public class CompartmentType extends SBase
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. A CompartmentType
has no mathematical meaning in
SBML&mdashit has 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.
Compartment
,
ListOfCompartmentTypes
,
SpeciesType
,
ListOfSpeciesTypes
Constructor and Description |
---|
CompartmentType(CompartmentType orig)
Copy constructor creates a copy of this
CompartmentType object. |
CompartmentType(long level,
long version)
|
CompartmentType(SBMLNamespaces sbmlns)
|
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 . |
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 . |
int |
setName(java.lang.String name)
Sets the value of the 'name' attribute of this
CompartmentType . |
int |
unsetName()
Unsets the value of the 'name' attribute of this
CompartmentType object. |
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getObjectVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setIdAttribute, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public CompartmentType(long level, long version) throws SBMLConstructorException
level
- a long integer, the SBML Level to assign to this
CompartmentType
.
version
- a long integer, the SBML Version to assign to this
CompartmentType
.
SBMLConstructorException
- Thrown if the given level
and version
combination are invalid
or if this object is incompatible with the given level and version.
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.public CompartmentType(SBMLNamespaces sbmlns) throws SBMLConstructorException
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).
sbmlns
- an SBMLNamespaces
object.
SBMLConstructorException
- Thrown if the given sbmlns
is inconsistent or incompatible
with this object.
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.public CompartmentType(CompartmentType orig) throws SBMLConstructorException
CompartmentType
object.
orig
- the object 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 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.
public CompartmentType cloneObject()
CompartmentType
object.
cloneObject
 in class SBase
CompartmentType
object.public java.lang.String getId()
CompartmentType
.
getId
 in class SBase
CompartmentType
.
SBase.getIdAttribute()
,
SBase.setIdAttribute(String sid)
,
SBase.isSetIdAttribute()
,
SBase.unsetIdAttribute()
The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always SId
or a type derived
from that, such as UnitSId
, depending on the object in
question. All data types are defined as follows:
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. This applies to all uses of SId
,
SIdRef
, and derived types.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, check, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The exception to this rule is that for InitialAssignment
, EventAssignment
,
AssignmentRule
, and RateRule
objects, the getId() function and the isSetId()
functions (though not the setId() or unsetId() functions) would instead
reference the value of the 'variable' attribute (for the rules and event
assignments) or the 'symbol' attribute (for initial assignments).
The AlgebraicRule
fell into this category as well, though because it
contained neither a 'variable' nor a 'symbol' attribute, getId() would
always return an empty string, and isSetId() would always return false.
For this reason, four new functions are now provided
(getIdAttribute(), setIdAttribute(String),
isSetIdAttribute(), and unsetIdAttribute()) that will always
act on the actual 'id' attribute, regardless of the object's type. The
new functions should be used instead of the old ones unless the old behavior
is somehow necessary.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
public java.lang.String getName()
CompartmentType
object.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The 'name' attribute is
optional and is not intended to be used for cross-referencing purposes
within a model. Its purpose instead is to provide a human-readable
label for the component. The data type of 'name' is the type
string
defined in XML Schema. SBML imposes no
restrictions as to the content of 'name' attributes beyond those
restrictions defined by the string
type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
getName
 in class SBase
SBase.getIdAttribute()
,
CompartmentType.isSetName()
,
CompartmentType.setName(String sid)
,
CompartmentType.unsetName()
public boolean isSetId()
isSetId
 in class SBase
true
if the 'id' attribute of this SBML object is
set, false
otherwise.
SBase.getIdAttribute()
,
SBase.setIdAttribute(String sid)
,
SBase.unsetIdAttribute()
,
SBase.isSetIdAttribute()
The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always SId
or a type derived
from that, such as UnitSId
, depending on the object in
question. All data types are defined as follows:
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. This applies to all uses of SId
,
SIdRef
, and derived types.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, check, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The exception to this rule is that for InitialAssignment
, EventAssignment
,
AssignmentRule
, and RateRule
objects, the getId() function and the isSetId()
functions (though not the setId() or unsetId() functions) would instead
reference the value of the 'variable' attribute (for the rules and event
assignments) or the 'symbol' attribute (for initial assignments).
The AlgebraicRule
fell into this category as well, though because it
contained neither a 'variable' nor a 'symbol' attribute, getId() would
always return an empty string, and isSetId() would always return false.
