org.sbml.jsbml.ext.qual

Class FunctionTerm

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractMathContainer

org.sbml.jsbml.ext.qual.FunctionTerm

All Implemented Interfaces:

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

public class FunctionTerm
extends AbstractMathContainer

Each FunctionTerm is also associated with a result and in addition to a Boolean function inside a Math element that can be used to set the conditions under which this term is selected.

Since:

1.0

Version:

$Rev: 1725 $

Author:

Nicolas Rodriguez, Finja Büchel, Florian Mittag

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	defaultTerm
private java.lang.Integer	resultLevel
private static long	serialVersionUID Generated serial version identifier.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
FunctionTerm() Default constructor
FunctionTerm(ASTNode math, int level, int version)
FunctionTerm(FunctionTerm ft) Creates a FunctionTerm instance from a given FunctionTerm.
FunctionTerm(int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
FunctionTerm	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
int	getResultLevel() Returns the resultLevel if it is set, otherwise throw a PropertyUndefinedError Exception.
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isDefaultTerm() Returns true if it is a defaultTerm.
boolean	isResultLevelMandatory() Return false, resultLevel is not mandatory.
boolean	isSetResultLevel() Returns true if resultLevel is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setDefaultTerm(boolean defaultTerm) Sets if this FunctionTerm is a defaultTerm.
void	setResultLevel(int resultLevel) The result of a term is described by a resultLevel.
java.lang.String	toString()
boolean	unsetResultLevel() Unsets the resultLevel.
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.AbstractMathContainer

containsUndeclaredUnits, getAllowsChildren, getChildAt, getChildCount, getDerivedUnitDefinition, getDerivedUnits, getFormula, getMath, getMathMLString, isSetMath, setFormula, setMath, unsetFormula, unsetMath

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, 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, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, 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, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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, 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, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, 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, 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, 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

resultLevel

private java.lang.Integer resultLevel

defaultTerm

private boolean defaultTerm

Constructor Detail

FunctionTerm

public FunctionTerm()

Default constructor

FunctionTerm

public FunctionTerm(int level,
            int version)

Parameters:

level -

version -

FunctionTerm

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

Parameters:

math -

level -

version -

FunctionTerm

public FunctionTerm(FunctionTerm ft)

Creates a FunctionTerm instance from a given FunctionTerm.

Parameters:

ft - an FunctionTerm object to clone

Method Detail

clone

public FunctionTerm 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 AbstractMathContainer

Returns:

a copy of this object

isResultLevelMandatory

public boolean isResultLevelMandatory()

Return false, resultLevel is not mandatory.

Returns:

false

isSetResultLevel

public boolean isSetResultLevel()

Returns true if resultLevel is set.

Returns:

true if resultLevel is set.

getResultLevel

public int getResultLevel()

Returns the resultLevel if it is set, otherwise throw a PropertyUndefinedError Exception.

Returns:

the resultLevel if it is set.

Throws:

PropertyUndefinedError

setResultLevel

public void setResultLevel(int resultLevel)

The result of a term is described by a resultLevel. This attribute is required. The resultLevel is a non-negative integer describing a level. The resultLevel is used; possibly together with the thresholdLevel or outputLevel to determine the level of a QualitativeSpecies resulting from the Transition.

Parameters:

resultLevel - the resultLevel to set

unsetResultLevel

public boolean unsetResultLevel()

Unsets the resultLevel.

Returns:

true is the resultLevel was set beforehand.

equals

public boolean equals(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isDefaultTerm

public boolean isDefaultTerm()

Returns true if it is a defaultTerm.

Returns:

true if it is a defaultTerm.

setDefaultTerm

public void setDefaultTerm(boolean defaultTerm)

Sets if this FunctionTerm is a defaultTerm. The defaultTerm defines the default result of a Transition. This term is used if there are no other FunctionTerm elements or if none of the Math elements of the FunctionTerm elements evaluates to "true".

Parameters:

defaultTerm - the defaultTerm to set

toString

public java.lang.String toString()

Overrides:

toString in class AbstractMathContainer

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 AbstractMathContainer

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.

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 AbstractMathContainer

Returns:

a Map containing the XML attributes of this object.