Submodel (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.CompBase
  - - org.sbml.libsbml.Submodel

```
public class Submodel
extends CompBase
```
comp A model instance inside another model.
The Submodel class was introduced by the SBML Level 3 'Hierarchical Model Composition' package (&ldquocomp&rdquo) as the principle way by which models are structured hierarchically. Submodels are instantiations of models contained within other models. They reference another Model that is to be instantiated within its parent Model, and additionally define how that Model is to be modified before instantiation.
The Submodel object class has a required attribute 'modelRef', which must reference another Model or ExternalModelDefinition object present in the SBML Document. This referenced Model is the model to be instantiated.
It also has a required attribute, 'id', to give the submodel a unique identifier by which other parts of an SBML model definition can refer to it, and an optional 'name' attribute of type string. Identifiers and names must be used according to the guidelines described in the SBML specification.
The Submodel class also provides constructs that define how the referenced Model object is to be modified before it is instantiated in the enclosing model. If numerical values in the referenced model must be changed in order to fit them into their new context as part of the submodel, the changes can be handled through conversion factors. If one or more structural features in the referenced model are undesirable and should be removed, the changes can be handled through deletions. (For example, an initial assignment or reaction may not be relevant in its new context and should be removed.)
In some cases, the referenced Model may have been written with different units than the containing model. For most model elements, this is not a problem: it is already possible to have Species and Parameter objects with different units in a single model, for example, so in this case the resulting hierarchical model would be treated in exactly the same way as any other model with Species and Parameters with different units.
However, two units in SBML models are fixed and must not vary between SBML elements: time and extent. The units of time are set once per model, and affect the core elements of RateRule, KineticLaw, Delay, and the csymbols 'time' and 'delay'. Even if the model does not explicitly state what the units of time actually are, they are defined to be consistent across the model, and therefore might differ from the units of time across a parent model. To correct this imbalance, the optional attribute 'timeConversionFactor' may be used, which, if defined, must reference a constant parameter in the parent model. The value of the time conversion factor should be defined such that a single unit of time in the Submodel multiplied by the time conversion factor should equal a single unit of time in the parent model.
Extent is the unit in SBML that defines how the KineticLaw of a Reaction affects species quantities: kinetic laws are defined to be in units of extent/time. No other SBML core construct is defined in terms of extent. If the effective units of extent in a submodel differ from the effective units of extent in the parent model (regardless of whether either defined what those units actually are), the optional attribute 'extentConversionFactor' may be used, which, if defined, must reference a constant parameter in the parent model. The value of the extent conversion factor should be defined such that a single unit of extent in the Submodel multiplied by the extent conversion factor should equal a single unit of extent in the parent model.
If features of the referenced model must be removed, a Deletion should be added to the Submodel object. A Submodel may contain a child ListOfDeletions, which in turn may contain one or more Deletion items. Each Deletion references a single element of the referenced Model that must be removed before instantiating that Model as a submodel of the parent Model.

