QualitativeSpecies (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.QualitativeSpecies

```
public class QualitativeSpecies
extends SBase
```
qual Extension of 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 Summary

Constructors
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.

Method Summary

All Methods Instance Methods Concrete Methods
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.
`java.lang.String`	`getCompartment()` Returns the value of the 'compartment' attribute of this `QualitativeSpecies`.
`boolean`	`getConstant()` Returns the value of the 'constant' attribute of this `QualitativeSpecies`.
`java.lang.String`	`getElementName()` Returns the XML name of this object.
`java.lang.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`.
`java.lang.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(java.lang.String oldid, java.lang.String newid)` Replaces all uses of a given `SIdRef` type attribute value with another value.
`int`	`setCompartment(java.lang.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(java.lang.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(java.lang.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`.

Methods inherited from class org.sbml.libsbml.SBase
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

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - QualitativeSpecies
```
public QualitativeSpecies(long level,
                          long version,
                          long pkgVersion)
                   throws SBMLConstructorException
```
    Creates a new QualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - QualitativeSpecies
```
public QualitativeSpecies(long level,
                          long version)
                   throws SBMLConstructorException
```
    Creates a new QualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - QualitativeSpecies
```
public QualitativeSpecies(long level)
                   throws SBMLConstructorException
```
    Creates a new QualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - QualitativeSpecies
```
public QualitativeSpecies()
                   throws SBMLConstructorException
```
    Creates a new QualitativeSpecies with the given level, version, and package version.
    
    Parameters:
    
    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
    
    Throws:
    
    SBMLConstructorException
  - QualitativeSpecies
```
public QualitativeSpecies(QualPkgNamespaces qualns)
                   throws SBMLConstructorException
```
    Creates a new QualitativeSpecies with the given QualPkgNamespaces object.
    
    Parameters:
    
    qualns - the QualPkgNamespaces object
    
    Throws:
    
    SBMLConstructorException
  - QualitativeSpecies
```
public QualitativeSpecies(QualitativeSpecies orig)
                   throws SBMLConstructorException
```
    Copy constructor for QualitativeSpecies.
    
    Parameters:
    
    orig - the QualitativeSpecies instance to copy.
    
    Throws:
    
