public class SpeciesGlyph extends GraphicalObject
Species
in the
&ldquolayout&rdquo package.
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)
Ctor.
|
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)
Renames all the
SIdRef attributes on this element, including any
found in MathML content (if such exists). |
void |
setSpeciesId(java.lang.String id)
Sets the id of the associated species object.
|
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 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.SBMLConstructorException
public SpeciesGlyph(LayoutPkgNamespaces layoutns) throws SBMLConstructorException
SBMLConstructorException
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(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.SBMLConstructorException
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.SBMLConstructorException
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.SBMLConstructorException
public SpeciesGlyph(SpeciesGlyph source) throws SBMLConstructorException
SBMLConstructorException
public SpeciesGlyph(XMLNode node) throws SBMLConstructorException
SpeciesGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesGlyph(XMLNode node, long l2version) throws SBMLConstructorException
SpeciesGlyph
from the given XMLNode
SBMLConstructorException
public SpeciesGlyph cloneObject()
SpeciesGlyph
.
cloneObject
 in class GraphicalObject
SpeciesGlyph
.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 java.lang.String getElementName()
getElementName
 in class GraphicalObject
public java.lang.String getSpeciesId()
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_SPECIESGLYPH
SpeciesGlyph.getElementName()
,
SBase.getPackageName()
public void initDefaults()
GraphicalObject
.initDefaults
 in class GraphicalObject
public boolean isSetSpeciesId()
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 setSpeciesId(java.lang.String id)
public XMLNode toXML()
XMLNode
object from this.toXML
 in class GraphicalObject