Constructor Summary

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`addDeletion(Deletion deletion)` Adds a copy of the given `Deletion` object to the list of deletions.
`void`	`clearInstantiation()` Delete the instantiated `Model`, if it exists.
`SBase`	`cloneObject()` Creates and returns a deep copy of this `Submodel` object.
`void`	`connectToChild()`
`int`	`convertTimeAndExtent()` Convert all references to time and extent in the instantiated `Model`, according to the timeConversionFactor and extentConversionFactor attributes.
`Deletion`	`createDeletion()` Creates a `Deletion` object, adds it to the end of the deletion objects list and returns a pointer to the newly created object.
`void`	`delete()` Explicitly deletes the underlying native object.
`Deletion`	`getDeletion(long n)` Returns the deletion with the given index.
`Deletion`	`getDeletion(java.lang.String id)` Returns the deletion with the given `id`.
`SBase`	`getElementByMetaId(java.lang.String metaid)` Returns the first child element it can find with the given `metaid`, or itself if it has the given `metaid`, or `null` if no such object is found.
`SBase`	`getElementBySId(java.lang.String id)` Returns the first child element found that has the given `id` in the model-wide SId namespace, or `null` if no such object is found.
`java.lang.String`	`getElementName()` Returns the XML element name of this SBML object.
`java.lang.String`	`getExtentConversionFactor()` Returns the value of the 'extentConversionFactor' attribute of this `Submodel`.
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `Submodel`.
`Model`	`getInstantiation()` Get the instantiated `Model` this `Submodel` contains rules to create.
`SBaseList`	`getListOfAllInstantiatedElements()`
`ListOfDeletions`	`getListOfDeletions()` Returns the `ListOf` object that holds all deletions.
`java.lang.String`	`getModelRef()` Returns the value of the 'modelRef' attribute of this `Submodel`.
`java.lang.String`	`getName()` Returns the value of the 'name' attribute of this `Submodel`.
`long`	`getNumDeletions()` Returns the number of deletions for this `Submodel`.
`java.lang.String`	`getSubstanceConversionFactor()` Returns an empty string, since 'substanceConversionFactor' is not a part of the comp spec.
`java.lang.String`	`getTimeConversionFactor()` Returns the value of the 'timeConversionFactor' attribute of this `Submodel`.
`int`	`getTypeCode()` Returns the libSBML type code of this object instance.
`boolean`	`hasRequiredAttributes()` Returns true if the 'submodel' attribute is set, and if getNumReferents() is exactly 1.
`int`	`instantiate()` Find and create a local copy of the `Model` object referenced by this `Submodel`.
`boolean`	`isSetExtentConversionFactor()` Predicate returning `true` or `false` depending on whether this `Submodel`'s 'extentConversionFactor' attribute has been set.
`boolean`	`isSetId()` Predicate returning `true` or `false` depending on whether this `Submodel`'s 'id' attribute has been set.
`boolean`	`isSetModelRef()` Predicate returning `true` or `false` depending on whether this `Submodel`'s 'modelRef' attribute has been set.
`boolean`	`isSetName()` Predicate returning `true` or `false` depending on whether this `Submodel`'s 'name' attribute has been set.
`boolean`	`isSetSubstanceConversionFactor()` Returns `false`, since 'substanceConversionFactor' is not a part of the comp spec.
`boolean`	`isSetTimeConversionFactor()` Predicate returning `true` or `false` depending on whether this `Submodel`'s 'timeConversionFactor' attribute has been set.
`int`	`performDeletions()` Delete elements in the instantiated submodel, based on any Deletions from this `Submodel`'s listOfDeletions.
`Deletion`	`removeDeletion(long index)` Removes the deletion with the given index from the `Submodel`.
`Deletion`	`removeDeletion(java.lang.String sid)` Removes the deletion with the given identifier from the `Submodel`.
`void`	`renameSIdRefs(java.lang.String oldid, java.lang.String newid)` Renames the conversion factor attributes on this element if `oldid` matches.
`int`	`replaceElement(SBase toReplace, SBase replacement)` Delete the element in question from the stored instantiated `Model`, and replace all references to it with references to the replacement object.
`int`	`setExtentConversionFactor(java.lang.String id)` Sets the value of the 'extentConversionFactor' attribute of this `Submodel`.
`int`	`setId(java.lang.String id)` Sets the value of the 'id' attribute of this `Submodel`.
`int`	`setModelRef(java.lang.String modelRef)` Sets the value of the 'modelRef' attribute of this `Submodel`.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `Submodel`.
`int`	`setSubstanceConversionFactor(java.lang.String id)` Automatically fails, since 'substanceConversionFactor' is not a part of the comp spec.
`int`	`setTimeConversionFactor(java.lang.String id)` Sets the value of the 'timeConversionFactor' attribute of this `Submodel`.
`int`	`unsetExtentConversionFactor()` Unsets the value of the 'extentConversionFactor' attribute of this `Submodel`.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `Submodel`.
`int`	`unsetModelRef()` Unsets the value of the 'modelRef' attribute of this `Submodel`.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `Submodel`.
`int`	`unsetSubstanceConversionFactor()` Automatically fails, since 'substanceConversionFactor' is not a part of the comp spec.
`int`	`unsetTimeConversionFactor()` Unsets the value of the 'timeConversionFactor' attribute of this `Submodel`.

