org.sbml.jsbml.ext.qual

Class Transition

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.qual.Transition

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class Transition
extends AbstractNamedSBase
implements UniqueNamedSBase

A Transition defines the changes in level associated with the QualitativeSpecies that occur when a Transition is enabled.

In logical models a Transition is used to specify the logical rule associated with a QualitativeSpecies (that appears as an Output of this Transition). For example, the rule if A > 1 : B = 2 would be encapsulated as a Transition with QualitativeSpecies "A" as an Input and "B" as an Output; the if A > 1 rule being encoded by the math element of a FunctionTerm with the resultLevel attribute having a value "2".

In Petri net models a Transition is interpreted, using the common Petri net semantics, as events that might occur within the system causing tokens to be moved. See the package specification for an example.

Since:

1.0

Author:

Nicolas Rodriguez, Finja Büchel, Florian Mittag

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
Transition() Creates a new Transition instance.
Transition(int level, int version) Creates a new Transition instance.
Transition(String id) Creates a new Transition instance.
Transition(String id, int level, int version) Creates a new Transition instance.
Transition(String id, String name, int level, int version) Creates a new Transition instance.
Transition(Transition t) Creates a new Transition instance.

Method Summary

Modifier and Type	Method and Description
boolean	addFunctionTerm(FunctionTerm functionTerm)
boolean	addInput(Input input)
boolean	addOutput(Output output)
Transition	clone()
FunctionTerm	createFunctionTerm() Creates a new instance of FunctionTerm and adds it to this Transition's listOfFunctionTerms.
FunctionTerm	createFunctionTerm(ASTNode math) Creates a new instance of FunctionTerm with the given mathematical expression (encoded in an ASTNode) and adds it to this Transition's listOfFunctionTerms.
Input	createInput()
Input	createInput(String id)
Input	createInput(String id, QualitativeSpecies qualitativeSpecies, InputTransitionEffect transitionEffect)
Input	createInput(String id, String input_species_id, InputTransitionEffect transitionEffect)
Output	createOutput()
Output	createOutput(String id)
Output	createOutput(String id, QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect)
Output	createOutput(String id, String output_species_id, OutputTransitionEffect transitionEffect)
boolean	equals(Object obj)
TreeNode	getChildAt(int index)
int	getChildCount()
int	getFunctionTermCount()
int	getInputCount()
ListOf<FunctionTerm>	getListOfFunctionTerms()
ListOf<Input>	getListOfInputs()
ListOf<Output>	getListOfOutputs()
int	getOutputCount()
int	hashCode()
void	initDefaults()
boolean	isIdMandatory()
boolean	isListOfFunctionTermsMandatory()
boolean	isListOfInputsMandatory()
boolean	isListOfOutputsMandatory()
boolean	isSetListOfFunctionTerms()
boolean	isSetListOfInputs()
boolean	isSetListOfOutputs()
boolean	isSignMandatory()
boolean	readAttribute(String attributeName, String prefix, String value)
boolean	removeFunctionTerm(FunctionTerm functionTerm)
void	removeFunctionTerm(int i)
boolean	removeInput(Input input)
void	removeInput(int i)
void	removeOutput(int i)
boolean	removeOutput(Output output)
void	setListOfFunctionTerms(ListOf<FunctionTerm> loft) The Transition element contains exactly one list of FunctionTerms.
void	setListOfInputs(ListOf<Input> loi) The Transition element contains at most one list of Inputs.
void	setListOfOutputs(ListOf<Output> loo) The Transition element contains at most one list of Outputs.
boolean	unsetListOfFunctionTerms()
boolean	unsetListOfInputs()
boolean	unsetListOfOutputs()
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, 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, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, 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, setMetaId, setName, setNamespace, setNotes, setNotes, 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, isCloningInProgress, isInvalidSBMLAllowed, 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.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, 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, getAllowsChildren, getIndex, getParent, isLeaf

Constructor Detail

Transition

public Transition()

Creates a new Transition instance.

Transition

public Transition(int level,
                  int version)

Creates a new Transition instance.

Parameters:

level - the SBML level

version - the SBML version

Transition

public Transition(String id)

Creates a new Transition instance.

Parameters:

id - the id

Transition

public Transition(String id,
                  int level,
                  int version)

Creates a new Transition instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

Transition

public Transition(String id,
                  String name,
                  int level,
                  int version)

Creates a new Transition instance.

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

Transition

public Transition(Transition t)

Creates a new Transition instance.

Parameters:

t - the Transition instance to clone

Method Detail

addFunctionTerm

public boolean addFunctionTerm(FunctionTerm functionTerm)

Parameters:

functionTerm - true if the FunctionTerm was added to the list or false if adding the new FunctionTerm was not successful.

