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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, 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

Version:

$Rev: 1822 $

Author:

Nicolas Rodriguez, Finja Büchel, Florian Mittag

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private ListOf<FunctionTerm>	listOfFunctionTerms
private ListOf<Input>	listOfInputs
private ListOf<Output>	listOfOutputs
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
Transition()
Transition(int level, int version)
Transition(java.lang.String id)
Transition(java.lang.String id, int level, int version)
Transition(java.lang.String id, java.lang.String name, int level, int version)
Transition(Transition t)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	addFunctionTerm(FunctionTerm functionTerm)
boolean	addInput(Input input)
boolean	addOutput(Output output)
Transition	clone() Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.
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(java.lang.String id)
Input	createInput(java.lang.String id, QualitativeSpecies qualitativeSpecies, InputTransitionEffect transitionEffect)
Input	createInput(java.lang.String id, java.lang.String input_species_id, InputTransitionEffect transitionEffect)
Output	createOutput()
Output	createOutput(java.lang.String id)
Output	createOutput(java.lang.String id, QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect)
Output	createOutput(java.lang.String id, java.lang.String output_species_id, OutputTransitionEffect transitionEffect)
boolean	equals(java.lang.Object obj) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
int	getFunctionTermCount()
int	getInputCount()
ListOf<FunctionTerm>	getListOfFunctionTerms()
ListOf<Input>	getListOfInputs()
ListOf<Output>	getListOfOutputs()
int	getOutputCount()
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults()
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isListOfFunctionTermsMandatory()
boolean	isListOfInputsMandatory()
boolean	isListOfOutputsMandatory()
boolean	isSetListOfFunctionTerms()
boolean	isSetListOfInputs()
boolean	isSetListOfOutputs()
boolean	isSignMandatory()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
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()
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.AbstractNamedSBase

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

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, getAllowsChildren, 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.NamedSBase

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

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, getAllowsChildren, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

listOfFunctionTerms

private ListOf<FunctionTerm> listOfFunctionTerms

listOfInputs

private ListOf<Input> listOfInputs

listOfOutputs

private ListOf<Output> listOfOutputs

Constructor Detail

Transition

public Transition()

Transition

public Transition(int level,
          int version)

Parameters:

level -

version -

Transition

public Transition(java.lang.String id)

Parameters:

id -

Transition

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

Parameters:

id -

level -

version -

Transition

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

Parameters:

id -

name -

level -

version -

Transition

public Transition(Transition t)

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.

addInput

public boolean addInput(Input input)

Parameters:

input - the input to add

addOutput

public boolean addOutput(Output output)

Parameters:

output - the output to add

clone

public Transition 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

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(java.lang.String id)

Parameters:

id -

Returns:

createInput

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

Parameters:

id -

qualitativeSpecies -

transitionEffect -

Returns:

createInput

public Input createInput(java.lang.String id,
                java.lang.String input_species_id,
                InputTransitionEffect transitionEffect)

Parameters:

id -

input_species_id -

transitionEffect -

Returns:

createOutput

public Output createOutput()

Returns:

createOutput

public Output createOutput(java.lang.String id)

Parameters:

id -

Returns:

createOutput

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

Parameters:

id -

qualitativeSpecies -

transitionEffect -

Returns:

createOutput

public Output createOutput(java.lang.String id,
                  java.lang.String output_species_id,
                  OutputTransitionEffect transitionEffect)

Parameters:

id -

output_species_id -

transitionEffect -

Returns:

equals

public boolean equals(java.lang.Object obj)

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 AbstractNamedSBase

Parameters:

obj - 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.

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

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()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractNamedSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

initDefaults

public void initDefaults()

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

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(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 AbstractNamedSBase

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.

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:

java.lang.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:

java.lang.IndexOutOfBoundsException - if the index is invalid.

removeOutput

public void removeOutput(int i)

Parameters:

i - position in the listOfOutputs which should be deleted

Throws:

java.lang.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 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 AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.