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, 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, 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
  - Submodel
```
public Submodel(long level,
                long version,
                long pkgVersion)
         throws SBMLConstructorException
```
    Creates a new Submodel 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
  - Submodel
```
public Submodel(long level,
                long version)
         throws SBMLConstructorException
```
    Creates a new Submodel 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
  - Submodel
```
public Submodel(long level)
         throws SBMLConstructorException
```
    Creates a new Submodel 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
  - Submodel
```
public Submodel()
         throws SBMLConstructorException
```
    Creates a new Submodel 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
  - Submodel
```
public Submodel(CompPkgNamespaces compns)
         throws SBMLConstructorException
```
    Creates a new Submodel with the given CompPkgNamespaces object.
    
    Parameters:
    
    compns - the namespace to use
    
    Throws:
    
    SBMLConstructorException
  - Submodel
```
public Submodel(Submodel source)
         throws SBMLConstructorException
```
    Copy constructor.
    
    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 Submodel.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 Submodel.delete() themselves.
    
    Overrides:
    
    delete in class CompBase
  - cloneObject
```
public SBase cloneObject()
```
    Creates and returns a deep copy of this Submodel object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this Submodel object
  - getElementBySId
```
public SBase getElementBySId(java.lang.String id)
```
    Returns the first child element found that has the given id in the model-wide SId namespace, or null if no such object is found.
    
    Overrides:
    
    getElementBySId in class SBase
    
    Parameters:
    
    id - string representing the id of objects to find
    
    Returns:
    
    a pointer to the SBase element with the given id.
  - getElementByMetaId
```
public SBase getElementByMetaId(java.lang.String metaid)
```
    Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or null if no such object is found.
    
    Overrides:
    
    getElementByMetaId in class SBase
    
    Parameters:
    
    metaid - string representing the metaid of objects to find
    
    Returns:
    
    a pointer to the SBase element with the given metaid.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this Submodel.
    
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the value of the 'id' attribute of this Submodel.
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true or false depending on whether this Submodel's 'id' attribute has been set.
    
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if this Submodel's 'id' 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 Submodel. Fails if the id is not a valid syntax for an SId.
    Overrides:
    
    setId in class SBase
    
    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 Submodel.
    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
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this Submodel.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the value of the 'name' attribute of this Submodel.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true or false depending on whether this Submodel's 'name' attribute has been set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if this Submodel's 'name' attribute has been set, otherwise false is returned.
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this Submodel. Fails if the name is empty.
    Overrides:
    
    setName in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this Submodel.
    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
  - getModelRef
```
public java.lang.String getModelRef()
```
    Returns the value of the 'modelRef' attribute of this Submodel.
    
    Returns:
    
    the value of the 'modelRef' attribute of this Submodel.
  - isSetModelRef
```
public boolean isSetModelRef()
```
    Predicate returning true or false depending on whether this Submodel's 'modelRef' attribute has been set.
    
    Returns:
    
    true if this Submodel's 'modelRef' attribute has been set, otherwise false is returned.
  - setModelRef
```
public int setModelRef(java.lang.String modelRef)
```
    Sets the value of the 'modelRef' attribute of this Submodel. Fails if the modelRef is not a valid syntax for an SIdRef.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetModelRef
```
public int unsetModelRef()
```
    Unsets the value of the 'modelRef' attribute of this Submodel.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getSubstanceConversionFactor
```
public java.lang.String getSubstanceConversionFactor()
```
    Returns an empty string, since 'substanceConversionFactor' is not a part of the comp spec.
    
    Returns:
    
    an empty string
  - isSetSubstanceConversionFactor
```
public boolean isSetSubstanceConversionFactor()
```
    Returns false, since 'substanceConversionFactor' is not a part of the comp spec.
    
    Returns:
    
    false.
  - setSubstanceConversionFactor
```
public int setSubstanceConversionFactor(java.lang.String id)
```
    Automatically fails, since 'substanceConversionFactor' is not a part of the comp spec.
    Returns:
    integer value indicating success/failure of the operation. The possible return value is:
    
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetSubstanceConversionFactor
```
public int unsetSubstanceConversionFactor()
```
    Automatically fails, since 'substanceConversionFactor' is not a part of the comp spec.
    Returns:
    integer value indicating success/failure of the operation. The possible return value is:
    
    LIBSBML_OPERATION_FAILED
  - getTimeConversionFactor
```
public java.lang.String getTimeConversionFactor()
```
    Returns the value of the 'timeConversionFactor' attribute of this Submodel.
    