For this reason, four new functions are now provided
(getIdAttribute(), setIdAttribute(String),
isSetIdAttribute(), and unsetIdAttribute()) that will always
act on the actual 'id' attribute, regardless of the object's type. The
new functions should be used instead of the old ones unless the old behavior
is somehow necessary.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
public boolean isSetName()
true
if this CompartmentType
object's 'name'
attribute is set.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The 'name' attribute is
optional and is not intended to be used for cross-referencing purposes
within a model. Its purpose instead is to provide a human-readable
label for the component. The data type of 'name' is the type
string
defined in XML Schema. SBML imposes no
restrictions as to the content of 'name' attributes beyond those
restrictions defined by the string
type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
isSetName
 in class SBase
true
if the 'name' attribute of this SBML object is
set, false
otherwise.
CompartmentType.getName()
,
CompartmentType.setName(String sid)
,
CompartmentType.unsetName()
public int setId(java.lang.String sid)
CompartmentType
.
The string sid
is copied.
The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always SId
or a type derived
from that, such as UnitSId
, depending on the object in
question. All data types are defined as follows:
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. This applies to all uses of SId
,
SIdRef
, and derived types.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, check, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The exception to this rule is that for InitialAssignment
, EventAssignment
,
AssignmentRule
, and RateRule
objects, the getId() function and the isSetId()
functions (though not the setId() or unsetId() functions) would instead
reference the value of the 'variable' attribute (for the rules and event
assignments) or the 'symbol' attribute (for initial assignments).
The AlgebraicRule
fell into this category as well, though because it
contained neither a 'variable' nor a 'symbol' attribute, getId() would
always return an empty string, and isSetId() would always return false.
For this reason, four new functions are now provided
(getIdAttribute(), setIdAttribute(String),
isSetIdAttribute(), and unsetIdAttribute()) that will always
act on the actual 'id' attribute, regardless of the object's type. The
new functions should be used instead of the old ones unless the old behavior
is somehow necessary.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have identifiers). If the object in question does not posess an 'id' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the identifier to be set, nor will it read or write 'id' attributes for those objects.
setId
 in class SBase
sid
- the string to use as the identifier of this object.
SBase.getIdAttribute()
,
SBase.setIdAttribute(String sid)
,
SBase.isSetIdAttribute()
,
SBase.unsetIdAttribute()
public int setName(java.lang.String name)
public int unsetName()
CompartmentType
object.
In SBML Level 3 Version 2, the 'id' and 'name' attributes were
moved to SBase
directly, instead of being defined individually for many
(but not all) objects. Libsbml has for a long time provided functions
defined on SBase
itself to get, set, and unset those attributes, which
would fail or otherwise return empty strings if executed on any object
for which those attributes were not defined. Now that all SBase
objects
define those attributes, those functions now succeed for any object with
the appropriate level and version.
The 'name' attribute is
optional and is not intended to be used for cross-referencing purposes
within a model. Its purpose instead is to provide a human-readable
label for the component. The data type of 'name' is the type
string
defined in XML Schema. SBML imposes no
restrictions as to the content of 'name' attributes beyond those
restrictions defined by the string
type in XML Schema.
The recommended practice for handling 'name' is as follows. If a software tool has the capability for displaying the content of 'name' attributes, it should display this content to the user as a component's label instead of the component's 'id'. If the user interface does not have this capability (e.g., because it cannot display or use special characters in symbol names), or if the 'name' attribute is missing on a given component, then the user interface should display the value of the 'id' attribute instead. (Script language interpreters are especially likely to display 'id' instead of 'name'.)
As a consequence of the above, authors of systems that automatically generate the values of 'id' attributes should be aware some systems may display the 'id''s to the user. Authors therefore may wish to take some care to have their software create 'id' values that are: (a) reasonably easy for humans to type and read and (b) likely to be meaningful, for example by making the 'id' attribute be an abbreviated form of the name attribute value.
An additional point worth mentioning is although there are restrictions on the uniqueness of 'id' values, there are no restrictions on the uniqueness of 'name' values in a model. This allows software applications leeway in assigning component identifiers.
Regardless of the level and version of the SBML, these functions allow client applications to use more generalized code in some situations (for instance, when manipulating objects that are all known to have names). If the object in question does not posess a 'name' attribute according to the SBML specification for the Level and Version in use, libSBML will not allow the name to be set, nor will it read or write 'name' attributes for those objects.
unsetName
 in class SBase
CompartmentType.getName()
,
CompartmentType.setName(String sid)
,
CompartmentType.isSetName()
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_COMPARTMENT_TYPE
(default).
CompartmentType.getElementName()
,
SBase.getPackageName()
public java.lang.String getElementName()
For CompartmentType
, the element name is always 'compartmentType'.
getElementName
 in class SBase
CompartmentType.getTypeCode()
,
SBase.getPackageName()
public boolean hasRequiredAttributes()
true
if all the required attributes for this
CompartmentType
object have been set.
The required attributes for a CompartmentType
object are:
hasRequiredAttributes
 in class SBase
true
if the required attributes have been set, false
otherwise.