CompartmentGlyph (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.GraphicalObject
  - - org.sbml.libsbml.CompartmentGlyph

public class CompartmentGlyph
extends GraphicalObject

layout A glyph for an SBML compartment.

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

All Methods Instance Methods Concrete 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)` 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.
`int`	`unsetOrder()` Sets the compartment order

Methods inherited from class org.sbml.libsbml.GraphicalObject
connectToChild, 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, 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

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

- Constructor Detail
  - 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(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)
                 throws SBMLConstructorException
```
    Default Constructor which creates a new CompartmentGlyph. Id and associated compartment id are unset.
    
    Throws:
    
    SBMLConstructorException
  - CompartmentGlyph
```
public CompartmentGlyph()
                 throws SBMLConstructorException
```
    Default Constructor which creates a new CompartmentGlyph. Id and associated compartment id are unset.
    
    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(XMLNode node,
                        long l2version)
                 throws SBMLConstructorException
```
    Creates a new CompartmentGlyph from the given XMLNode
    (FOR BACKWARD COMPATIBILITY)
    
    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(CompartmentGlyph source)
                 throws SBMLConstructorException
```
    Copy constructor.
    
    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 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.
  - setCompartmentId
```
public int setCompartmentId(java.lang.String id)
```
    Sets the id of the associated compartment.
  - isSetCompartmentId
```
public boolean isSetCompartmentId()
```
    Returns true if the id of the associated compartment is not the empty string.
  - getOrder
```
public double getOrder()
```
    Returns the compartment order.
  - setOrder
```
public int setOrder(double order)
```
    Sets the compartment order
  - unsetOrder
```
public int unsetOrder()
```
    Sets the compartment order
  - 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)
```
    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 SIdRefin 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.
    
    Overrides:
    
    renameSIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - initDefaults
```
public void initDefaults()
```
    Calls initDefaults from GraphicalObject.
    
    Overrides:
    
    initDefaults in class GraphicalObject
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this SBML object.
    
    Overrides:
    
    getElementName in class GraphicalObject
    
    Returns:
    
    the string of the name of this element.
  - 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.
  - 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 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 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().
  - toXML
```
public XMLNode toXML()
```
    Creates an XMLNode object from this.
    
    Overrides:
    
    toXML in class GraphicalObject

Class CompartmentGlyph

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.GraphicalObject

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

CompartmentGlyph

Method Detail

delete

getCompartmentId

setCompartmentId

isSetCompartmentId

getOrder

setOrder

unsetOrder

isSetOrder

renameSIdRefs

initDefaults

getElementName

cloneObject

getTypeCode

toXML