    Returns:
    
    the value of the 'timeConversionFactor' attribute of this Submodel.
  - isSetTimeConversionFactor
```
public boolean isSetTimeConversionFactor()
```
    Predicate returning true or false depending on whether this Submodel's 'timeConversionFactor' attribute has been set.
    
    Returns:
    
    true if this Submodel's 'timeConversionFactor' attribute has been set, otherwise false is returned.
  - setTimeConversionFactor
```
public int setTimeConversionFactor(java.lang.String id)
```
    Sets the value of the 'timeConversionFactor' attribute of this Submodel. Fails if the id is not a valid syntax for an SIdRef.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetTimeConversionFactor
```
public int unsetTimeConversionFactor()
```
    Unsets the value of the 'timeConversionFactor' attribute of this Submodel.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getExtentConversionFactor
```
public java.lang.String getExtentConversionFactor()
```
    Returns the value of the 'extentConversionFactor' attribute of this Submodel.
    
    Returns:
    
    the value of the 'extentConversionFactor' attribute of this Submodel.
  - isSetExtentConversionFactor
```
public boolean isSetExtentConversionFactor()
```
    Predicate returning true or false depending on whether this Submodel's 'extentConversionFactor' attribute has been set.
    
    Returns:
    
    true if this Submodel's 'extentConversionFactor' attribute has been set, otherwise false is returned.
  - setExtentConversionFactor
```
public int setExtentConversionFactor(java.lang.String id)
```
    Sets the value of the 'extentConversionFactor' attribute of this Submodel. Fails if the id is not a valid syntax for an SIdRef.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - unsetExtentConversionFactor
```
public int unsetExtentConversionFactor()
```
    Unsets the value of the 'extentConversionFactor' attribute of this Submodel.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getListOfDeletions
```
public ListOfDeletions getListOfDeletions()
```
    Returns the ListOf object that holds all deletions.
    
    Returns:
    
    the ListOf object that holds all deletions.
  - getDeletion
```
public Deletion getDeletion(long n)
```
    Returns the deletion with the given index. If the index is invalid, null is returned.
    
    Parameters:
    
    n - the index number of the Deletion to get.
    
    Returns:
    
    the nth Deletion in the ListOfDeletions.
  - getDeletion
```
public Deletion getDeletion(java.lang.String id)
```
    Returns the deletion with the given id. If the id is invalid, null is returned.
    
    Parameters:
    
    id - the id of the Deletion to get.
    
    Returns:
    
    the Deletion in the ListOfDeletions with the given id.
  - addDeletion
```
public int addDeletion(Deletion deletion)
```
    Adds a copy of the given Deletion object to the list of deletions.
    Parameters:
    
    deletion - the Deletion object to be added to the list of deletions. Fails if the added deletion is null, does not match the level/version/package of the parent object, or cannot be added to the list of deletions.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT
    LIBSBML_LEVEL_MISMATCH
    LIBSBML_VERSION_MISMATCH
    LIBSBML_PKG_VERSION_MISMATCH
  - getNumDeletions
```
public long getNumDeletions()
```
    Returns the number of deletions for this Submodel.
    
    Returns:
    
    the number of deletions for this Submodel.
  - createDeletion
```
public Deletion createDeletion()
```
    Creates a Deletion object, adds it to the end of the deletion objects list and returns a pointer to the newly created object.
    
    Returns:
    
    a newly created Deletion object
  - removeDeletion
```
public Deletion removeDeletion(long index)
```
    Removes the deletion with the given index from the Submodel. A pointer to the deletion that was removed is returned. If no deletion has been removed, null is returned.
    
    Parameters:
    
    index - the index of the Deletion object to remove
    
    Returns:
    
    the Deletion object removed. As mentioned above, the caller owns the returned object. null is returned if the given index is out of range.
  - removeDeletion
```
public Deletion removeDeletion(java.lang.String sid)
```
    Removes the deletion with the given identifier from the Submodel. A pointer to the deletion that was removed is returned. If no deletion has been removed, null is returned.
    
