GraphicalObject (LibSBML Java API)

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

Direct Known Subclasses:

CompartmentGlyph, GeneralGlyph, ReactionGlyph, ReferenceGlyph, SpeciesGlyph, SpeciesReferenceGlyph, TextGlyph
```
public class GraphicalObject
extends SBase
```
layout Base class of objects that store layouts.
All the more specific layout elements (CompartmentGlyph, GeneralGlyph, SpeciesGlyph, ReactionGlyph, ReferenceGlyph, TextGlyph, and SpeciesReferenceGlyph) are derived from the class GraphicalObject. Each object of class GraphicalObject has a mandatory BoundingBox, which specifies the position and the size of the object. While GraphicalObject is the base class for most elements in the &ldquolayout&rdquo package, it is not an abstract class. It can be instantiated when used in the listOfAdditionalGraphicalObjects to describe additional elements and relationships. Since it only describes a BoundingBox, programs are encouraged to add Annotation objects that describe program-specific graphical information.

Constructor Summary

Constructors
Constructor and Description
`GraphicalObject()` Creates a new `GraphicalObject`.
`GraphicalObject(GraphicalObject source)` Copy constructor.
`GraphicalObject(LayoutPkgNamespaces layoutns)` Creates a new `GraphicalObject` with the given `LayoutPkgNamespaces`
`GraphicalObject(LayoutPkgNamespaces layoutns, java.lang.String id)` Creates a new `GraphicalObject` with the given `id`.
`GraphicalObject(LayoutPkgNamespaces layoutns, java.lang.String id, BoundingBox bb)` Creates a new `GraphicalObject` with the given `id` and 3D coordinates for the bounding box.
`GraphicalObject(LayoutPkgNamespaces layoutns, java.lang.String id, double x, double y, double w, double h)` Creates a new `GraphicalObject` with the given `id` and 2D coordinates for the bounding box.
`GraphicalObject(LayoutPkgNamespaces layoutns, java.lang.String id, double x, double y, double z, double w, double h, double d)` Creates a new `GraphicalObject` with the given `id` and 3D coordinates for the bounding box.
`GraphicalObject(LayoutPkgNamespaces layoutns, java.lang.String id, Point p, Dimensions d)` Creates a new `GraphicalObject` with the given `id` and 3D coordinates for the bounding box.
`GraphicalObject(long level)` Creates a new `GraphicalObject`.
`GraphicalObject(long level, long version)` Creates a new `GraphicalObject`.
`GraphicalObject(long level, long version, long pkgVersion)` Creates a new `GraphicalObject`.
`GraphicalObject(XMLNode node)` Creates a new `GraphicalObject` from the given `XMLNode`
`GraphicalObject(XMLNode node, long l2version)` Creates a new `GraphicalObject` from the given `XMLNode`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`GraphicalObject`	`cloneObject()` Creates and returns a deep copy of this `GraphicalObject`.
`void`	`connectToChild()`
`void`	`delete()` Explicitly deletes the underlying native object.
`BoundingBox`	`getBoundingBox()` Returns the bounding box for the `GraphicalObject`.
`boolean`	`getBoundingBoxExplicitlySet()`
`java.lang.String`	`getElementName()` Returns the XML element name of this SBML object.
`java.lang.String`	`getId()` Returns the value of the 'id' attribute of this `GraphicalObject`.
`java.lang.String`	`getMetaIdRef()` Returns the value of the 'metaidRef' attribute of this `GraphicalObject`.
`int`	`getTypeCode()` Returns the libSBML type code of this object instance.
`void`	`initDefaults()` Does nothing.
`boolean`	`isSetId()` Predicate returning `true` or `false` depending on whether this `GraphicalObject`'s 'id' attribute has been set.
`boolean`	`isSetMetaIdRef()` Predicate returning `true` or `false` depending on whether this `GraphicalObject`'s 'metaidRef' attribute has been set.
`void`	`renameMetaIdRefs(java.lang.String oldid, java.lang.String newid)` Renames all the `MetaIdRef` attributes on this element.
`void`	`setBoundingBox(BoundingBox bb)` Sets the boundingbox for the `GraphicalObject`.
`int`	`setId(java.lang.String id)` Sets the value of the 'id' attribute of this `GraphicalObject`.
`int`	`setMetaIdRef(java.lang.String metaid)` Sets the value of the 'metaidRef' attribute of this `GraphicalObject`.
`XMLNode`	`toXML()` Creates an `XMLNode` object from this.
`int`	`unsetId()` Unsets the value of the 'id' attribute of this `GraphicalObject`.
`int`	`unsetMetaIdRef()` Unsets the value of the 'metaidRef' attribute of this `GraphicalObject`.

