Constructor and Description |
---|
Layout()   |
Layout(Layout source)   |
Layout(LayoutPkgNamespaces layoutns)   |
Layout(LayoutPkgNamespaces layoutns,
String id,
Dimensions dimensions)   |
Layout(long level)   |
Layout(long level,
long version)   |
Layout(long level,
long version,
long pkgVersion)   |
Layout(XMLNode node)   |
Layout(XMLNode node,
long l2version)   |
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm
public Layout() throws SBMLConstructorException
SBMLConstructorException
public Layout(Layout source) throws SBMLConstructorException
SBMLConstructorException
public Layout(LayoutPkgNamespaces layoutns) throws SBMLConstructorException
SBMLConstructorException
public Layout(LayoutPkgNamespaces layoutns, String id, Dimensions dimensions) throws SBMLConstructorException
SBMLConstructorException
public Layout(long level) throws SBMLConstructorException
SBMLConstructorException
public Layout(long level, long version) throws SBMLConstructorException
SBMLConstructorException
public Layout(long level, long version, long pkgVersion) throws SBMLConstructorException
SBMLConstructorException
public Layout(XMLNode node) throws SBMLConstructorException
SBMLConstructorException
public Layout(XMLNode node, long l2version) throws SBMLConstructorException
SBMLConstructorException
public void addAdditionalGraphicalObject(GraphicalObject glyph)
public void addCompartmentGlyph(CompartmentGlyph glyph)
public void addGeneralGlyph(GeneralGlyph glyph)
public void addReactionGlyph(ReactionGlyph glyph)
public void addSpeciesGlyph(SpeciesGlyph glyph)
public void addTextGlyph(TextGlyph glyph)
public Layout cloneObject()
SBase
object.
cloneObject
 in class SBase
SBase
object.public GraphicalObject createAdditionalGraphicalObject()
public CompartmentGlyph createCompartmentGlyph()
public CubicBezier createCubicBezier()
public GeneralGlyph createGeneralGlyph()
public LineSegment createLineSegment()
public ReactionGlyph createReactionGlyph()
public SpeciesGlyph createSpeciesGlyph()
public SpeciesReferenceGlyph createSpeciesReferenceGlyph()
public TextGlyph createTextGlyph()
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 Layout.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 Layout.delete()
themselves.
public GraphicalObject getAdditionalGraphicalObject(long index)
public GraphicalObject getAdditionalGraphicalObject(String id)
public CompartmentGlyph getCompartmentGlyph(long index)
public CompartmentGlyph getCompartmentGlyph(String id)
public Dimensions getDimensions()
public String getElementName()
This is overridden by subclasses to return a string appropriate to the
SBML component. For example, Model
defines it as returning
'model'
, CompartmentType
defines it as returning 'compartmentType'
,
and so on.
getElementName
 in class SBase
public GeneralGlyph getGeneralGlyph(long index)
public GeneralGlyph getGeneralGlyph(String id)
public ListOfGraphicalObjects getListOfAdditionalGraphicalObjects()
public ListOfCompartmentGlyphs getListOfCompartmentGlyphs()
public ListOfReactionGlyphs getListOfReactionGlyphs()
public ListOfSpeciesGlyphs getListOfSpeciesGlyphs()
public ListOfTextGlyphs getListOfTextGlyphs()
public long getNumAdditionalGraphicalObjects()
public long getNumCompartmentGlyphs()
public long getNumGeneralGlyphs()
public long getNumReactionGlyphs()
public long getNumSpeciesGlyphs()
public long getNumTextGlyphs()
public ReactionGlyph getReactionGlyph(long index)
public ReactionGlyph getReactionGlyph(String id)
public SpeciesGlyph getSpeciesGlyph(long index)
public SpeciesGlyph getSpeciesGlyph(String id)
public TextGlyph getTextGlyph(long index)
public TextGlyph getTextGlyph(String id)
public int getTypeCode()
This method may return the type code of this SBML object, or it may
return SBML_UNKNOWN
. This
is because subclasses of SBase
are not required to implement this
method to return a type code. This method is meant primarily for the
LibSBML C interface, in which class and subclass information is not
readily available.
getTypeCode
 in class SBase
SBML_UNKNOWN
(the default).
Layout.getElementName()
,
SBase.getPackageName()
public void initDefaults()
public GraphicalObject removeAdditionalGraphicalObject(long index)
public GraphicalObject removeAdditionalGraphicalObject(String id)
public CompartmentGlyph removeCompartmentGlyph(long index)
public CompartmentGlyph removeCompartmentGlyph(String id)
public ReactionGlyph removeReactionGlyph(long index)
public ReactionGlyph removeReactionGlyph(String id)
public SpeciesGlyph removeSpeciesGlyph(long index)
public SpeciesGlyph removeSpeciesGlyph(String id)
public SpeciesReferenceGlyph removeSpeciesReferenceGlyph(String id)
public TextGlyph removeTextGlyph(long index)
public TextGlyph removeTextGlyph(String id)
public void setDimensions(Dimensions dimensions)
public int unsetId()
Most (but not all) objects in SBML include two common attributes: 'id'
and 'name'. The identifier given by an object's 'id' attribute value
is used to identify the object within the SBML model definition.
Other objects can refer to the component using this identifier. The
data type of 'id' is always either Sid
or
UnitSId
, depending on the object in question. Both
data types are defined as follows:
letter .= 'a'..'z','A'..'Z' digit .= '0'..'9' idChar .= letter | digit | '_' SId .= ( letter | '_' ) idChar*
The equality of SId
and UnitSId
type values
in SBML is determined by an exact character sequence match i.e.,
comparisons of these identifiers must be performed in a case-sensitive
manner. This applies to all uses of SId
and
UnitSId
.