org.sbml.libsbml

Class ReactionGlyph

java.lang.Object

org.sbml.libsbml.SBase

org.sbml.libsbml.GraphicalObject

org.sbml.libsbml.ReactionGlyph

public class ReactionGlyph
extends GraphicalObject

layout The ReactionGlyph is used to represent Reaction elements in the layout.

Analogous to how a Reaction object has to at least have one reactant or product, the ReactionGlyph has to at least have one SpeciesReferenceGlyph stored in the ListOfSpeciesReferenceGlyphs. Figure 12 on the following page provides the UML diagram for the class definition. The ReactionGlyph inherits from GraphicalObject. In addition to the attributes inherited from GraphicalObject, the ReactionGlyph is described by an attribute reaction, a Curve element and a listOfSpeciesReferenceGlyphs element. The Curve describes the center section of a ReactionGlyph. The center section is frequently used by tools to separate the point where substrates arcs come together, from the point where product arcs split off. The Curve is optional, and when not present the dimensions of the inherited BoundingBox describes the center section, by storing its position and dimension.

Constructor Summary

Constructors

Constructor and Description
ReactionGlyph() Creates a new ReactionGlyph.
ReactionGlyph(LayoutPkgNamespaces layoutns) Creates a new ReactionGlyph with the given LayoutPkgNamespaces object.
ReactionGlyph(LayoutPkgNamespaces layoutns, java.lang.String id) Creates a ResctionGlyph with the given LayoutPkgNamespaces and id.
ReactionGlyph(LayoutPkgNamespaces layoutns, java.lang.String id, java.lang.String reactionId) Creates a ResctionGlyph with the given LayoutPkgNamespaces, id and set the id of the associated reaction to the second argument.
ReactionGlyph(long level) Creates a new ReactionGlyph.
ReactionGlyph(long level, long version) Creates a new ReactionGlyph.
ReactionGlyph(long level, long version, long pkgVersion) Creates a new ReactionGlyph.
ReactionGlyph(ReactionGlyph source) Copy constructor.
ReactionGlyph(XMLNode node) Creates a new ReactionGlyph from the given XMLNode
ReactionGlyph(XMLNode node, long l2version) Creates a new ReactionGlyph from the given XMLNode

Method Summary

Methods

Modifier and Type	Method and Description
void	addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph) Adds a new species reference glyph to the list.
ReactionGlyph	cloneObject() Creates and returns a deep copy of this ReactionGlyph object.
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.
SpeciesReferenceGlyph	createSpeciesReferenceGlyph() Creates a new SpeciesReferenceGlyph object, adds it to the end of the list of species reference objects 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 reaction glyph
boolean	getCurveExplicitlySet()
java.lang.String	getElementName() Returns the XML element name of this SBML object.
long	getIndexForSpeciesReferenceGlyph(java.lang.String id) Returns the index of the species reference glyph with the given id.
ListOfSpeciesReferenceGlyphs	getListOfSpeciesReferenceGlyphs() Returns the ListOf object that hold the species reference glyphs.
long	getNumSpeciesReferenceGlyphs() Returns the number of species reference glyph objects.
java.lang.String	getReactionId() Returns the id of the associated reaction.
SpeciesReferenceGlyph	getSpeciesReferenceGlyph(long index) Returns the species reference glyph with the given index.
int	getTypeCode() Returns the libSBML type code of this object instance.
void	initDefaults() Calls initDefaults from GraphicalObject.
boolean	isSetCurve() Returns true if the curve consists of one or more segments.
boolean	isSetReactionId() Returns true if the id of the associated reaction is not the empty string.
SpeciesReferenceGlyph	removeSpeciesReferenceGlyph(long index) Remove the species reference glyph with the given index.
SpeciesReferenceGlyph	removeSpeciesReferenceGlyph(java.lang.String id) Remove the species reference glyph with the given id.
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 reaction glyph.
int	setReactionId(java.lang.String id) Sets the id of the associated reaction.
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

ReactionGlyph

public ReactionGlyph()
              throws SBMLConstructorException

Creates a new ReactionGlyph. The list of species reference glyph is empty and the id of the associated reaction is set to the empty string.

Throws:

SBMLConstructorException

ReactionGlyph

public ReactionGlyph(LayoutPkgNamespaces layoutns)
              throws SBMLConstructorException

Creates a new ReactionGlyph with the given LayoutPkgNamespaces object.

