CompartmentType (LibSBML Java API)

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

```
public class CompartmentType
extends SBase
```
A compartment type in SBML Level 2.
SBML Level 2 Versions 2&ndash4 provide the compartment type as a grouping construct that can be used to establish a relationship between multiple Compartment objects. A CompartmentType object only has an identity, and this identity can only be used to indicate that particular Compartment objects in the model belong to this type. This may be useful for conveying a modeling intention, such as when a model contains many similar compartments, either by their biological function or the reactions they carry. Without a compartment type construct, it would be impossible within SBML itself to indicate that all of the compartments share an underlying conceptual relationship because each SBML compartment must be given a unique and separate identity. Compartment types have no mathematical meaning in SBML&mdashthey have no effect on a model's mathematical interpretation. Simulators and other numerical analysis software may ignore CompartmentType definitions and references to them in a model.
There is no mechanism in SBML Level 2 for representing hierarchies of compartment types. One CompartmentType instance cannot be the subtype of another CompartmentType instance SBML provides no means of defining such relationships.
As with other major structures in SBML, CompartmentType has a mandatory attribute, 'id', used to give the compartment type an identifier. The identifier must be a text string conforming to the identifer syntax permitted in SBML. CompartmentType also has an optional 'name' attribute, of type string. The 'id' and 'name' must be used according to the guidelines described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification).
CompartmentType was introduced in SBML Level 2 Version 2. It is not available in SBML Level 1 nor in Level 3.

See Also:

Compartment, ListOfCompartmentTypes, SpeciesType, ListOfSpeciesTypes

Constructor Summary

Constructors
Constructor and Description
`CompartmentType(CompartmentType orig)` Copy constructor creates a copy of this `CompartmentType` object.
`CompartmentType(long level, long version)` Creates a new `CompartmentType` object using the given SBML `level` and `version` values.
`CompartmentType(SBMLNamespaces sbmlns)` Creates a new `CompartmentType` object using the given `SBMLNamespaces` object `sbmlns`.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`CompartmentType`	`cloneObject()` Creates and returns a deep copy of this `CompartmentType` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getElementName()` Returns the XML element name of this object
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `CompartmentType` object.
`java.lang.String`	`getName()` Returns the value of the 'name' attribute of this `CompartmentType` object.
`int`	`getTypeCode()` Returns the libSBML type code for this SBML object.
`boolean`	`hasRequiredAttributes()` Predicate returning `true` if all the required attributes for this `CompartmentType` object have been set.
`boolean`	`isSetId()` Predicate returning `true` if this `CompartmentType` object's 'id' attribute is set.
`boolean`	`isSetName()` Predicate returning `true` if this `CompartmentType` object's 'name' attribute is set.
`int`	`setId(java.lang.String sid)` Sets the value of the 'id' attribute of this `CompartmentType` object.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `CompartmentType` object.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `CompartmentType` object.

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, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData

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

- Constructor Detail
  - CompartmentType
```
public CompartmentType(long level,
                       long version)
                throws SBMLConstructorException
```
    Creates a new CompartmentType object using the given SBML level and version values.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this CompartmentType
    
    version - a long integer, the SBML Version to assign to this CompartmentType
    
    Throws:
    
    SBMLConstructorException - Thrown if the given level and version combination are invalid or if this object is incompatible with the given level and version.
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.
  - CompartmentType
```
public CompartmentType(SBMLNamespaces sbmlns)
                throws SBMLConstructorException
```
    Creates a new CompartmentType object using the given SBMLNamespaces object sbmlns.
    
    The SBMLNamespaces object encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and (in Level 3) packages used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an SBMLNamespaces object somewhere in a program once, then hand that object as needed to object constructors that accept SBMLNamespaces as arguments.
    It is worth emphasizing that although this constructor does not take an identifier argument, in SBML Level 2 and beyond, the 'id' (identifier) attribute of a CompartmentType object is required to have a value. Thus, callers are cautioned to assign a value after calling this constructor. Setting the identifier can be accomplished using the method setId(String).
    
    Parameters:
    
    sbmlns - an SBMLNamespaces object.
    
