public class SpeciesReferenceGlyph extends GraphicalObject
Reaction
in the &ldquolayout&rdquo package.
The SpeciesReferenceGlyph element describes the graphical connection
between a SpeciesGlyph
and a ReactionGlyph
(which would be an arrow or
some curve in most cases). A SpeciesReferenceGlyph
inherits from
GraphicalObject
, and adds a mandatory attribute 'speciesGlyph' and two
optional attributes 'speciesReference' and 'role'. Optionally, the
SpeciesReferenceGlyph
also has a child element 'curve'.
If the curve is specified, it overrides the inherited bounding box.
Constructor and Description |
---|
SpeciesReferenceGlyph()
Creates a new
SpeciesReferenceGlyph with the given SBML level, version and
package version. |
SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns)
Ctor.
|
SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns,
java.lang.String sid,
java.lang.String speciesGlyphId,
java.lang.String speciesReferenceId,
int role)
Creates a new
SpeciesReferenceGlyph . |
SpeciesReferenceGlyph(long level)
Creates a new
SpeciesReferenceGlyph with the given SBML level, version and
package version. |
SpeciesReferenceGlyph(long level,
long version)
Creates a new
SpeciesReferenceGlyph with the given SBML level, version and
package version. |
SpeciesReferenceGlyph(long level,
long version,
long pkgVersion)
Creates a new
SpeciesReferenceGlyph with the given SBML level, version and
package version. |
SpeciesReferenceGlyph(SpeciesReferenceGlyph source)
Copy constructor.
|
SpeciesReferenceGlyph(XMLNode node)
Creates a new
SpeciesReferenceGlyph from the given XMLNode |
SpeciesReferenceGlyph(XMLNode node,
long l2version)
Creates a new
SpeciesReferenceGlyph from the given XMLNode |
Modifier and Type | Method and Description |
---|---|
SpeciesReferenceGlyph |
cloneObject()
Creates and returns a deep copy of this
SpeciesReferenceGlyph . |
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 species reference glyph
|
boolean |
getCurveExplicitlySet()   |
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
int |
getRole()
Returns the role.
|
java.lang.String |
getRoleString()
Returns a string representation of the role.
|
java.lang.String |
getSpeciesGlyphId()
Returns the id of the associated
SpeciesGlyph . |
java.lang.String |
getSpeciesReferenceId()
Returns the id of the associated species reference.
|
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
void |
initDefaults()
Calls initDefaults on
GraphicalObject and sets role to
SPECIES_ROLE_UNDEFINED. |
boolean |
isSetCurve()
Returns true if the curve consists of one or more segments.
|
boolean |
isSetRole()
Returns true of role is different from SPECIES_ROLE_UNDEFINED.
|
boolean |
isSetSpeciesGlyphId()
Returns true if the id of the associated species glyph is not the
empty string.
|
boolean |
isSetSpeciesReferenceId()
Returns true if the id of the associated species reference is not 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 species reference glyph.
|
void |
setRole(int role)
Sets the role.
|
void |
setRole(java.lang.String role)
Sets the role based on a string.
|
void |
setSpeciesGlyphId(java.lang.String speciesGlyphId)
Sets the id of the associated species glyph.
|
void |
setSpeciesReferenceId(java.lang.String id)
Sets the id of the associated species reference.
|
XMLNode |
toXML()
Creates an
XMLNode object from this. |
getBoundingBox, getBoundingBoxExplicitlySet, getId, getMetaIdRef, isSetId, isSetMetaIdRef, renameMetaIdRefs, setBoundingBox, setId, setMetaIdRef, unsetId, unsetMetaIdRef
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
public SpeciesReferenceGlyph() throws SBMLConstructorException
SpeciesReferenceGlyph
with the given SBML level, version and
package version. The id if the associated species
reference and the id of the associated species glyph are set to the
empty string. The role is set to SPECIES_ROLE_UNDEFINED.SBMLConstructorException
public SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns) throws SBMLConstructorException
SBMLConstructorException
public SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns, java.lang.String sid, java.lang.String speciesGlyphId, java.lang.String speciesReferenceId, int role) throws SBMLConstructorException
SpeciesReferenceGlyph
. The id is given as the first
argument, the id of the associated species glyph is given as the
second argument. The third argument is the id of the associated
species reference and the fourth argument is the role.SBMLConstructorException
public SpeciesReferenceGlyph(long level) throws SBMLConstructorException
SpeciesReferenceGlyph
with the given SBML level, version and
package version. The id if the associated species
reference and the id of the associated species glyph are set to the
empty string. The role is set to SPECIES_ROLE_UNDEFINED.SBMLConstructorException
public SpeciesReferenceGlyph(long level, long version) throws SBMLConstructorException
SpeciesReferenceGlyph
with the given SBML level, version and
package version. The id if the associated species
reference and the id of the associated species glyph are set to the
empty string. The role is set to SPECIES_ROLE_UNDEFINED.SBMLConstructorException
public SpeciesReferenceGlyph(long level, long version, long pkgVersion) throws SBMLConstructorException
SpeciesReferenceGlyph
with the given SBML level, version and
package version. The id if the associated species
reference and the id of the associated species glyph are set to the
empty string. The role is set to SPECIES_ROLE_UNDEFINED.SBMLConstructorException
public SpeciesReferenceGlyph(SpeciesReferenceGlyph source) throws SBMLConstructorException
SBMLConstructorException
public SpeciesReferenceGlyph(XMLNode node) throws SBMLConstructorException
SpeciesReferenceGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesReferenceGlyph(XMLNode node, long l2version) throws SBMLConstructorException
SpeciesReferenceGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesReferenceGlyph cloneObject()
SpeciesReferenceGlyph
.
cloneObject
 in class GraphicalObject
SpeciesReferenceGlyph
.public CubicBezier createCubicBezier()
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.public LineSegment createLineSegment()
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.public void delete()
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 SpeciesReferenceGlyph.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 SpeciesReferenceGlyph.delete()
themselves.
delete
 in class GraphicalObject
public boolean getCurveExplicitlySet()
public java.lang.String getElementName()
getElementName
 in class GraphicalObject
public int getRole()
public java.lang.String getRoleString()
public java.lang.String getSpeciesGlyphId()
SpeciesGlyph
.public java.lang.String getSpeciesReferenceId()
public int getTypeCode()
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.
getTypeCode
 in class GraphicalObject
SBML_LAYOUT_SPECIESREFERENCEGLYPH
SpeciesReferenceGlyph.getElementName()
,
SBase.getPackageName()
public void initDefaults()
GraphicalObject
and sets role to
SPECIES_ROLE_UNDEFINED.initDefaults
 in class GraphicalObject
public boolean isSetCurve()
public boolean isSetRole()
public boolean isSetSpeciesGlyphId()
public boolean isSetSpeciesReferenceId()
public void renameSIdRefs(java.lang.String oldid, java.lang.String newid)
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.
renameSIdRefs
 in class SBase
oldid
- the old identifiernewid
- the new identifierpublic void setCurve(Curve curve)
public void setRole(int role)
public void setRole(java.lang.String role)
public void setSpeciesGlyphId(java.lang.String speciesGlyphId)
public void setSpeciesReferenceId(java.lang.String id)
public XMLNode toXML()
XMLNode
object from this.toXML
 in class GraphicalObject