public class QualitativeSpecies extends SBase
Species
.
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.
In a Petri net, qualitative species refer to the places of the model, while in a logical model, they refer to the variables of this model (i.e. nodes of the influence graph).
A QualitativeSpecies
describes a pool of indistinguishable entities in a
Compartment
. It is associated with a level (an integer representing
e.g. an activity state, or a functional level of concentration, etc.)
Constructor and Description |
---|
QualitativeSpecies()
Creates a new
QualitativeSpecies with the given level, version, and package version. |
QualitativeSpecies(long level)
Creates a new
QualitativeSpecies with the given level, version, and package version. |
QualitativeSpecies(long level,
long version)
Creates a new
QualitativeSpecies with the given level, version, and package version. |
QualitativeSpecies(long level,
long version,
long pkgVersion)
Creates a new
QualitativeSpecies with the given level, version, and package version. |
QualitativeSpecies(QualitativeSpecies orig)
Copy constructor for
QualitativeSpecies . |
QualitativeSpecies(QualPkgNamespaces qualns)
Creates a new
QualitativeSpecies with the given QualPkgNamespaces object. |
Modifier and Type | Method and Description |
---|---|
QualitativeSpecies |
cloneObject()
Creates and returns a deep copy of this
QualitativeSpecies object. |
void |
delete()
Explicitly deletes the underlying native object.
|
String |
getCompartment()
Returns the value of the 'compartment' attribute of this
QualitativeSpecies . |
boolean |
getConstant()
Returns the value of the 'constant' attribute of this
QualitativeSpecies . |
String |
getElementName()
Returns the XML name of this object.
|
String |
getId()
Returns the value of the 'id' attribute of this
QualitativeSpecies . |
int |
getInitialLevel()
Returns the value of the 'initialLevel' attribute of this
QualitativeSpecies . |
int |
getMaxLevel()
Returns the value of the 'maxLevel' attribute of this
QualitativeSpecies . |
String |
getName()
Returns the value of the 'name' attribute of this
QualitativeSpecies . |
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if all the required attributes
for this QualitativeSpecies object have been set. |
boolean |
isSetCompartment()
Predicate returning
true or false depending on whether this
QualitativeSpecies 's 'compartment' attribute has been set. |
boolean |
isSetConstant()
Predicate returning
true or false depending on whether this
QualitativeSpecies 's 'constant' attribute has been set. |
boolean |
isSetId()
Predicate returning
true or false depending on whether this
QualitativeSpecies 's 'id' attribute has been set. |
boolean |
isSetInitialLevel()
Predicate returning
true or false depending on whether this
QualitativeSpecies 's 'initialLevel' attribute has been set. |
boolean |
isSetMaxLevel()
Predicate returning
true or false depending on whether this
QualitativeSpecies 's 'maxLevel' attribute has been set. |
boolean |
isSetName()
Predicate returning
true or false depending on whether this
QualitativeSpecies 's 'name' attribute has been set. |
void |
renameSIdRefs(String oldid,
String newid)
Replaces all uses of a given
SIdRef type attribute value with another
value. |
int |
setCompartment(String compartment)
Sets the value of the 'compartment' attribute of this
QualitativeSpecies . |
int |
setConstant(boolean constant)
Sets the value of the 'constant' attribute of this
QualitativeSpecies . |
int |
setId(String id)
Sets the value of the 'id' attribute of this
QualitativeSpecies . |
int |
setInitialLevel(int initialLevel)
Sets the value of the 'initialLevel' attribute of this
QualitativeSpecies . |
int |
setMaxLevel(int maxLevel)
Sets the value of the 'maxLevel' attribute of this
QualitativeSpecies . |
int |
setName(String name)
Sets the value of the 'name' attribute of this
QualitativeSpecies . |
int |
unsetCompartment()
Unsets the value of the 'compartment' attribute of this
QualitativeSpecies . |
int |
unsetConstant()
Unsets the value of the 'constant' attribute of this
QualitativeSpecies . |
int |
unsetId()
Unsets the value of the 'id' attribute of this
QualitativeSpecies . |
int |
unsetInitialLevel()
Unsets the value of the 'initialLevel' attribute of this
QualitativeSpecies . |
int |
unsetMaxLevel()
Unsets the value of the 'maxLevel' attribute of this
QualitativeSpecies . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
QualitativeSpecies . |
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public QualitativeSpecies(long level, long version, long pkgVersion) throws SBMLConstructorException
QualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this QualitativeSpecies
version
- a long integer, the SBML Version to assign to this QualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this QualitativeSpecies
SBMLConstructorException
public QualitativeSpecies(long level, long version) throws SBMLConstructorException
QualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this QualitativeSpecies
version
- a long integer, the SBML Version to assign to this QualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this QualitativeSpecies
SBMLConstructorException
public QualitativeSpecies(long level) throws SBMLConstructorException
QualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this QualitativeSpecies
version
- a long integer, the SBML Version to assign to this QualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this QualitativeSpecies
SBMLConstructorException
public QualitativeSpecies() throws SBMLConstructorException
QualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this QualitativeSpecies
version
- a long integer, the SBML Version to assign to this QualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this QualitativeSpecies
SBMLConstructorException
public QualitativeSpecies(QualPkgNamespaces qualns) throws SBMLConstructorException
QualitativeSpecies
with the given QualPkgNamespaces
object.
qualns
- the QualPkgNamespaces
objectSBMLConstructorException
public QualitativeSpecies(QualitativeSpecies orig) throws SBMLConstructorException
QualitativeSpecies
.
orig
- the QualitativeSpecies
instance to copy.SBMLConstructorException
public void delete()
In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize()
methods for the objects. The finalize()
methods in turn call the QualitativeSpecies.delete()
method on the libSBML object.
