org.sbml.jsbml

Class AbstractMathContainer

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, MathContainer, SBase, SBaseWithDerivedUnit, TreeNodeWithChangeSupport

Direct Known Subclasses:

Constraint, Delay, EventAssignment, FunctionDefinition, InitialAssignment, KineticLaw, Priority, Rule, StoichiometryMath, Trigger

public abstract class AbstractMathContainer
extends AbstractSBase
implements MathContainer

Base class for all the SBML components which contain MathML nodes.

Since:

0.8

Author:

Andreas Dräger, marine

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static org.apache.log4j.Logger	logger A logger for user-messages.
private ASTNode	math The math formula as an abstract syntax tree.
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
AbstractMathContainer() Creates a MathContainer instance.
AbstractMathContainer(AbstractMathContainer sb) Creates a MathContainer instance from a given MathContainer.
AbstractMathContainer(ASTNode math, int level, int version) Creates a MathContainer instance from an ASTNode, level and version.
AbstractMathContainer(int level, int version) Creates a MathContainer instance from a level and version.
AbstractMathContainer(java.lang.String id, int level, int version) Creates a new MathContainer instance.

Method Summary

Modifier and Type	Method and Description
abstract AbstractMathContainer	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	containsUndeclaredUnits() Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units.
boolean	getAllowsChildren()
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
UnitDefinition	getDerivedUnitDefinition() Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model.
java.lang.String	getDerivedUnits() Derives the unit of this quantity.
java.lang.String	getFormula() Deprecated.
ASTNode	getMath() If MathContainer.isSetMath() returns true, this method returns the ASTNode belonging to this MathContainer.
java.lang.String	getMathMLString() If MathContainer.isSetMath() returns true, this method returns the corresponding MathML String, otherwise an empty String will be returned.
boolean	isSetMath() Checks if an ASTNode has been set for this MathContainer.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setFormula(java.lang.String formula) Deprecated.
void	setMath(ASTNode math) Sets the math ASTNode of this MathContainer to the given value.
void	unsetFormula() Deprecated.
void	unsetMath() Sets the current ASTNode math element of this MathContainer to null and notifies all TreeNodeChangeListeners assigned to this object about this change.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setLevelAndVersion, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageNamespaceAndVersion, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, equals, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hashCode, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isIdMandatory, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

logger

private static final transient org.apache.log4j.Logger logger

A logger for user-messages.

math

private ASTNode math

The math formula as an abstract syntax tree.

Constructor Detail

AbstractMathContainer

public AbstractMathContainer()

Creates a MathContainer instance. By default, the math object is null.

AbstractMathContainer

public AbstractMathContainer(AbstractMathContainer sb)

Creates a MathContainer instance from a given MathContainer.

Parameters:

sb - an AbstractMathContainer object to clone

AbstractMathContainer

public AbstractMathContainer(ASTNode math,
                             int level,
                             int version)

Creates a MathContainer instance from an ASTNode, level and version. By default, the math is null.

Parameters:

math - the ASTNode representing the math.

level - the SBML level

version - the SBML version

AbstractMathContainer

public AbstractMathContainer(int level,
                             int version)

Creates a MathContainer instance from a level and version. By default, the formula, math and mathBuffer are null.

Parameters:

level - the SBML level

version - the SBML version

AbstractMathContainer

public AbstractMathContainer(java.lang.String id,
                             int level,
                             int version)

Creates a new MathContainer instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

Method Detail

clone

public abstract AbstractMathContainer clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

containsUndeclaredUnits

public boolean containsUndeclaredUnits()

Description copied from interface: SBaseWithDerivedUnit

Returns true or false depending on whether this SBaseWithDerivedUnit refers to elements such as parameters or numbers with undeclared units. A return value of true indicates that the UnitDefinition returned by SBaseWithDerivedUnit.getDerivedUnitDefinition() may not accurately represent the units of the expression.