    SBMLConstructorException
- Method Detail
  - delete
```
public void delete()
```
    Explicitly deletes the underlying native object.
    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.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public QualitativeSpecies cloneObject()
```
    Creates and returns a deep copy of this QualitativeSpecies object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this QualitativeSpecies object.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this QualitativeSpecies.
    
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the value of the 'id' attribute of this QualitativeSpecies as a string.
  - getCompartment
```
public java.lang.String getCompartment()
```
    Returns the value of the 'compartment' attribute of this QualitativeSpecies.
    
    Returns:
    
    the value of the 'compartment' attribute of this QualitativeSpecies as a string.
  - getConstant
```
public boolean getConstant()
```
    Returns the value of the 'constant' attribute of this QualitativeSpecies.
    
    Returns:
    
    the value of the 'constant' attribute of this QualitativeSpecies as a boolean.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this QualitativeSpecies.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the value of the 'name' attribute of this QualitativeSpecies as a string.
  - getInitialLevel
```
public int getInitialLevel()
```
    Returns the value of the 'initialLevel' attribute of this QualitativeSpecies.
    
    Returns:
    
    the value of the 'initialLevel' attribute of this QualitativeSpecies as a integer.
  - getMaxLevel
```
public int getMaxLevel()
```
    Returns the value of the 'maxLevel' attribute of this QualitativeSpecies.
    
    Returns:
    
    the value of the 'maxLevel' attribute of this QualitativeSpecies as a integer.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true or false depending on whether this QualitativeSpecies's 'id' attribute has been set.
    
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if this QualitativeSpecies's 'id' attribute has been set, otherwise false is returned.
  - isSetCompartment
```
public boolean isSetCompartment()
```
    Predicate returning true or false depending on whether this QualitativeSpecies's 'compartment' attribute has been set.
    
    Returns:
    
    true if this QualitativeSpecies's 'compartment' attribute has been set, otherwise false is returned.
  - isSetConstant
```
public boolean isSetConstant()
```
    Predicate returning true or false depending on whether this QualitativeSpecies's 'constant' attribute has been set.
    
    Returns:
    
    true if this QualitativeSpecies's 'constant' attribute has been set, otherwise false is returned.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true or false depending on whether this QualitativeSpecies's 'name' attribute has been set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if this QualitativeSpecies's 'name' attribute has been set, otherwise false is returned.
  - isSetInitialLevel
```
public boolean isSetInitialLevel()
```
    Predicate returning true or false depending on whether this QualitativeSpecies's 'initialLevel' attribute has been set.
    
    Returns:
    
    true if this QualitativeSpecies's 'initialLevel' attribute has been set, otherwise false is returned.
  - isSetMaxLevel
```
public boolean isSetMaxLevel()
```
    Predicate returning true or false depending on whether this QualitativeSpecies's 'maxLevel' attribute has been set.
    
    Returns:
    
    true if this QualitativeSpecies's 'maxLevel' attribute has been set, otherwise false is returned.
  - setId
```
public int setId(java.lang.String id)
```
    Sets the value of the 'id' attribute of this QualitativeSpecies.
    Overrides:
    
    setId in class SBase
    
    Parameters:
    
    id - String value of the 'id' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setCompartment
```
public int setCompartment(java.lang.String compartment)
```
    Sets the value of the 'compartment' attribute of this QualitativeSpecies.
    Parameters:
    
    compartment - String value of the 'compartment' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setConstant
```
public int setConstant(boolean constant)
```
    Sets the value of the 'constant' attribute of this QualitativeSpecies.
    Parameters:
    
    constant - boolean value of the 'constant' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this QualitativeSpecies.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - String value of the 'name' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setInitialLevel
```
public int setInitialLevel(int initialLevel)
```
    Sets the value of the 'initialLevel' attribute of this QualitativeSpecies.
    Parameters:
    
    initialLevel - int value of the 'initialLevel' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setMaxLevel
```
public int setMaxLevel(int maxLevel)
```
    Sets the value of the 'maxLevel' attribute of this QualitativeSpecies.
    Parameters:
    
    maxLevel - int value of the 'maxLevel' attribute to be set
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetId
```
public int unsetId()
```
    Unsets the value of the 'id' attribute of this QualitativeSpecies.
    Overrides:
    
    unsetId in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetCompartment
```
public int unsetCompartment()
```
    Unsets the value of the 'compartment' attribute of this QualitativeSpecies.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetConstant
```
public int unsetConstant()
```
    Unsets the value of the 'constant' attribute of this QualitativeSpecies.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this QualitativeSpecies.
    Overrides:
    
    unsetName in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetInitialLevel
```
public int unsetInitialLevel()
```
    Unsets the value of the 'initialLevel' attribute of this QualitativeSpecies.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetMaxLevel
```
public int unsetMaxLevel()
```
    Unsets the value of the 'maxLevel' attribute of this QualitativeSpecies.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - renameSIdRefs
```
public void renameSIdRefs(java.lang.String oldid,
                          java.lang.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 SIdRefin 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.
    
    Overrides:
    
    renameSIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML name of this object.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code of this object instance.
    
    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.
    
    Overrides:
    
    getTypeCode in class SBase
    
    Returns:
    
    the SBML type code for this object: SBML_QUAL_QUALITATIVE_SPECIES
    
    See Also:
    
    QualitativeSpecies.getElementName(), SBase.getPackageName()
    
    "Warning:"
    
    The specific integer values of the possible type codes may be reused by different Level 3 package plug-ins. Thus, to identifiy the correct code, it is necessary to invoke both getTypeCode() and getPackageName().
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required attributes for this QualitativeSpecies object have been set.
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    a boolean value indicating whether all the required attributes for this object have been defined.
    
    "Note:"
    The required attributes for a QualitativeSpecies object are:
    
    'id'
    'compartment'
    'constant'

Class QualitativeSpecies

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

QualitativeSpecies

QualitativeSpecies

QualitativeSpecies

QualitativeSpecies

QualitativeSpecies

QualitativeSpecies

Method Detail

delete

cloneObject

getId

getCompartment

getConstant

getName

getInitialLevel

getMaxLevel

isSetId

isSetCompartment

isSetConstant

isSetName

isSetInitialLevel

isSetMaxLevel

setId

setCompartment

setConstant

setName

setInitialLevel

setMaxLevel

unsetId

unsetCompartment

unsetConstant

unsetName

unsetInitialLevel

unsetMaxLevel

renameSIdRefs

getElementName

getTypeCode

hasRequiredAttributes