Package org.sbml.jsbml.ext.qual

Class QualitativeSpecies

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.qual.QualitativeSpecies

All Implemented Interfaces:

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

public class QualitativeSpecies
extends AbstractNamedSBase
implements CompartmentalizedSBase, UniqueNamedSBase

Similarly to the Species in SBML, the components of qualitative models refer to pools of entities that are considered indistinguishable and are each located in a specific Compartment. However, here components are characterised by their qualitative influences rather than by taking part in reactions. Therefore, we define the QualitativeSpecies element to represent such pools of entities.

Since:

1.0

Author:

Nicolas Rodriguez, Finja Büchel, Clemens Wrzodek

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	Description
QualitativeSpecies()	Creates a new QualitativeSpecies instance.
QualitativeSpecies(int level, int version)	Creates a new QualitativeSpecies instance.
QualitativeSpecies(java.lang.String id)	Creates a new QualitativeSpecies instance.
QualitativeSpecies(java.lang.String id, int level, int version)	Creates a new QualitativeSpecies instance.
QualitativeSpecies(java.lang.String id, java.lang.String name, int level, int version)	Creates a new QualitativeSpecies instance.
QualitativeSpecies(QualitativeSpecies qualSpecies)	Creates a new QualitativeSpecies instance.
QualitativeSpecies(Species species)	Creates a new QualitativeSpecies instance.

Method Summary

Modifier and Type	Method	Description
QualitativeSpecies	clone()
boolean	equals(java.lang.Object object)
java.lang.String	getCompartment()
Compartment	getCompartmentInstance()
boolean	getConstant()
int	getInitialLevel()
int	getMaxLevel()
int	hashCode()
void	initDefaults()
boolean	isCompartmentMandatory()
boolean	isIdMandatory()
boolean	isInitialLevelMandatory()
boolean	isMaxLevelMandatory()
boolean	isSetCompartment()
boolean	isSetCompartmentInstance()
boolean	isSetConstant()
boolean	isSetConstantMandatory()
boolean	isSetInitialLevel()
boolean	isSetMaxLevel()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
boolean	setCompartment(java.lang.String compartment)
boolean	setCompartment(Compartment compartment)
void	setConstant(boolean constant)	Sets the constant attribute.
void	setInitialLevel(int initialLevel)	Sets the initialLevel attribute.
void	setMaxLevel(int maxLevel)	Sets the maxLevel attribute.
boolean	unsetCompartment()
boolean	unsetConstant()
boolean	unsetInitialLevel()
boolean	unsetMaxLevel()
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, 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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 interface org.sbml.jsbml.NamedSBase

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

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, 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, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

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

Constructor Detail

QualitativeSpecies

public QualitativeSpecies()

Creates a new QualitativeSpecies instance.

QualitativeSpecies

public QualitativeSpecies(int level,
                          int version)

Creates a new QualitativeSpecies instance.

Parameters:

level - the SBML level

version - the SBML version

QualitativeSpecies

public QualitativeSpecies(QualitativeSpecies qualSpecies)

Creates a new QualitativeSpecies instance.

Copy constructor that clones all variables of qualSpecies.

Parameters:

qualSpecies - the QualitativeSpecies to clone

QualitativeSpecies

public QualitativeSpecies(Species species)

Creates a new QualitativeSpecies instance.

Copy constructor that clones all values from the input species that are also available in QualitativeSpecies.

You should consider setting a new id and meta_id afterwards to avoid duplicate identifiers.

Parameters:

species - the species to be used to initialize the new instance

QualitativeSpecies

public QualitativeSpecies(java.lang.String id)

Creates a new QualitativeSpecies instance.

Parameters:

id - the id

QualitativeSpecies

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

Creates a new QualitativeSpecies instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

QualitativeSpecies

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

Creates a new QualitativeSpecies instance.

