ModelDefinition (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.Model
  - - org.sbml.libsbml.ModelDefinition

```
public class ModelDefinition
extends Model
```
comp A model used in model composition.
The 'Hierarchical Model Composition' package (&ldquocomp&rdquo) allows multiple Model objects to be defined in a single SBMLDocument. While these new Model objects are not new SBML classes, they are given a new name, <modelDefinition>, and reside in ListOfModelDefinition objects. In libSBML, this class inherits from the Model class, changing only the expected parent of the object, and the XML name.
An additional restriction is placed on the 'id' attribute of ModelDefinition objects: not only must it be unique across all such attributes of type SId within the ModelDefintion, it must also be unique across all Model, ModelDefinition, and ExternalModelDefinition objects in the same SBMLDocument.

Constructor Summary

Constructors
Constructor and Description
`ModelDefinition()` Creates a new `ModelDefinition` with the given level, version, and package version.
`ModelDefinition(CompPkgNamespaces compns)` Creates a new `ModelDefinition` with the given `CompPkgNamespaces` object.
`ModelDefinition(long level)` Creates a new `ModelDefinition` with the given level, version, and package version.
`ModelDefinition(long level, long version)` Creates a new `ModelDefinition` with the given level, version, and package version.
`ModelDefinition(long level, long version, long pkgVersion)` Creates a new `ModelDefinition` with the given level, version, and package version.
`ModelDefinition(Model source)` Copy constructor from base `Model` object.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`ModelDefinition`	`cloneObject()` Creates and returns a deep copy of this `ModelDefinition` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getElementName()` Returns the XML element name of this object.
`int`	`getTypeCode()` Returns the libSBML type code of this object instance.
`int`	`removeFromParentAndDelete()` Finds this `Model`'s parent `ListOfModelDefinitions` and removes itself from it and deletes itself.

Methods inherited from class org.sbml.libsbml.Model
addCompartment, addCompartmentType, addConstraint, addEvent, addFunctionDefinition, addInitialAssignment, addParameter, addReaction, addRule, addSpecies, addSpeciesType, addUnitDefinition, appendAnnotation, appendAnnotation, appendFrom, connectToChild, createAlgebraicRule, createAssignmentRule, createCompartment, createCompartmentType, createConstraint, createDelay, createEvent, createEventAssignment, createFunctionDefinition, createInitialAssignment, createKineticLaw, createKineticLawLocalParameter, createKineticLawParameter, createModifier, createParameter, createProduct, createRateRule, createReactant, createReaction, createSpecies, createSpeciesType, createTrigger, createUnit, createUnitDefinition, getAreaUnits, getAssignmentRule, getAssignmentRuleByVariable, getCompartment, getCompartment, getCompartmentType, getCompartmentType, getConstraint, getConversionFactor, getElementByMetaId, getElementBySId, getEvent, getEvent, getExtentUnits, getFunctionDefinition, getFunctionDefinition, getId, getInitialAssignment, getInitialAssignment, getInitialAssignmentBySymbol, getLengthUnits, getListOfCompartments, getListOfCompartmentTypes, getListOfConstraints, getListOfEvents, getListOfFunctionDefinitions, getListOfInitialAssignments, getListOfParameters, getListOfReactions, getListOfRules, getListOfSpecies, getListOfSpeciesTypes, getListOfUnitDefinitions, getModifierSpeciesReference, getName, getNumCompartments, getNumCompartmentTypes, getNumConstraints, getNumEvents, getNumFunctionDefinitions, getNumInitialAssignments, getNumParameters, getNumReactions, getNumRules, getNumSpecies, getNumSpeciesTypes, getNumSpeciesWithBoundaryCondition, getNumUnitDefinitions, getParameter, getParameter, getRateRule, getRateRuleByVariable, getReaction, getReaction, getRule, getRule, getRuleByVariable, getSpecies, getSpecies, getSpeciesReference, getSpeciesType, getSpeciesType, getSubstanceUnits, getTimeUnits, getUnitDefinition, getUnitDefinition, getVolumeUnits, hasRequiredElements, isPopulatedListFormulaUnitsData, isSetAreaUnits, isSetConversionFactor, isSetExtentUnits, isSetId, isSetLengthUnits, isSetName, isSetSubstanceUnits, isSetTimeUnits, isSetVolumeUnits, populateListFormulaUnitsData, removeCompartment, removeCompartment, removeCompartmentType, removeCompartmentType, removeConstraint, removeEvent, removeEvent, removeFunctionDefinition, removeFunctionDefinition, removeInitialAssignment, removeInitialAssignment, removeParameter, removeParameter, removeReaction, removeReaction, removeRule, removeRule, removeRuleByVariable, removeSpecies, removeSpecies, removeSpeciesType, removeSpeciesType, removeUnitDefinition, removeUnitDefinition, renameIDs, renameSIdRefs, renameUnitSIdRefs, setAnnotation, setAnnotation, setAreaUnits, setConversionFactor, setExtentUnits, setId, setLengthUnits, setName, setSubstanceUnits, setTimeUnits, setVolumeUnits, unsetAreaUnits, unsetConversionFactor, unsetExtentUnits, unsetId, unsetLengthUnits, unsetName, unsetSubstanceUnits, unsetTimeUnits, unsetVolumeUnits

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, 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, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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
  - ModelDefinition
```
public ModelDefinition(long level,
                       long version,
                       long pkgVersion)
                throws SBMLConstructorException
```
    Creates a new ModelDefinition with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ModelDefinition
```
public ModelDefinition(long level,
                       long version)
                throws SBMLConstructorException
```
    Creates a new ModelDefinition with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ModelDefinition
```
public ModelDefinition(long level)
                throws SBMLConstructorException
```
    Creates a new ModelDefinition with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ModelDefinition
```
public ModelDefinition()
                throws SBMLConstructorException
```
    Creates a new ModelDefinition with the given level, version, and package version.
    
    Parameters:
    
    level - the SBML Level
    
    version - the Version within the SBML Level
    
    pkgVersion - the version of the package
    
    Throws:
    
    SBMLConstructorException
  - ModelDefinition
```
public ModelDefinition(CompPkgNamespaces compns)
                throws SBMLConstructorException
```
    Creates a new ModelDefinition with the given CompPkgNamespaces object.
    
    Parameters:
    
    compns - the namespace to use
    
    Throws:
    
    SBMLConstructorException
  - ModelDefinition
```
public ModelDefinition(Model source)
                throws SBMLConstructorException
```
    Copy constructor from base Model object.
    
    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 ModelDefinition.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 ModelDefinition.delete() themselves.
    
    Overrides:
    
    delete in class Model
  - cloneObject
```
public ModelDefinition cloneObject()
```
    Creates and returns a deep copy of this ModelDefinition object.
    
    Overrides:
    
    cloneObject in class Model
    
    Returns:
    
    a (deep) copy of this ModelDefinition object
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object.
    The only difference between a Model and a ModelDefinition is the element name ('modelDefinition').
    
    Overrides:
    
    getElementName in class Model
    
    Returns:
    
    the name of this element, as a text string.
    
    See Also:
    
    ModelDefinition.getTypeCode()
  - 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 Model
    
    Returns:
    
    the SBML type code for this object: SBML_COMP_MODELDEFINITION
    
    See Also:
    
    ModelDefinition.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().
  - removeFromParentAndDelete
```
public int removeFromParentAndDelete()
```
    Finds this Model's parent ListOfModelDefinitions and removes itself from it and deletes itself.
    This method actually just calls the SBase function, since the Model class overrides it, but that's actually what we want to happen here.
    Overrides:
    
    removeFromParentAndDelete in class Model
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED

Class ModelDefinition

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.Model

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

ModelDefinition

ModelDefinition

ModelDefinition

ModelDefinition

ModelDefinition

ModelDefinition

Method Detail

delete

cloneObject

getElementName

getTypeCode

removeFromParentAndDelete