org.sbml.libsbml

Class ReferenceGlyph

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.GraphicalObject

org.sbml.libsbml.ReferenceGlyph

public class ReferenceGlyph
extends GraphicalObject

layout The ReferenceGlyph is used by the &ldquolayout&rdquo package to connect a GraphicalObject and a GeneralGlyph.

The ReferenceGlyph element describes the graphical connection between an arbitrary GraphicalObject (or derived element) and a GeneralGlyph (which would be an arrow or some curve in most cases). A ReferenceGlyph inherits from GraphicalObject. Additionally it has a mandatory attribute 'glyph' and two optional attributes 'reference' and 'role'. Optionally, the ReferenceGlyph also has an element 'curve'. The ReferenceGlyph should either contain a bounding box or a curve specification. If both are given, the bounding box should be ignored.

Constructor Summary

Constructors

Constructor and Description
ReferenceGlyph() Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(LayoutPkgNamespaces layoutns) Ctor.
ReferenceGlyph(LayoutPkgNamespaces layoutns, java.lang.String sid, java.lang.String glyphId, java.lang.String referenceId, java.lang.String role) Creates a new ReferenceGlyph.
ReferenceGlyph(long level) Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(long level, long version) Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(long level, long version, long pkgVersion) Creates a new ReferenceGlyph with the given SBML level, version and package version.
ReferenceGlyph(ReferenceGlyph source) Copy constructor.
ReferenceGlyph(XMLNode node) Creates a new ReferenceGlyph from the given XMLNode
ReferenceGlyph(XMLNode node, long l2version) Creates a new ReferenceGlyph from the given XMLNode

Method Summary

Methods

Modifier and Type	Method and Description
ReferenceGlyph	cloneObject() Creates and returns a deep copy of this ReferenceGlyph.
CubicBezier	createCubicBezier() Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
LineSegment	createLineSegment() Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.
void	delete() Explicitly deletes the underlying native object.
Curve	getCurve() Returns the curve object for the reference glyph
boolean	getCurveExplicitlySet()
java.lang.String	getElementName() Returns the XML element name of this SBML object.
java.lang.String	getGlyphId() Returns the id of the associated glyph.
java.lang.String	getReferenceId() Returns the id of the associated sbml reference.
java.lang.String	getRole() Returns a string representation of the role.
int	getTypeCode() Returns the libSBML type code of this object instance.
void	initDefaults() Calls initDefaults on GraphicalObject
boolean	isSetCurve() Returns true if the curve consists of one or more segments.
boolean	isSetGlyphId() Returns true if the id of the associated glyph is not the empty string.
boolean	isSetReferenceId() Returns true if the id of the associated reference is not the empty string.
boolean	isSetRole() Returns true of role is different from the empty string.
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).
void	setCurve(Curve curve) Sets the curve object for the reference glyph.
void	setGlyphId(java.lang.String glyphId) Sets the id of the associated glyph.
void	setReferenceId(java.lang.String id) Sets the id of the associated sbml reference.
void	setRole(java.lang.String role) Sets the role.
XMLNode	toXML() Creates an XMLNode object from this.

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

ReferenceGlyph

public ReferenceGlyph()
               throws SBMLConstructorException

Creates a new ReferenceGlyph with the given SBML level, version and package version. The id if the associated reference and the id of the associated glyph are set to the empty string. The role is set to empty.

Throws:

SBMLConstructorException

ReferenceGlyph

public ReferenceGlyph(LayoutPkgNamespaces layoutns)
               throws SBMLConstructorException

Ctor.

Throws:

SBMLConstructorException

ReferenceGlyph

public ReferenceGlyph(LayoutPkgNamespaces layoutns,
              java.lang.String sid,
              java.lang.String glyphId,
              java.lang.String referenceId,
              java.lang.String role)
               throws SBMLConstructorException

Creates a new ReferenceGlyph. The id is given as the first argument, the id of the associated glyph is given as the second argument. The third argument is the id of the associated reference and the fourth argument is the role.

Throws:

SBMLConstructorException

ReferenceGlyph

public ReferenceGlyph(long level)
               throws SBMLConstructorException

Creates a new ReferenceGlyph with the given SBML level, version and package version. The id if the associated reference and the id of the associated glyph are set to the empty string. The role is set to empty.

Throws:

SBMLConstructorException

ReferenceGlyph

public ReferenceGlyph(long level,
              long version)
               throws SBMLConstructorException

Creates a new ReferenceGlyph with the given SBML level, version and package version. The id if the associated reference and the id of the associated glyph are set to the empty string. The role is set to empty.

Throws:

SBMLConstructorException

ReferenceGlyph

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

Creates a new ReferenceGlyph with the given SBML level, version and package version. The id if the associated reference and the id of the associated glyph are set to the empty string. The role is set to empty.

Throws:

SBMLConstructorException

ReferenceGlyph

public ReferenceGlyph(ReferenceGlyph source)
               throws SBMLConstructorException

Copy constructor.

Throws:

SBMLConstructorException

ReferenceGlyph

public ReferenceGlyph(XMLNode node)
               throws SBMLConstructorException

Creates a new ReferenceGlyph from the given XMLNode

Throws:

SBMLConstructorException

ReferenceGlyph

public ReferenceGlyph(XMLNode node,
              long l2version)
               throws SBMLConstructorException

Creates a new ReferenceGlyph from the given XMLNode

Throws:

SBMLConstructorException

Method Detail

cloneObject

public ReferenceGlyph cloneObject()

Creates and returns a deep copy of this ReferenceGlyph.

Overrides:

cloneObject in class GraphicalObject

Returns:

a (deep) copy of this ReferenceGlyph.

createCubicBezier

public CubicBezier createCubicBezier()

Creates a new CubicBezier object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.

createLineSegment

public LineSegment createLineSegment()

Creates a new LineSegment object, adds it to the end of the list of curve segment objects of the curve and returns a reference to the newly created object.

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 ReferenceGlyph.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 ReferenceGlyph.delete() themselves.

Overrides:

delete in class GraphicalObject

getCurve

public Curve getCurve()

Returns the curve object for the reference glyph

getCurveExplicitlySet

public boolean getCurveExplicitlySet()

getElementName

public java.lang.String getElementName()

Returns the XML element name of this SBML object.

Overrides:

getElementName in class GraphicalObject

getGlyphId

public java.lang.String getGlyphId()

Returns the id of the associated glyph.

getReferenceId

public java.lang.String getReferenceId()

Returns the id of the associated sbml reference.

getRole

public java.lang.String getRole()

Returns a string representation of the role.

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_REFERENCEGLYPH

See Also:

ReferenceGlyph.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 on GraphicalObject

Overrides:

initDefaults in class GraphicalObject

isSetCurve

public boolean isSetCurve()

Returns true if the curve consists of one or more segments.

isSetGlyphId

public boolean isSetGlyphId()

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

isSetReferenceId

public boolean isSetReferenceId()

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

isSetRole

public boolean isSetRole()

Returns true of role is different from the empty string.

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

setCurve

public void setCurve(Curve curve)

Sets the curve object for the reference glyph.

setGlyphId

public void setGlyphId(java.lang.String glyphId)

Sets the id of the associated glyph.

setReferenceId

public void setReferenceId(java.lang.String id)

Sets the id of the associated sbml reference.

setRole

public void setRole(java.lang.String role)

Sets the role.

toXML

public XMLNode toXML()

Creates an XMLNode object from this.

Overrides:

toXML in class GraphicalObject