This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke QualitativeSpecies.delete()
themselves.
public QualitativeSpecies cloneObject()
QualitativeSpecies
object.
cloneObject
 in class SBase
QualitativeSpecies
object.public String getId()
QualitativeSpecies
.
getId
 in class SBase
QualitativeSpecies
as a string.public String getCompartment()
QualitativeSpecies
.
QualitativeSpecies
as a string.public boolean getConstant()
QualitativeSpecies
.
QualitativeSpecies
as a boolean.public String getName()
QualitativeSpecies
.
getName
 in class SBase
QualitativeSpecies
as a string.public int getInitialLevel()
QualitativeSpecies
.
QualitativeSpecies
as a integer.public int getMaxLevel()
QualitativeSpecies
.
QualitativeSpecies
as a integer.public boolean isSetId()
true
or false
depending on whether this
QualitativeSpecies
's 'id' attribute has been set.
isSetId
 in class SBase
true
if this QualitativeSpecies
's 'id' attribute has been set,
otherwise false
is returned.public boolean isSetCompartment()
true
or false
depending on whether this
QualitativeSpecies
's 'compartment' attribute has been set.
true
if this QualitativeSpecies
's 'compartment' attribute has been set,
otherwise false
is returned.public boolean isSetConstant()
true
or false
depending on whether this
QualitativeSpecies
's 'constant' attribute has been set.
true
if this QualitativeSpecies
's 'constant' attribute has been set,
otherwise false
is returned.public boolean isSetName()
true
or false
depending on whether this
QualitativeSpecies
's 'name' attribute has been set.
isSetName
 in class SBase
true
if this QualitativeSpecies
's 'name' attribute has been set,
otherwise false
is returned.public boolean isSetInitialLevel()
true
or false
depending on whether this
QualitativeSpecies
's 'initialLevel' attribute has been set.
true
if this QualitativeSpecies
's 'initialLevel' attribute has been set,
otherwise false
is returned.public boolean isSetMaxLevel()
true
or false
depending on whether this
QualitativeSpecies
's 'maxLevel' attribute has been set.
true
if this QualitativeSpecies
's 'maxLevel' attribute has been set,
otherwise false
is returned.public int setId(String id)
QualitativeSpecies
.
public int setCompartment(String compartment)
QualitativeSpecies
.
compartment
- String value of the 'compartment' attribute to be set
public int setConstant(boolean constant)
QualitativeSpecies
.
constant
- boolean value of the 'constant' attribute to be set
public int setName(String name)
QualitativeSpecies
.
public int setInitialLevel(int initialLevel)
QualitativeSpecies
.
initialLevel
- int value of the 'initialLevel' attribute to be set
public int setMaxLevel(int maxLevel)
QualitativeSpecies
.
maxLevel
- int value of the 'maxLevel' attribute to be set
public int unsetId()
QualitativeSpecies
.
public int unsetCompartment()
QualitativeSpecies
.
public int unsetConstant()
QualitativeSpecies
.
public int unsetName()
QualitativeSpecies
.
public int unsetInitialLevel()
QualitativeSpecies
.
public int unsetMaxLevel()
QualitativeSpecies
.
public void renameSIdRefs(String oldid, String newid)
Replaces all uses of a given SIdRef
type attribute value with another
value.
In SBML, object identifiers are of a data type called SId
.
In SBML Level 3, an explicit data type called SIdRef
was
introduced for attribute values that refer to SId
values in
previous Levels of SBML, this data type did not exist and attributes were
simply described to as 'referring to an identifier', but the effective
data type was the same as SIdRef
in Level 3. These and
other methods of libSBML refer to the type SIdRef
for all
Levels of SBML, even if the corresponding SBML specification did not
explicitly name the data type.
This method works by looking at all attributes and (if appropriate)
mathematical formulas in MathML content, comparing the referenced
identifiers to the value of oldid
. If any matches are found, the
matching values are replaced with newid
. The method does not
descend into child elements.
renameSIdRefs
 in class SBase
oldid
- the old identifiernewid
- the new identifierpublic String getElementName()
getElementName
 in class SBase
public int getTypeCode()
LibSBML attaches an identifying code to every kind of SBML object. These
are integer constants known as SBML type codes. The names of all
the codes begin with the characters SBML_
.
In the Java language interface for libSBML, the
type codes are defined as static integer constants in the interface class
libsbmlConstants
. Note that different Level 3
package plug-ins may use overlapping type codes to identify the package
to which a given object belongs, call the getPackageName()
method on the object.
getTypeCode
 in class SBase
SBML_QUAL_QUALITATIVE_SPECIES
QualitativeSpecies.getElementName()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes
for this QualitativeSpecies
object have been set.
hasRequiredAttributes
 in class SBase
QualitativeSpecies
object are: