public class CompartmentGlyph extends GraphicalObject
Constructor and Description |
---|
CompartmentGlyph()
Default Constructor which creates a new
CompartmentGlyph . |
CompartmentGlyph(CompartmentGlyph source)
Copy constructor.
|
CompartmentGlyph(LayoutPkgNamespaces layoutns)
Ctor.
|
CompartmentGlyph(LayoutPkgNamespaces layoutns,
String id)
Constructor which creates a new
CompartmentGlyph with the given id . |
CompartmentGlyph(LayoutPkgNamespaces layoutns,
String id,
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.
|
String |
getCompartmentId()
Returns the id of the associated compartment.
|
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(String oldid,
String newid)
Replaces all uses of a given
SIdRef type attribute value with another
value. |
int |
setCompartmentId(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. |
int |
unsetOrder()
Sets 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, 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, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
public CompartmentGlyph(long level, long version, long pkgVersion) throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.SBMLConstructorException
public CompartmentGlyph(long level, long version) throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.SBMLConstructorException
public CompartmentGlyph(long level) throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.SBMLConstructorException
public CompartmentGlyph() throws SBMLConstructorException
CompartmentGlyph
. Id and
associated compartment id are unset.SBMLConstructorException
public CompartmentGlyph(LayoutPkgNamespaces layoutns) throws SBMLConstructorException
SBMLConstructorException
public CompartmentGlyph(LayoutPkgNamespaces layoutns, String id) throws SBMLConstructorException
SBMLConstructorException
public CompartmentGlyph(LayoutPkgNamespaces layoutns, String id, 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
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 String getCompartmentId()
public int setCompartmentId(String id)
public boolean isSetCompartmentId()
public double getOrder()
public int setOrder(double order)
public int unsetOrder()
public boolean isSetOrder()
public void renameSIdRefs(String oldid, 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 identifiernewid
- the new identifierpublic void initDefaults()
GraphicalObject
.initDefaults
 in class GraphicalObject
public 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 getPackageName()
method on the object.
getTypeCode
 in class GraphicalObject
SBML_LAYOUT_COMPARTMENTGLYPH
CompartmentGlyph.getElementName()
,
SBase.getPackageName()
public XMLNode toXML()
XMLNode
object from this.toXML
 in class GraphicalObject