org.sbml.libsbml

Class CompartmentGlyph

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.GraphicalObject

org.sbml.libsbml.CompartmentGlyph

public class CompartmentGlyph
extends GraphicalObject

layout Representation of a compartment glyph.

Constructor Summary

Constructors

Constructor and Description
CompartmentGlyph() Default Constructor which creates a new CompartmentGlyph.
CompartmentGlyph(CompartmentGlyph source) Copy constructor.
CompartmentGlyph(LayoutPkgNamespaces layoutns) Ctor.
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

Method Summary

Methods

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) Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).
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.
int	unsetOrder() Sets the compartment order

Methods inherited from class org.sbml.libsbml.GraphicalObject

getBoundingBox, getBoundingBoxExplicitlySet, getId, getMetaIdRef, isSetId, isSetMetaIdRef, renameMetaIdRefs, setBoundingBox, setId, setMetaIdRef, unsetId, unsetMetaIdRef

Methods inherited from class org.sbml.libsbml.SBase

addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, 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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CompartmentGlyph

public CompartmentGlyph()
                 throws SBMLConstructorException

Default Constructor which creates a new CompartmentGlyph. Id and associated compartment id are unset.

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(CompartmentGlyph source)
                 throws SBMLConstructorException

Copy constructor.

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(LayoutPkgNamespaces layoutns)
                 throws SBMLConstructorException

Ctor.

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(LayoutPkgNamespaces layoutns,
                java.lang.String id)
                 throws SBMLConstructorException

Constructor which creates a new CompartmentGlyph with the given id.

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(LayoutPkgNamespaces layoutns,
                java.lang.String id,
                java.lang.String compartmentId)
                 throws SBMLConstructorException

Constructor which creates a new CompartmentGlyph. Id and associated compartment id are set to copies of the values given as arguments.

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(long level)
                 throws SBMLConstructorException

Default Constructor which creates a new CompartmentGlyph. Id and associated compartment id are unset.

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(long level,
                long version)
                 throws SBMLConstructorException

Default Constructor which creates a new CompartmentGlyph. Id and associated compartment id are unset.

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(long level,
                long version,
                long pkgVersion)
                 throws SBMLConstructorException

Default Constructor which creates a new CompartmentGlyph. Id and associated compartment id are unset.

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(XMLNode node)
                 throws SBMLConstructorException

Creates a new CompartmentGlyph from the given XMLNode

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

CompartmentGlyph

public CompartmentGlyph(XMLNode node,
                long l2version)
                 throws SBMLConstructorException

Creates a new CompartmentGlyph from the given XMLNode

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

Method Detail

cloneObject

public CompartmentGlyph cloneObject()

Creates and returns a deep copy of this CompartmentGlyph.

Overrides:

cloneObject in class GraphicalObject

Returns:

a (deep) copy of this CompartmentGlyph.

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 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.

Overrides:

delete in class GraphicalObject

getCompartmentId

public java.lang.String getCompartmentId()

Returns the id of the associated compartment.

getElementName

public java.lang.String getElementName()

Returns the XML element name of this SBML object.

Overrides:

getElementName in class GraphicalObject

getOrder

public double getOrder()

Returns the compartment order.

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 &ldquoSBML_&rdquo. 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 GraphicalObject

Returns:

the SBML type code for this object: SBML_LAYOUT_COMPARTMENTGLYPH

See Also:

CompartmentGlyph.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().

initDefaults

public void initDefaults()

Calls initDefaults from GraphicalObject.

Overrides:

initDefaults in class GraphicalObject

isSetCompartmentId

public boolean isSetCompartmentId()

Returns true if the id of the associated compartment is not the empty string.

isSetOrder

public boolean isSetOrder()

Returns true if the compartment order has been set

renameSIdRefs

public void renameSIdRefs(java.lang.String oldid,
                 java.lang.String newid)

Renames all the SIdRef attributes on this element, including any found in MathML content (if such exists).

This method works by looking at all attributes and (if appropriate) mathematical formulas, comparing the identifiers to the value of oldid. If any matches are found, the matching identifiers are replaced with newid. The method does not descend into child elements.

Overrides:

renameSIdRefs in class SBase

Parameters:

oldid - the old identifier

newid - the new identifier

setCompartmentId

public int setCompartmentId(java.lang.String id)

Sets the id of the associated compartment.

setOrder

public int setOrder(double order)

Sets the compartment order

toXML

public XMLNode toXML()

Creates an XMLNode object from this.

Overrides:

toXML in class GraphicalObject

unsetOrder

public int unsetOrder()

Sets the compartment order