public class QualitativeSpecies extends AbstractNamedSBase implements CompartmentalizedSBase, 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.ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageNamelistOfListeners, parent, resourceBundle| Constructor and Description |
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QualitativeSpecies()
Creates a new
QualitativeSpecies instance. |
QualitativeSpecies(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. |
QualitativeSpecies(String id)
Creates a new
QualitativeSpecies instance. |
QualitativeSpecies(String id,
int level,
int version)
Creates a new
QualitativeSpecies instance. |
QualitativeSpecies(String id,
String name,
int level,
int version)
Creates a new
QualitativeSpecies instance. |
isValidIdaddCVTerm, 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, getChildAt, getChildCount, 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, unsetSBOTermaddAllChangeListeners, 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, userObjectKeySetfinalize, getClass, notify, notifyAll, wait, wait, waitgetId, getName, isSetId, isSetName, setId, setName, unsetId, unsetNameaddCVTerm, 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, unsetSBOTermaddAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySetchildren, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeafpublic QualitativeSpecies()
QualitativeSpecies instance.public QualitativeSpecies(int level,
int version)
QualitativeSpecies instance.level - the SBML levelversion - the SBML versionpublic QualitativeSpecies(QualitativeSpecies qualSpecies)
QualitativeSpecies instance.
Copy constructor that clones all variables of qualSpecies.
qualSpecies - the QualitativeSpecies to clonepublic QualitativeSpecies(Species species)
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.
species - the species to be used to initialize the new instancepublic QualitativeSpecies(String id)
QualitativeSpecies instance.id - the idpublic QualitativeSpecies(String id, int level, int version)
QualitativeSpecies instance.id - the idlevel - the SBML levelversion - the SBML versionpublic QualitativeSpecies(String id, String name, int level, int version)
QualitativeSpecies instance.id - the idname - the namelevel - the SBML levelversion - the SBML versionpublic QualitativeSpecies clone()
clone in interface SBaseclone in class AbstractSBasepublic boolean equals(Object object)
equals in interface SBaseequals in class AbstractSBasepublic String getCompartment()
getCompartment in interface CompartmentalizedSBasepublic Compartment getCompartmentInstance()
getCompartmentInstance in interface CompartmentalizedSBasepublic boolean getConstant()
public int getInitialLevel()
public int getMaxLevel()
public int hashCode()
hashCode in interface SBasehashCode in class AbstractSBasepublic void initDefaults()
public boolean isCompartmentMandatory()
isCompartmentMandatory in interface CompartmentalizedSBasepublic boolean isIdMandatory()
isIdMandatory in interface NamedSBaseisIdMandatory in interface SBaseisIdMandatory in class AbstractSBasepublic boolean isInitialLevelMandatory()
public boolean isMaxLevelMandatory()
public boolean isSetCompartment()
isSetCompartment in interface CompartmentalizedSBasepublic boolean isSetCompartmentInstance()
isSetCompartmentInstance in interface CompartmentalizedSBasepublic boolean isSetConstant()
public boolean isSetConstantMandatory()
public boolean isSetInitialLevel()
public boolean isSetMaxLevel()
public boolean readAttribute(String attributeName, String prefix, String value)
readAttribute in interface SBasereadAttribute in class AbstractSBasepublic boolean setCompartment(Compartment compartment)
setCompartment in interface CompartmentalizedSBasepublic boolean setCompartment(String compartment)
setCompartment in interface CompartmentalizedSBasepublic 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 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 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 unsetCompartment()
unsetCompartment in interface CompartmentalizedSBasepublic boolean unsetConstant()
true if the unset of the constant attribute was successfulpublic boolean unsetInitialLevel()
true if unset initialLevel attribute was successfulpublic boolean unsetMaxLevel()
true if unset maxLevel attribute was successfulpublic Map<String,String> writeXMLAttributes()
writeXMLAttributes in interface SBasewriteXMLAttributes in class AbstractSBaseCopyright © 2009–2017. All rights reserved.