    Throws:
    
    SBMLConstructorException - Thrown if the given sbmlns is inconsistent or incompatible with this object.
    
    "Note:"
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute.
  - CompartmentType
```
public CompartmentType(CompartmentType orig)
                throws SBMLConstructorException
```
    Copy constructor creates a copy of this CompartmentType object.
    
    Parameters:
    
    orig - the object 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 CompartmentType.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 CompartmentType.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public CompartmentType cloneObject()
```
    Creates and returns a deep copy of this CompartmentType object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    the (deep) copy of this CompartmentType object.
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this CompartmentType object.
    
    Overrides:
    
    getId in class SBase
    
    Returns:
    
    the identifier of this CompartmentType object.
    
    See Also:
    
    CompartmentType.getName(), CompartmentType.setId(String), SBase.unsetId(), CompartmentType.isSetId()
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this CompartmentType object.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the name of this CompartmentType object.
    
    See Also:
    
    CompartmentType.getId(), CompartmentType.isSetName(), CompartmentType.setName(String), CompartmentType.unsetName()
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true if this CompartmentType object's 'id' attribute is set.
    
    Overrides:
    
    isSetId in class SBase
    
    Returns:
    
    true if the 'id' attribute of this CompartmentType object is set, false otherwise.
    
    See Also:
    
    CompartmentType.getId(), SBase.unsetId(), CompartmentType.setId(String)
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true if this CompartmentType object's 'name' attribute is set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if the 'name' attribute of this CompartmentType object is set, false otherwise.
    
    See Also:
    
    CompartmentType.getName(), CompartmentType.setName(String), CompartmentType.unsetName()
  - setId
```
public int setId(java.lang.String sid)
```
    Sets the value of the 'id' attribute of this CompartmentType object.
    The string sid is copied.
    
    SBML has strict requirements for the syntax of identifiers, that is, the values of the 'id' attribute present on most types of SBML objects. The following is a summary of the definition of the SBML identifier type SId, which defines the permitted syntax of identifiers. We express the syntax using an extended form of BNF notation:
```
 letter .= 'a'..'z','A'..'Z'
 digit  .= '0'..'9'
 idChar .= letter | digit | '_'
 SId    .= ( letter | '_' ) idChar*
```
    The characters ( and ) are used for grouping, the character * 'zero or more times', and the character | indicates logical 'or'. The equality of SBML identifiers is determined by an exact character sequence match i.e., comparisons must be performed in a case-sensitive manner. In addition, there are a few conditions for the uniqueness of identifiers in an SBML model. Please consult the SBML specifications for the exact details of the uniqueness requirements.
    Overrides:
    
    setId in class SBase
    
    Parameters:
    
    sid - the string to use as the identifier of this CompartmentType
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    
    CompartmentType.getId(), SBase.unsetId(), CompartmentType.isSetId()
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this CompartmentType object.
    The string in name is copied.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - the new name for the CompartmentType
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
    See Also:
    
    CompartmentType.getName(), CompartmentType.isSetName(), CompartmentType.unsetName()
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this CompartmentType object.
    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
    See Also:
    
    CompartmentType.getName(), CompartmentType.setName(String), CompartmentType.isSetName()
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code for this SBML object.
    
    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_COMPARTMENT_TYPE (default).
    
    See Also:
    
    CompartmentType.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().
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this object
    For CompartmentType, the element name is always 'compartmentType'.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element.
    
    See Also:
    
    CompartmentType.getTypeCode(), SBase.getPackageName()
  - hasRequiredAttributes
```
public boolean hasRequiredAttributes()
```
    Predicate returning true if all the required attributes for this CompartmentType object have been set.
    The required attributes for a CompartmentType object are:
    - 'id'
    Overrides:
    
    hasRequiredAttributes in class SBase
    
    Returns:
    
    true if the required attributes have been set, false otherwise.

Class CompartmentType

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

CompartmentType

CompartmentType

CompartmentType

Method Detail

delete

cloneObject

getId

getName

isSetId

isSetName

setId

setName

unsetName

getTypeCode

getElementName

hasRequiredAttributes