Specified by:

containsUndeclaredUnits in interface SBaseWithDerivedUnit

Returns:

true if the math expression of this SBaseWithDerivedUnit includes parameters/numbers with undeclared units, false otherwise.

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface javax.swing.tree.TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount in class AbstractSBase

getDerivedUnitDefinition

public UnitDefinition getDerivedUnitDefinition()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity and tries to identify an equivalent UnitDefinition within the corresponding Model. If no equivalent unit definition can be found, a new unit definition will be created that is not part of the model but represents the unit of this quantity. If it is not possible to derive a unit for this quantity, null will be returned.

Specified by:

getDerivedUnitDefinition in interface SBaseWithDerivedUnit

Returns:

a UnitDefinition that represent the derived unit of this quantity, or null if it is not possible to derive a unit.

getDerivedUnits

public java.lang.String getDerivedUnits()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity. If the model that contains this quantity already contains a unit that is equivalent to the derived unit, the corresponding identifier will be returned. In case that the unit cannot be derived or that no equivalent unit exists within the model, or if the model has not been defined yet, null will be returned. In case that this quantity represents a basic Unit.Kind this method will return the String representation of this Unit.Kind.

Specified by:

getDerivedUnits in interface SBaseWithDerivedUnit

Returns:

a String that represent the id of a UnitDefinition. This UnitDefinition represent the derived unit of this quantity. If it is not possible to derive a unit for this quantity or if no equivalent UnitDefinition can be found in the Model, null is returned.

getFormula

@Deprecated
public java.lang.String getFormula()

Deprecated.

Description copied from interface: MathContainer

Converts this MathContainer's internal ASTNode to a C-like String according to the SBML Level 1 specifications and returns it.

Specified by:

getFormula in interface MathContainer

Returns:

the math ASTNode of this object as a String. It returns the empty String if the math ASTNode is not set.

See Also:

MathContainer.getMath()

getMath

public ASTNode getMath()

Description copied from interface: MathContainer

If MathContainer.isSetMath() returns true, this method returns the ASTNode belonging to this MathContainer.

Specified by:

getMath in interface MathContainer

Returns:

the math ASTNode of this object. It return null if the math ASTNode is not set.

getMathMLString

public java.lang.String getMathMLString()

Description copied from interface: MathContainer

If MathContainer.isSetMath() returns true, this method returns the corresponding MathML String, otherwise an empty String will be returned.

Specified by:

getMathMLString in interface MathContainer

Returns:

the MathML representation of this MathContainer's math element.

isSetMath

public boolean isSetMath()

Description copied from interface: MathContainer

Checks if an ASTNode has been set for this MathContainer.

Specified by:

isSetMath in interface MathContainer

Returns:

true if the math ASTNode of this object is not null.

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

setFormula

@Deprecated
public void setFormula(java.lang.String formula)
                            throws ParseException

Deprecated.

Description copied from interface: MathContainer

Sets the mathematical expression of this MathContainer instance to the given formula. This method parses the given String and stores the result in an ASTNode object.

Specified by:

setFormula in interface MathContainer

Parameters:

formula - a C-like String according to the definition in the SBML Level 1 specifications.

Throws:

ParseException - If the given formula is invalid or cannot be parsed properly.

setMath

public void setMath(ASTNode math)

Description copied from interface: MathContainer

Sets the math ASTNode of this MathContainer to the given value.

Specified by:

setMath in interface MathContainer

Parameters:

math - an abstract syntax tree.

unsetFormula

@Deprecated
public void unsetFormula()

Deprecated.

Specified by:

unsetFormula in interface MathContainer

unsetMath

public void unsetMath()

Description copied from interface: MathContainer

Sets the current ASTNode math element of this MathContainer to null and notifies all TreeNodeChangeListeners assigned to this object about this change.

Specified by:

unsetMath in interface MathContainer

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:

a Map containing the XML attributes of this object.