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

Method Detail

clone

public QualitativeSpecies clone()

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

equals

public boolean equals(java.lang.Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

getCompartment

public java.lang.String getCompartment()

Specified by:

getCompartment in interface CompartmentalizedSBase

getCompartmentInstance

public Compartment getCompartmentInstance()

Specified by:

getCompartmentInstance in interface CompartmentalizedSBase

getConstant

public boolean getConstant()

Returns:

the constant

getInitialLevel

public int getInitialLevel()

Returns:

the initialLevel

getMaxLevel

public int getMaxLevel()

Returns:

the maxLevel

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

initDefaults

public void initDefaults()

isCompartmentMandatory

public boolean isCompartmentMandatory()

Specified by:

isCompartmentMandatory in interface CompartmentalizedSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isInitialLevelMandatory

public boolean isInitialLevelMandatory()

Returns:

false

isMaxLevelMandatory

public boolean isMaxLevelMandatory()

Returns:

false

isSetCompartment

public boolean isSetCompartment()

Specified by:

isSetCompartment in interface CompartmentalizedSBase

isSetCompartmentInstance

public boolean isSetCompartmentInstance()

Specified by:

isSetCompartmentInstance in interface CompartmentalizedSBase

isSetConstant

public boolean isSetConstant()

Returns:

isSetConstantMandatory

public boolean isSetConstantMandatory()

Returns:

true

isSetInitialLevel

public boolean isSetInitialLevel()

Returns:

isSetMaxLevel

public boolean isSetMaxLevel()

Returns:

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

setCompartment

public boolean setCompartment(Compartment compartment)

Specified by:

setCompartment in interface CompartmentalizedSBase

setCompartment

public boolean setCompartment(java.lang.String compartment)

Specified by:

setCompartment in interface CompartmentalizedSBase

setConstant

public void setConstant(boolean constant)

Sets the constant attribute.

The required attribute constant, of type boolean, is used to indicate that the level of the QualitativeSpecies is fixed or can be varied. This attribute is comparable with the constant attribute on the Species element. Typically, in a regulatory or influence graph a QualitativeSpecies may receive no interaction and if so, would appear only as an Input in the Model and have the value of the constant attribute set to "true". In other influence graphs or in Petri net models a QualitativeSpecies may occur as an Input whose level is changed by the Transition and would have constant set to "false". The nature of changes to a QualitativeSpecies resulting from a Transition is also recorded using the transitionEffect attribute on the Input and may be set to "none" to indicate there is no change. This duplication of information provides a means of validating the modeller's intent and also allows entities on the borders of a system to be easily identified.

Parameters:

constant - the constant to set

setInitialLevel

public void setInitialLevel(int initialLevel)

Sets the initialLevel attribute.

The initialLevel is a non-negative integer that defines the initial level of the QualitativeSpecies in its Compartment. This attribute is optional but cannot exceed the value of the maxLevel attribute, if both are set.

Parameters:

initialLevel - the initialLevel to set

setMaxLevel

public void setMaxLevel(int maxLevel)

Sets the maxLevel attribute.

The maxLevel is a non-negative integer that sets the maximal level of the QualitativeSpecies. This attribute is optional but when set, the level of the QualitativeSpecies must not exceed this value at any point in a simulation. In logical models, the maxLevel must be coherent with the resultLevel values in the function terms defined for the corresponding transition, i.e. the Model must not contain a FunctionTerm that attempts to set a level that exceeds this value. In Petri nets, this attribute is meant to define place capacities. Hence, a Transition is not enabled if the value resulting from its firing would exceed the maxLevel of one of its output places. The attribute is not required and even if explicitly stated, the restriction imposed by place capacities in a Petri net model must be encapsulated within the math element of the FunctionTerm elements. This attribute can also be used to indicate the range of possible levels for a QualitativeSpecies whose constant attribute is true. This may seem a little contradictory, since if the constant attribute is true then the level associated with the QualitativeSpecies cannot vary. However, it provides additional information regarding the possible levels particularly in the case where no initialLevel has been set.

Parameters:

maxLevel - the maxLevel to set

unsetCompartment

public boolean unsetCompartment()

Specified by:

unsetCompartment in interface CompartmentalizedSBase

unsetConstant

public boolean unsetConstant()

Returns:

true if the unset of the constant attribute was successful

unsetInitialLevel

public boolean unsetInitialLevel()

Returns:

true if unset initialLevel attribute was successful

unsetMaxLevel

public boolean unsetMaxLevel()

Returns:

true if unset maxLevel attribute was successful

writeXMLAttributes

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

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase