public class CompartmentGlyph extends GraphicalObject
Constructor and Description |
---|
CompartmentGlyph()
Default Constructor which creates a new
CompartmentGlyph . |
CompartmentGlyph(CompartmentGlyph source)
Copy constructor.
|
CompartmentGlyph(LayoutPkgNamespaces layoutns)
Constructor.
|
CompartmentGlyph(LayoutPkgNamespaces layoutns,
java.lang.String id)
Constructor which creates a new
CompartmentGlyph with the given id . |
CompartmentGlyph(LayoutPkgNamespaces layoutns,
java.lang.String id,
java.lang.String compartmentId)
Constructor which creates a new
CompartmentGlyph . |
CompartmentGlyph(long level)
Default Constructor which creates a new
CompartmentGlyph . |
CompartmentGlyph(long level,
long version)
Default Constructor which creates a new
CompartmentGlyph . |
CompartmentGlyph(long level,
long version,
long pkgVersion)
Default Constructor which creates a new
CompartmentGlyph . |
CompartmentGlyph(XMLNode node)
Creates a new
CompartmentGlyph from the given XMLNode |
CompartmentGlyph(XMLNode node,
long l2version)
Creates a new
CompartmentGlyph from the given XMLNode |
Modifier and Type | Method and Description |
---|---|
CompartmentGlyph |
cloneObject()
Creates and returns a deep copy of this
CompartmentGlyph . |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getCompartmentId()
Returns the id of the associated compartment.
|
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
double |
getOrder()
Returns the compartment order.
|
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
void |
initDefaults()
Calls initDefaults from
GraphicalObject . |
boolean |
isSetCompartmentId()
Returns
true if the id of the associated compartment is not the empty
string. |
boolean |
isSetOrder()
Returns
true if the compartment order 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 |
setCompartmentId(java.lang.String id)
Sets the id of the associated compartment.
|
int |
setOrder(double order)
Sets the compartment order.
|
XMLNode |
toXML()
Creates an
XMLNode object from this CompartmentGlyph . |
int |
unsetOrder()
Unsets the compartment order.
|
connectToChild, getBoundingBox, getBoundingBoxExplicitlySet, getId, getMetaIdRef, isSetId, isSetMetaIdRef, renameMetaIdRefs, setBoundingBox, setId, setMetaIdRef, unsetId, unsetMetaIdRef
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
public CompartmentGlyph(long level, long version, long pkgVersion) throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
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. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public CompartmentGlyph(long level, long version) throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
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. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public CompartmentGlyph(long level) throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
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. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public CompartmentGlyph() throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
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. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public CompartmentGlyph(LayoutPkgNamespaces layoutns) throws SBMLConstructorException
The package namespaces object used in this constructor is derived from a
SBMLNamespaces
object, which encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and
package version and name information used in addition to SBML Level 3 Core. A
common approach to using libSBML's SBMLNamespaces
facilities is to create an
package namespace object somewhere in a program once, then hand that object
as needed to object constructors of that package that accept it as and
argument, such as this one.
layoutns
- the LayoutPkgNamespaces
object.
SBMLConstructorException
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. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public CompartmentGlyph(LayoutPkgNamespaces layoutns, java.lang.String id) throws SBMLConstructorException
SBMLConstructorException
public CompartmentGlyph(LayoutPkgNamespaces layoutns, java.lang.String id, java.lang.String compartmentId) throws SBMLConstructorException
CompartmentGlyph
. Id and associated
compartment id are set to copies of the values given as arguments.
(FOR BACKWARD COMPATIBILITY)
SBMLConstructorException
public CompartmentGlyph(XMLNode node, long l2version) throws SBMLConstructorException
SBMLConstructorException
public CompartmentGlyph(XMLNode node) throws SBMLConstructorException
SBMLConstructorException
public CompartmentGlyph(CompartmentGlyph source) throws SBMLConstructorException
source
- the instance 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 CompartmentGlyph.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 CompartmentGlyph.delete()
themselves.
delete
 in class GraphicalObject
public java.lang.String getCompartmentId()
public int setCompartmentId(java.lang.String id)
id
- the identifier of a Compartment
object defined elsewhere
in this Model
.
public boolean isSetCompartmentId()
true
if the id of the associated compartment is not the empty
string.
true
if the 'compartment' attribute of this CompartmentGlyph
is
set, false
otherwise.public double getOrder()
public int setOrder(double order)
order
- the value to use for the 'order' attribute.
public int unsetOrder()
public boolean isSetOrder()
true
if the compartment order has been set.
true
if the 'order' attribute of this CompartmentGlyph
is
set, false
otherwise.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 SIdRef
in 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.
renameSIdRefs
 in class SBase
oldid
- the old identifier.newid
- the new identifier.public void initDefaults()
GraphicalObject
.initDefaults
 in class GraphicalObject
public java.lang.String getElementName()
getElementName
 in class GraphicalObject
public CompartmentGlyph cloneObject()
CompartmentGlyph
.
cloneObject
 in class GraphicalObject
CompartmentGlyph
.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
method on the object.
SBase.getPackageName()
getTypeCode
 in class GraphicalObject
SBML_LAYOUT_COMPARTMENTGLYPH
CompartmentGlyph.getElementName()
,
SBase.getPackageName()
public XMLNode toXML()
XMLNode
object from this CompartmentGlyph
.
toXML
 in class GraphicalObject
XMLNode
object based off of the information in this CompartmentGlyph
.