Returns:

addInput

public boolean addInput(Input input)

Parameters:

input - the input to add

Returns:

addOutput

public boolean addOutput(Output output)

Parameters:

output - the output to add

Returns:

clone

public Transition clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

createFunctionTerm

public FunctionTerm createFunctionTerm()

Creates a new instance of FunctionTerm and adds it to this Transition's listOfFunctionTerms. In case that this operation fails, null will be returned. In case of success, this method will return the newly created FunctionTerm.

Returns:

the newly created FunctionTerm or null if adding the new FunctionTerm was not successful.

See Also:

createFunctionTerm(ASTNode)

createFunctionTerm

public FunctionTerm createFunctionTerm(ASTNode math)

Creates a new instance of FunctionTerm with the given mathematical expression (encoded in an ASTNode) and adds it to this Transition's listOfFunctionTerms. In case that this operation fails, null will be returned. In case of success, this method will return the newly created FunctionTerm.

Parameters:

math - The mathematical expression for the new FunctionTerm.

Returns:

newly created FunctionTerm or null if adding the new FunctionTerm was not successful.

createInput

public Input createInput()

Returns:

createInput

public Input createInput(String id)

Parameters:

id -

Returns:

createInput

public Input createInput(String id,
                         QualitativeSpecies qualitativeSpecies,
                         InputTransitionEffect transitionEffect)

Parameters:

id -

qualitativeSpecies -

transitionEffect -

Returns:

createInput

public Input createInput(String id,
                         String input_species_id,
                         InputTransitionEffect transitionEffect)

Parameters:

id -

input_species_id -

transitionEffect -

Returns:

createOutput

public Output createOutput()

Returns:

createOutput

public Output createOutput(String id)

Parameters:

id -

Returns:

createOutput

public Output createOutput(String id,
                           QualitativeSpecies qualitativeSpecies,
                           OutputTransitionEffect transitionEffect)

Parameters:

id -

qualitativeSpecies -

transitionEffect -

Returns:

createOutput

public Output createOutput(String id,
                           String output_species_id,
                           OutputTransitionEffect transitionEffect)

Parameters:

id -

output_species_id -

transitionEffect -

Returns:

equals

public boolean equals(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getFunctionTermCount

public int getFunctionTermCount()

Returns:

getInputCount

public int getInputCount()

Returns:

getListOfFunctionTerms

public ListOf<FunctionTerm> getListOfFunctionTerms()

Returns:

the listOfFunctionTerms

getListOfInputs

public ListOf<Input> getListOfInputs()

Returns:

the listOfInputs

getListOfOutputs

public ListOf<Output> getListOfOutputs()

Returns:

the listOfOutputs

getOutputCount

public int getOutputCount()

Returns:

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

initDefaults

public void initDefaults()

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

Returns:

false

isListOfFunctionTermsMandatory

public boolean isListOfFunctionTermsMandatory()

Returns:

false

isListOfInputsMandatory

public boolean isListOfInputsMandatory()

Returns:

false

isListOfOutputsMandatory

public boolean isListOfOutputsMandatory()

Returns:

true

isSetListOfFunctionTerms

public boolean isSetListOfFunctionTerms()

Returns:

isSetListOfInputs

public boolean isSetListOfInputs()

Returns:

isSetListOfOutputs

public boolean isSetListOfOutputs()

Returns:

isSignMandatory

public boolean isSignMandatory()

Returns:

false

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

removeFunctionTerm

public boolean removeFunctionTerm(FunctionTerm functionTerm)

Parameters:

functionTerm - to remove from the listOfFunctionTerms

Returns:

true if the operation was successful

removeFunctionTerm

public void removeFunctionTerm(int i)

Parameters:

i - position in the listOfFunctionTerms which should be deleted

Throws:

IndexOutOfBoundsException - if the index is invalid.

removeInput

public boolean removeInput(Input input)

Parameters:

input - to remove from the listOfInputs

Returns:

true if the operation was successful

removeInput

public void removeInput(int i)

Parameters:

i - position in the listOfInputs which should be deleted

Throws:

IndexOutOfBoundsException - if the index is invalid.

removeOutput

public void removeOutput(int i)

Parameters:

i - position in the listOfOutputs which should be deleted

Throws:

IndexOutOfBoundsException - if the index is not valid

removeOutput

public boolean removeOutput(Output output)

Parameters:

output - to remove from the listOfOutputs

Returns:

true if the operation was successful

setListOfFunctionTerms

public void setListOfFunctionTerms(ListOf<FunctionTerm> loft)

The Transition element contains exactly one list of FunctionTerms.

Parameters:

loft -

setListOfInputs

public void setListOfInputs(ListOf<Input> loi)

The Transition element contains at most one list of Inputs.

Parameters:

loi -

setListOfOutputs

public void setListOfOutputs(ListOf<Output> loo)

The Transition element contains at most one list of Outputs.

Parameters:

loo -

unsetListOfFunctionTerms

public boolean unsetListOfFunctionTerms()

Returns:

unsetListOfInputs

public boolean unsetListOfInputs()

Returns:

unsetListOfOutputs

public boolean unsetListOfOutputs()

Returns:

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase