public class ListOfReactionGlyphs extends ListOf
ReactionGlyph
objects.
The ListOfReactionGlyphs
is a container for the ReactionGlyph
elements of a Layout
.
The various ListOf___ classes in SBML
are merely containers used for organizing the main components of an SBML
model. In libSBML's implementation, ListOf___
classes are derived from the
intermediate utility class ListOf
, which
is not defined by the SBML specifications but serves as a useful
programmatic construct. ListOf
is itself is in turn derived from SBase
,
which provides all of the various ListOf___
classes with common features
defined by the SBML specification, such as 'metaid' attributes and
annotations.
The relationship between the lists and the rest of an SBML model is illustrated by the following (for SBML Level 2 Version 4):
Readers may wonder about the motivations for using the ListOf___
containers in SBML. A simpler approach in XML might be to place the
components all directly at the top level of the model definition. The
choice made in SBML is to group them within XML elements named after
ListOfClassname, in part because it helps organize the
components. More importantly, the fact that the container classes are
derived from SBase
means that software tools can add information about
the lists themselves into each list container's 'annotation'.
Constructor and Description |
---|
ListOfReactionGlyphs()
Ctor.
|
ListOfReactionGlyphs(LayoutPkgNamespaces layoutns)
Ctor.
|
ListOfReactionGlyphs(long level)
Ctor.
|
ListOfReactionGlyphs(long level,
long version)
Ctor.
|
ListOfReactionGlyphs(long level,
long version,
long pkgVersion)
Ctor.
|
Modifier and Type | Method and Description |
---|---|
ListOfReactionGlyphs |
cloneObject()
Creates and returns a deep copy of this
ListOfReactionGlyphs . |
void |
delete()
Explicitly deletes the underlying native object.
|
ReactionGlyph |
get(long n)
Get a
ReactionGlyph from the ListOfReactionGlyphs . |
ReactionGlyph |
get(String sid)
Get a
ReactionGlyph from the ListOfReactionGlyphs
based on its identifier. |
String |
getElementName()
Returns the XML element name of
this SBML object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the SBML objects
contained in this
ListOf object. |
ReactionGlyph |
remove(long n)
Removes the nth item from this
ListOfReactionGlyphs items and returns a pointer to
it. |
ReactionGlyph |
remove(String sid)
Removes item in this
ListOfReactionGlyphs items with the given identifier. |
XMLNode |
toXML()
Creates an
XMLNode object from this. |
append, appendAndOwn, appendFrom, clear, clear, connectToChild, getElementByMetaId, getElementBySId, getTypeCode, insert, insertAndOwn, removeFromParentAndDelete, size
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm, unsetUserData
public ListOfReactionGlyphs(long level, long version, long pkgVersion) throws SBMLConstructorException
SBMLConstructorException
public ListOfReactionGlyphs(long level, long version) throws SBMLConstructorException
SBMLConstructorException
public ListOfReactionGlyphs(long level) throws SBMLConstructorException
SBMLConstructorException
public ListOfReactionGlyphs() throws SBMLConstructorException
SBMLConstructorException
public ListOfReactionGlyphs(LayoutPkgNamespaces layoutns) throws SBMLConstructorException
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 ListOfReactionGlyphs.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 ListOfReactionGlyphs.delete()
themselves.
public ListOfReactionGlyphs cloneObject()
ListOfReactionGlyphs
.
cloneObject
 in class ListOf
ListOfReactionGlyphs
.public int getItemTypeCode()
ListOf
object.
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.
getItemTypeCode
 in class ListOf
SBML_LAYOUT_REACTIONGLYPH
(default).
ListOfReactionGlyphs.getElementName()
,
SBase.getPackageName()
public String getElementName()
getElementName
 in class ListOf
public ReactionGlyph get(long n)
ReactionGlyph
from the ListOfReactionGlyphs
.
get
 in class ListOf
n
- the index number of the ReactionGlyph
to get.
ReactionGlyph
in this ListOfReactionGlyphs
.
ListOf.size()
public ReactionGlyph get(String sid)
ReactionGlyph
from the ListOfReactionGlyphs
based on its identifier.
sid
- a string representing the identifier
of the ReactionGlyph
to get.
ReactionGlyph
in this ListOfReactionGlyphs
with the given sid
or null
if no such
ReactionGlyph
exists.
ListOfReactionGlyphs.get(long n)
,
ListOf.size()
public ReactionGlyph remove(long n)
ListOfReactionGlyphs
items and returns a pointer to
it.
The caller owns the returned item and is responsible for deleting it.
remove
 in class ListOf
n
- the index of the item to remove
ListOf.size()
public ReactionGlyph remove(String sid)
ListOfReactionGlyphs
items with the given identifier.
The caller owns the returned item and is responsible for deleting it.
If none of the items in this list have the identifier sid
, then
null
is returned.
sid
- the identifier of the item to remove