicRule()
public AlgebraicRule(AlgebraicRule ar)
AlgebraicRule
instance.ar - an AlgebraicRule to clone.public AlgebraicRule(ASTNode math, int level, int version)
math - the math of the AlgebraicRulelevel - the SBML levelversion - the SBML versionpublic AlgebraicRule(int level,
int version)
level - the SBML levelversion - the SBML versionpublic AlgebraicRule clone()
SBaseSBase with the same properties
like this one.public boolean isCompartmentVolume()
RuleisCompartmentVolume in class Ruletrue if this Rule is a CompartmentVolumeRule, false otherwise.public boolean isParameter()
RuleisParameter in class Ruletrue if this Rule is a ParameterRule, false otherwise.public Variable getDerivedVariable() throws ModelOverdeterminedException
OverdeterminationValidator instead of calling this method. Each
time you call this method, the bipartite matching between all
MathContainers in the model and all
NamedSBaseWithDerivedUnits will be executed again, leading to a
probably high computational effort.
An example of how to use the OverdeterminationValidator is given
here:
int ruleIndex = 0; // some arbitrary algebraic rule
AlgebraicRule ar = model.getRule(ruleIndex);
OverdeterminationValidator odv = new OverdeterminationValidator(model);
Variable variable;
if (!odv.isOverdetermined()) {
variable = (Variable) odv.getMatching().get(ar);
System.out.printf("Rule %d determines Variable %s.", ruleIndex, variable.getId());
}
Variable determined by this AlgebraicRuleModelOverdeterminedException - if the model containing this Rule is over determined.java.lang.NullPointerException - Calling this method requires that this Rule is
already part of a Model. If you just created a
Rule and didn't add it to a Model you'll
receive a NullPointerException.public boolean isSpeciesConcentration()
Ruletrue or false depending on
whether this Rule is an SpeciesConcentrationRule.isSpeciesConcentration in class Ruletrue if this Rule is a SpeciesConcentrationRule, false otherwise.