public class SpeciesGlyph extends GraphicalObject
In addition to the attributes it inherits from GraphicalObject
, the
SpeciesGlyph
object has an optional 'species' attribute.
Constructor and Description |
---|
SpeciesGlyph()
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string. |
SpeciesGlyph(LayoutPkgNamespaces layoutns)
Constructor.
|
SpeciesGlyph(LayoutPkgNamespaces layoutns,
java.lang.String id)
Creates a new
SpeciesGlyph with the given id . |
SpeciesGlyph(LayoutPkgNamespaces layoutns,
java.lang.String id,
java.lang.String speciesId)
Creates a new
SpeciesGlyph with the given id and the id of the
associated species object set to the second argument. |
SpeciesGlyph(long level)
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string. |
SpeciesGlyph(long level,
long version)
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string. |
SpeciesGlyph(long level,
long version,
long pkgVersion)
Creates a new
SpeciesGlyph with the given SBML level, version, and package version
and the id of the associated species set to the empty string. |
SpeciesGlyph(SpeciesGlyph source)
Copy constructor.
|
SpeciesGlyph(XMLNode node)
Creates a new
SpeciesGlyph from the given XMLNode |
SpeciesGlyph(XMLNode node,
long l2version)
Creates a new
SpeciesGlyph from the given XMLNode |
Modifier and Type | Method and Description |
---|---|
SpeciesGlyph |
cloneObject()
Creates and returns a deep copy of this
SpeciesGlyph . |
void |
delete()
Explicitly deletes the underlying native object.
|
java.lang.String |
getElementName()
Returns the XML element name of
this SBML object.
|
java.lang.String |
getSpeciesId()
Returns the id of the associated species object.
|
int |
getTypeCode()
Returns the libSBML type code of this object instance.
|
void |
initDefaults()
Calls initDefaults from
GraphicalObject . |
boolean |
isSetSpeciesId()
Returns
true if the id of the associated species object 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 |
setSpeciesId(java.lang.String id)
Sets the id of the associated species object.
|
XMLNode |
toXML()
Creates an
XMLNode object from this. |
connectToChild, 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, getObjectVersion, 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 SpeciesGlyph(long level, long version, long pkgVersion) throws SBMLConstructorException
SpeciesGlyph
with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
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 SpeciesGlyph(long level, long version) throws SBMLConstructorException
SpeciesGlyph
with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
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 SpeciesGlyph(long level) throws SBMLConstructorException
SpeciesGlyph
with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
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 SpeciesGlyph() throws SBMLConstructorException
SpeciesGlyph
with the given SBML level, version, and package version
and the id of the associated species set to the empty string.
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 SpeciesGlyph(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 SpeciesGlyph(LayoutPkgNamespaces layoutns, java.lang.String id) throws SBMLConstructorException
SBMLConstructorException
public SpeciesGlyph(LayoutPkgNamespaces layoutns, java.lang.String id, java.lang.String speciesId) throws SBMLConstructorException
SpeciesGlyph
with the given id
and the id of the
associated species object set to the second argument.
(FOR BACKWARD COMPATIBILITY)
SBMLConstructorException
public SpeciesGlyph(XMLNode node, long l2version) throws SBMLConstructorException
SpeciesGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesGlyph(XMLNode node) throws SBMLConstructorException
SpeciesGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesGlyph(SpeciesGlyph 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 SpeciesGlyph.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 SpeciesGlyph.delete()
themselves.
delete
 in class GraphicalObject
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 java.lang.String getSpeciesId()
public void setSpeciesId(java.lang.String id)
public boolean isSetSpeciesId()
true
if the id of the associated species object is not the
empty string.public void initDefaults()
GraphicalObject
.initDefaults
 in class GraphicalObject
public java.lang.String getElementName()
getElementName
 in class GraphicalObject
public SpeciesGlyph cloneObject()
SpeciesGlyph
.
cloneObject
 in class GraphicalObject
SpeciesGlyph
.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 getPackageName()
method on the object.
getTypeCode
 in class GraphicalObject
SBML_LAYOUT_SPECIESGLYPH
.
SpeciesGlyph.getElementName()
,
SBase.getPackageName()
public XMLNode toXML()
XMLNode
object from this.toXML
 in class GraphicalObject