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, NamedSBase, SBase, UniqueNamedSBase, TreeNodeWithChangeSupport

public class QualitativeSpecies
extends AbstractNamedSBase
implements 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

Version:

$Rev: 1834 $

Author:

Nicolas Rodriguez, Finja Büchel, Clemens Wrzodek

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.String	compartment
private java.lang.Boolean	constant
private java.lang.Integer	initialLevel
private java.lang.Integer	maxLevel
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
QualitativeSpecies()
QualitativeSpecies(int level, int version)
QualitativeSpecies(QualitativeSpecies qualSpecies) Copy constructor that clones all variables of qualSpecies.
QualitativeSpecies(Species species) Copy constructor that clones all values from the input species that are also available in QualitativeSpecies.
QualitativeSpecies(java.lang.String id)
QualitativeSpecies(java.lang.String id, int level, int version)
QualitativeSpecies(java.lang.String id, java.lang.String name, int level, int version)

Method Summary

Methods

Modifier and Type	Method and Description
QualitativeSpecies	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.
java.lang.String	getCompartment()
boolean	getConstant()
int	getInitialLevel()
int	getMaxLevel()
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults()
boolean	isBoundaryConditionMandatory()
boolean	isCompartmentMandatory()
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	isInitialLevelMandatory()
boolean	isMaxLevelMandatory()
boolean	isSetCompartment()
boolean	isSetConstant()
boolean	isSetConstantMandatory()
boolean	isSetInitialLevel()
boolean	isSetMaxLevel()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setCompartment(Compartment compartment)
void	setCompartment(java.lang.String compartment) Sets the compartment attribute.
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() 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, getChildAt, getChildCount, 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, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

compartment

private java.lang.String compartment

constant

private java.lang.Boolean constant

initialLevel

private java.lang.Integer initialLevel

maxLevel

private java.lang.Integer maxLevel

Constructor Detail

QualitativeSpecies

public QualitativeSpecies()

QualitativeSpecies

public QualitativeSpecies(java.lang.String id)

Parameters:

id -

QualitativeSpecies

public QualitativeSpecies(int level,
                  int version)

Parameters:

level -

version -

QualitativeSpecies

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

Parameters:

id -

level -

version -

QualitativeSpecies

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

Parameters:

id -

level -

version -

QualitativeSpecies

public QualitativeSpecies(Species species)

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 -

QualitativeSpecies

public QualitativeSpecies(QualitativeSpecies qualSpecies)

Copy constructor that clones all variables of qualSpecies.

Parameters:

qualSpecies -

Method Detail

initDefaults

public void initDefaults()

clone

public QualitativeSpecies 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

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:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

isCompartmentMandatory

public boolean isCompartmentMandatory()

Returns:

true

isSetCompartment

public boolean isSetCompartment()

Returns:

if compartment attribute is set

getCompartment

public java.lang.String getCompartment()

Returns:

the compartment

setCompartment

public void setCompartment(java.lang.String compartment)

Sets the compartment attribute.

The required attribute compartment is used to identify the Compartment in which the QualitativeSpecies is located. The attribute's value must be the identifier of an existing Compartment object in the model. This attribute is comparable with the compartment attribute on the Species element.

Parameters:

compartment - the compartment to set

setCompartment

public void setCompartment(Compartment compartment)

Parameters:

compartment -

unsetCompartment

public boolean unsetCompartment()

Returns:

true if the unset of the compartment attribute was successful

isBoundaryConditionMandatory

public boolean isBoundaryConditionMandatory()

Returns:

true

isSetConstantMandatory

public boolean isSetConstantMandatory()

Returns:

true

isSetConstant

public boolean isSetConstant()

Returns:

getConstant

public boolean getConstant()

Returns:

the constant

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

unsetConstant

public boolean unsetConstant()

Returns:

true if the unset of the constant attribute was successful

isInitialLevelMandatory

public boolean isInitialLevelMandatory()

Returns:

false

isSetInitialLevel

public boolean isSetInitialLevel()

Returns:

getInitialLevel

public int getInitialLevel()

Returns:

the initialLevel

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

unsetInitialLevel

public boolean unsetInitialLevel()

Returns:

true if unset initialLevel attribute was successful

isMaxLevelMandatory

public boolean isMaxLevelMandatory()

Returns:

false

isSetMaxLevel

public boolean isSetMaxLevel()

Returns:

getMaxLevel

public int getMaxLevel()

Returns:

the maxLevel

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

unsetMaxLevel

public boolean unsetMaxLevel()

Returns:

true if unset maxLevel attribute was successful

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 AbstractNamedSBase

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 AbstractNamedSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

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.

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.