    Parameters:
    
    sid - string representing the identifier of the Deletion object to remove
    
    Returns:
    
    the Deletion object removed. As mentioned above, the caller owns the returned object. null is returned if the given sid is not found.
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Returns true if the 'submodel' attribute is set, and if getNumReferents() is exactly 1.
    
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    boolean: 'true' if the attributes are correctly set 'false' if not.
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this SBML object.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, as a text string.
  - renameSIdRefs
```
public void renameSIdRefs(java.lang.String oldid,
                          java.lang.String newid)
```
    Renames the conversion factor attributes on this element if oldid matches.
    
    Overrides:
    
    renameSIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - 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_COMP_SUBMODEL
    
    See Also:
    
    Submodel.getElementName(), CompBase.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().
  - connectToChild
```
public void connectToChild()
```
    Overrides:
    
    connectToChild in class SBase
  - instantiate
```
public int instantiate()
```
    Find and create a local copy of the Model object referenced by this Submodel. Is recursive, in that if the instantiated Model contains any Submodel objects, those Submodels will themselves be instantiated. If an instantiated model previously existed, it is deleted and a new one is created. For this reason, call this function only once, or call Submodel.getInstantiation().
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT (which indicates this Submodel itself is invalid, and no Model can be instantiated from it)
    LIBSBML_OPERATION_FAILED
  - performDeletions
```
public int performDeletions()
```
    Delete elements in the instantiated submodel, based on any Deletions from this Submodel's listOfDeletions.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT (which indicates this Submodel itself is invalid, and no Model can be instantiated from it)
    LIBSBML_OPERATION_FAILED
  - replaceElement
```
public int replaceElement(SBase toReplace,
                          SBase replacement)
```
    Delete the element in question from the stored instantiated Model, and replace all references to it with references to the replacement object. LIBSBML_INVALID_OBJECT means that this Submodel itself or one of the passed-in objects are invalid. LIBSBML_OPERATION_FAILED means that the routine failed for some othe reason.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_OBJECT
    LIBSBML_OPERATION_FAILED
  - getInstantiation
```
public Model getInstantiation()
```
    Get the instantiated Model this Submodel contains rules to create. Calls instantiate() automatically if this operation has not yet been performed, and/or if the operation failed the last time it was called. Any modifictions that have been performed with performDeletions(), replaceElement(), or convertTimeAndExtent() function calls will be included.
    
    Returns:
    
    the instantiated Model object: a clone of the original, modified according to the performDeletions() and replaceElement() functions that have been called. Returns null if any error is encountered.
  - clearInstantiation
```
public void clearInstantiation()
```
    Delete the instantiated Model, if it exists.
  - convertTimeAndExtent
```
public int convertTimeAndExtent()
```
    Convert all references to time and extent in the instantiated Model, according to the timeConversionFactor and extentConversionFactor attributes.
  - getListOfAllInstantiatedElements
```
public SBaseList getListOfAllInstantiatedElements()
```

Class Submodel

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

Submodel

Submodel

Submodel

Submodel

Submodel

Submodel

Method Detail

delete

cloneObject

getElementBySId

getElementByMetaId

getId

isSetId

setId

unsetId

getName

isSetName

setName

unsetName

getModelRef

isSetModelRef

setModelRef

unsetModelRef

getSubstanceConversionFactor

isSetSubstanceConversionFactor

setSubstanceConversionFactor

unsetSubstanceConversionFactor

getTimeConversionFactor

isSetTimeConversionFactor

setTimeConversionFactor

unsetTimeConversionFactor

getExtentConversionFactor

isSetExtentConversionFactor

setExtentConversionFactor

unsetExtentConversionFactor

getListOfDeletions

getDeletion

getDeletion

addDeletion

getNumDeletions

createDeletion

removeDeletion

removeDeletion

hasRequiredAttributes

getElementName

renameSIdRefs

getTypeCode

connectToChild

instantiate

performDeletions

replaceElement

getInstantiation

clearInstantiation

convertTimeAndExtent

getListOfAllInstantiatedElements