public class SpeciesReferenceGlyph extends GraphicalObject
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)
Constructor.
|
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 . |
void |
connectToChild()   |
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_INVALID . |
boolean |
isSetCurve()
Returns
true if the curve consists of one or more segments. |
boolean |
isSetRole()
Returns
true of role is different from SPECIES_ROLE_INVALID . |
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)
Replaces all uses of a given
SIdRef type attribute value with another
value. |
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, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getName, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetName, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setIdAttribute, setMetaId, setModelHistory, setName, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
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_INVALID
.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.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_INVALID
.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.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_INVALID
.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.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_INVALID
.
level
- the SBML Level.version
- the Version within the SBML Level.pkgVersion
- the version of the package.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.public SpeciesReferenceGlyph(LayoutPkgNamespaces layoutns) throws SBMLConstructorException
The package namespaces object used in this constructor is derived from a
SBMLNamespaces
object, which encapsulates SBML Level/Version/namespaces
information. It is used to communicate the SBML Level, Version, and
package version and name information used in addition to SBML Level 3 Core. A
common approach to using libSBML's SBMLNamespaces
facilities is to create an
package namespace object somewhere in a program once, then hand that object
as needed to object constructors of that package that accept it as and
argument, such as this one.
layoutns
- the LayoutPkgNamespaces
object.
SBMLConstructorException
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute. For packages, this means that the
parent object to which this package element is being added must have
been created with the package namespace, or that the package namespace
was added to it, even if that parent is not a package object itself.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(XMLNode node, long l2version) throws SBMLConstructorException
SpeciesReferenceGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesReferenceGlyph(XMLNode node) throws SBMLConstructorException
SpeciesReferenceGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesReferenceGlyph(SpeciesReferenceGlyph source) throws SBMLConstructorException
source
- the instance to copy.SBMLConstructorException
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 java.lang.String getSpeciesGlyphId()
SpeciesGlyph
.public void setSpeciesGlyphId(java.lang.String speciesGlyphId)
public java.lang.String getSpeciesReferenceId()
public void setSpeciesReferenceId(java.lang.String id)
public java.lang.String getRoleString()
public int getRole()
public void setRole(java.lang.String role)
public void setRole(int role)
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 SIdRef
in 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.
renameSIdRefs
 in class SBase
oldid
- the old identifier.newid
- the new identifier.public void setCurve(Curve curve)
public boolean isSetCurve()
true
if the curve consists of one or more segments.public boolean getCurveExplicitlySet()
public boolean isSetSpeciesGlyphId()
true
if the id of the associated species glyph is not the
empty string.public boolean isSetSpeciesReferenceId()
true
if the id of the associated species reference is not the
empty string.public boolean isSetRole()
true
of role is different from SPECIES_ROLE_INVALID
.public void initDefaults()
GraphicalObject
and sets role to
SPECIES_ROLE_INVALID
.initDefaults
 in class GraphicalObject
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 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 java.lang.String getElementName()
getElementName
 in class GraphicalObject
public SpeciesReferenceGlyph cloneObject()
SpeciesReferenceGlyph
.
cloneObject
 in class GraphicalObject
SpeciesReferenceGlyph
.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 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
method on the object.
SBase.getPackageName()
getTypeCode
 in class GraphicalObject
SBML_LAYOUT_SPECIESREFERENCEGLYPH
.
SpeciesReferenceGlyph.getElementName()
,
SBase.getPackageName()
public XMLNode toXML()
XMLNode
object from this.toXML
 in class GraphicalObject
public void connectToChild()
connectToChild
 in class GraphicalObject