org.sbml.jsbml.ext.qual
public class QualitativeSpecies extends AbstractNamedSBase implements UniqueNamedSBase
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.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.
|
ignoredExtensions, ignoredXMLElements
listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS
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) |
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)
|
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. |
getId, getName, isSetId, isSetName, isValidId, setId, setName, toString, unsetId, unsetName
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
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
finalize, getClass, notify, notifyAll, wait, wait, wait
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
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
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
private static final long serialVersionUID
private java.lang.String compartment
private java.lang.Boolean constant
private java.lang.Integer initialLevel
private java.lang.Integer maxLevel
public QualitativeSpecies()
public QualitativeSpecies(java.lang.String id)
id
- public QualitativeSpecies(int level, int version)
level
- version
- public QualitativeSpecies(java.lang.String id, int level, int version)
id
- level
- version
- public QualitativeSpecies(java.lang.String id, java.lang.String name, int level, int version)
id
- level
- version
- public QualitativeSpecies(Species species)
species
that are also available in
QualitativeSpecies
.
You should consider setting a new id and meta_id afterwards to avoid duplicate identifiers.
species
- public QualitativeSpecies(QualitativeSpecies qualSpecies)
qualSpecies
.qualSpecies
- public void initDefaults()
public QualitativeSpecies clone()
SBase
SBase
with the same properties
like this one.clone
in interface SBase
clone
in class AbstractSBase
public boolean isIdMandatory()
NamedSBase
NamedSBase
is required to be defined (i.e., not null
)
in the definition of SBML.isIdMandatory
in interface NamedSBase
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.public boolean isCompartmentMandatory()
public boolean isSetCompartment()
public java.lang.String getCompartment()
public void setCompartment(java.lang.String compartment)
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.
compartment
- the compartment to setpublic void setCompartment(Compartment compartment)
compartment
- public boolean unsetCompartment()
true
if the unset of the compartment attribute was successfulpublic boolean isBoundaryConditionMandatory()
public boolean isSetConstantMandatory()
public boolean isSetConstant()
public boolean getConstant()
public void setConstant(boolean constant)
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.
constant
- the constant to setpublic boolean unsetConstant()
true
if the unset of the constant attribute was successfulpublic boolean isInitialLevelMandatory()
public boolean isSetInitialLevel()
public int getInitialLevel()
public void setInitialLevel(int initialLevel)
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.
initialLevel
- the initialLevel to setpublic boolean unsetInitialLevel()
true
if unset initialLevel attribute was successfulpublic boolean isMaxLevelMandatory()
public boolean isSetMaxLevel()
public int getMaxLevel()
public void setMaxLevel(int maxLevel)
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.
maxLevel
- the maxLevel to setpublic boolean unsetMaxLevel()
true
if unset maxLevel attribute was successfulpublic boolean equals(java.lang.Object object)
SBase
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractNamedSBase
SBase
instance.Object.hashCode()
public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBase
SBase
.
If the given attribute name is not recognized, nothing is done and
false
is returned.
readAttribute
in interface SBase
readAttribute
in class AbstractNamedSBase
attributeName
- localName of the XML attributeprefix
- prefix of the XML attributevalue
- value of the XML attributetrue
if the attribute has been successfully read.public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
SBase
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.
writeXMLAttributes
in interface SBase
writeXMLAttributes
in class AbstractNamedSBase
Map
containing the XML attributes of this object.