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, renameSIdRefs, 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
  - GraphicalObject
```
public GraphicalObject(long level,
                       long version,
                       long pkgVersion)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject.
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(long level,
                       long version)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject.
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(long level)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject.
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject()
                throws SBMLConstructorException
```
    Creates a new GraphicalObject.
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(LayoutPkgNamespaces layoutns)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject with the given LayoutPkgNamespaces
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(LayoutPkgNamespaces layoutns,
                       java.lang.String id)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject with the given id.
    (FOR BACKWARD COMPATIBILITY)
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(LayoutPkgNamespaces layoutns,
                       java.lang.String id,
                       double x,
                       double y,
                       double w,
                       double h)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject with the given id and 2D coordinates for the bounding box.
    (FOR BACKWARD COMPATIBILITY)
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(LayoutPkgNamespaces layoutns,
                       java.lang.String id,
                       double x,
                       double y,
                       double z,
                       double w,
                       double h,
                       double d)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject with the given id and 3D coordinates for the bounding box.
    (FOR BACKWARD COMPATIBILITY)
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(LayoutPkgNamespaces layoutns,
                       java.lang.String id,
                       Point p,
                       Dimensions d)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject with the given id and 3D coordinates for the bounding box.
    (FOR BACKWARD COMPATIBILITY)
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(LayoutPkgNamespaces layoutns,
                       java.lang.String id,
                       BoundingBox bb)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject with the given id and 3D coordinates for the bounding box.
    (FOR BACKWARD COMPATIBILITY)
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(XMLNode node,
                       long l2version)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject from the given XMLNode
    (FOR BACKWARD COMPATIBILITY)
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(XMLNode node)
                throws SBMLConstructorException
```
    Creates a new GraphicalObject from the given XMLNode
    (FOR BACKWARD COMPATIBILITY)
    
    Throws:
    
    SBMLConstructorException
  - GraphicalObject
```
public GraphicalObject(GraphicalObject 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 GraphicalObject.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 GraphicalObject.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - initDefaults
```
public void initDefaults()
```
    Does nothing. No defaults are defined for GraphicalObject.
  - renameMetaIdRefs
```
public void renameMetaIdRefs(java.lang.String oldid,
                             java.lang.String newid)
```
    Renames all the MetaIdRef attributes on this element.
    This method works by looking at all meta-attribute values, 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:
    
    renameMetaIdRefs in class SBase
    
    Parameters:
    
    oldid - the old identifier
    
    newid - the new identifier
  - getId
```
public java.lang.String getId()
```
    Returns the value of the 'id' attribute of this GraphicalObject.
    
    Overrides:
    
    getId in class SBase
  - isSetId
```
public boolean isSetId()
```
    Predicate returning true or false depending on whether this GraphicalObject's 'id' attribute has been set.
    
    Overrides:
    
    isSetId in class SBase
  - setId
```
public int setId(java.lang.String id)
```
    Sets the value of the 'id' attribute of this GraphicalObject.
    
    Overrides:
    
    setId in class SBase
  - unsetId
```
public int unsetId()
```
    Unsets the value of the 'id' attribute of this GraphicalObject.
    Overrides:
    
    unsetId in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - getMetaIdRef
```
public java.lang.String getMetaIdRef()
```
    Returns the value of the 'metaidRef' attribute of this GraphicalObject.
  - isSetMetaIdRef
```
public boolean isSetMetaIdRef()
```
    Predicate returning true or false depending on whether this GraphicalObject's 'metaidRef' attribute has been set.
  - setMetaIdRef
```
public int setMetaIdRef(java.lang.String metaid)
```
    Sets the value of the 'metaidRef' attribute of this GraphicalObject.
  - unsetMetaIdRef
```
public int unsetMetaIdRef()
```
    Unsets the value of the 'metaidRef' attribute of this GraphicalObject.
  - setBoundingBox
```
public void setBoundingBox(BoundingBox bb)
```
    Sets the boundingbox for the GraphicalObject.
  - getBoundingBox
```
public BoundingBox getBoundingBox()
```
    Returns the bounding box for the GraphicalObject.
  - getBoundingBoxExplicitlySet
```
public boolean getBoundingBoxExplicitlySet()
```
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this SBML object.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the string of the name of this element
  - cloneObject
```
public GraphicalObject cloneObject()
```
    Creates and returns a deep copy of this GraphicalObject.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this GraphicalObject.
  - 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 SBase
    
    Returns:
    
    the SBML type code for this object: SBML_LAYOUT_GRAPHICALOBJECT
    
    See Also:
    
    GraphicalObject.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.
  - connectToChild
```
public void connectToChild()
```
    Overrides:
    
    connectToChild in class SBase

Class GraphicalObject

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

GraphicalObject

Method Detail

delete

initDefaults

renameMetaIdRefs

getId

isSetId

setId

unsetId

getMetaIdRef

isSetMetaIdRef

setMetaIdRef

unsetMetaIdRef

setBoundingBox

getBoundingBox

getBoundingBoxExplicitlySet

getElementName

cloneObject

getTypeCode

toXML

connectToChild