Throws:

SBMLConstructorException

ReactionGlyph

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

Creates a ResctionGlyph with the given LayoutPkgNamespaces and id.

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

ReactionGlyph

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

Creates a ResctionGlyph with the given LayoutPkgNamespaces, id and set the id of the associated reaction to the second argument.

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

ReactionGlyph

public ReactionGlyph(long level)
              throws SBMLConstructorException

Creates a new ReactionGlyph. The list of species reference glyph is empty and the id of the associated reaction is set to the empty string.

Throws:

SBMLConstructorException

ReactionGlyph

public ReactionGlyph(long level,
             long version)
              throws SBMLConstructorException

Creates a new ReactionGlyph. The list of species reference glyph is empty and the id of the associated reaction is set to the empty string.

Throws:

SBMLConstructorException

ReactionGlyph

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

Creates a new ReactionGlyph. The list of species reference glyph is empty and the id of the associated reaction is set to the empty string.

Throws:

SBMLConstructorException

ReactionGlyph

public ReactionGlyph(ReactionGlyph source)
              throws SBMLConstructorException

Copy constructor.

Throws:

SBMLConstructorException

ReactionGlyph

public ReactionGlyph(XMLNode node)
              throws SBMLConstructorException

Creates a new ReactionGlyph from the given XMLNode

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

ReactionGlyph

public ReactionGlyph(XMLNode node,
             long l2version)
              throws SBMLConstructorException

Creates a new ReactionGlyph from the given XMLNode

(FOR BACKWARD COMPATIBILITY)

Throws:

SBMLConstructorException

Method Detail

addSpeciesReferenceGlyph

public void addSpeciesReferenceGlyph(SpeciesReferenceGlyph glyph)

Adds a new species reference glyph to the list.

cloneObject

public ReactionGlyph cloneObject()

Creates and returns a deep copy of this ReactionGlyph object.

Overrides:

cloneObject in class GraphicalObject

Returns:

a (deep) copy of this ReactionGlyph.

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.

createSpeciesReferenceGlyph

public SpeciesReferenceGlyph createSpeciesReferenceGlyph()

Creates a new SpeciesReferenceGlyph object, adds it to the end of the list of species reference objects 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 ReactionGlyph.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 ReactionGlyph.delete() themselves.

Overrides:

delete in class GraphicalObject

getCurve

public Curve getCurve()

Returns the curve object for the reaction 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

getIndexForSpeciesReferenceGlyph

public long getIndexForSpeciesReferenceGlyph(java.lang.String id)

Returns the index of the species reference glyph with the given id. If the reaction glyph does not contain a species reference glyph with this id, the value of the maximum long integer is returned as an indicator.

getListOfSpeciesReferenceGlyphs

public ListOfSpeciesReferenceGlyphs getListOfSpeciesReferenceGlyphs()

Returns the ListOf object that hold the species reference glyphs.

getNumSpeciesReferenceGlyphs

public long getNumSpeciesReferenceGlyphs()

Returns the number of species reference glyph objects.

getReactionId

public java.lang.String getReactionId()

Returns the id of the associated reaction.

getSpeciesReferenceGlyph

public SpeciesReferenceGlyph getSpeciesReferenceGlyph(long index)

Returns the species reference glyph with the given index. If the index is invalid, null is returned.

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_REACTIONGLYPH

See Also:

ReactionGlyph.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

isSetCurve

public boolean isSetCurve()

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

isSetReactionId

public boolean isSetReactionId()

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

removeSpeciesReferenceGlyph

public SpeciesReferenceGlyph removeSpeciesReferenceGlyph(long index)

Remove the species reference glyph with the given index. A pointer to the object is returned. If no object has been removed, null is returned.

removeSpeciesReferenceGlyph

public SpeciesReferenceGlyph removeSpeciesReferenceGlyph(java.lang.String id)

Remove the species reference glyph with the given id. A pointer to the object is returned. If no object has been removed, null is returned.

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 reaction glyph.

setReactionId

public int setReactionId(java.lang.String id)

Sets the id of the associated reaction.

toXML

public XMLNode toXML()

Creates an XMLNode object from this.

Overrides:

toXML in class GraphicalObject