public class ListOfQualitativeSpecies extends ListOf
QualitativeSpecies
objects.
The ListOfQualitativeSpecies
is a container for the QualitativeSpecies
elements of a Model
.
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 |
---|
ListOfQualitativeSpecies()
Creates a new
ListOfQualitativeSpecies with the given level, version, and package version. |
ListOfQualitativeSpecies(long level)
Creates a new
ListOfQualitativeSpecies with the given level, version, and package version. |
ListOfQualitativeSpecies(long level,
long version)
Creates a new
ListOfQualitativeSpecies with the given level, version, and package version. |
ListOfQualitativeSpecies(long level,
long version,
long pkgVersion)
Creates a new
ListOfQualitativeSpecies with the given level, version, and package version. |
ListOfQualitativeSpecies(QualPkgNamespaces qualns)
Creates a new
ListOfQualitativeSpecies with the given QualPkgNamespaces object. |
Modifier and Type | Method and Description |
---|---|
ListOfQualitativeSpecies |
cloneObject()
Creates and returns a deep copy of this
ListOfQualitativeSpecies object. |
void |
delete()
Explicitly deletes the underlying native object.
|
SBase |
get(long n)
Get a
QualitativeSpecies from the ListOfQualitativeSpecies . |
QualitativeSpecies |
get(String sid)
Get a
QualitativeSpecies from the ListOfQualitativeSpecies
based on its identifier. |
String |
getElementName()
Returns the XML name of this object.
|
int |
getItemTypeCode()
Returns the libSBML type code for the SBML objects
contained in this
ListOf object. |
SBase |
remove(long n)
Removes the nth
QualitativeSpecies from this ListOfQualitativeSpecies
and returns a pointer to it. |
QualitativeSpecies |
remove(String sid)
Removes the
QualitativeSpecies from this ListOfQualitativeSpecies with the given identifier
and returns a pointer to it. |
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 ListOfQualitativeSpecies(long level, long version, long pkgVersion) throws SBMLConstructorException
ListOfQualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
version
- a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
SBMLConstructorException
public ListOfQualitativeSpecies(long level, long version) throws SBMLConstructorException
ListOfQualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
version
- a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
SBMLConstructorException
public ListOfQualitativeSpecies(long level) throws SBMLConstructorException
ListOfQualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
version
- a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
SBMLConstructorException
public ListOfQualitativeSpecies() throws SBMLConstructorException
ListOfQualitativeSpecies
with the given level, version, and package version.
level
- a long integer, the SBML Level to assign to this ListOfQualitativeSpecies
version
- a long integer, the SBML Version to assign to this ListOfQualitativeSpecies
pkgVersion
- a long integer, the SBML Qual Version to assign to this ListOfQualitativeSpecies
SBMLConstructorException
public ListOfQualitativeSpecies(QualPkgNamespaces qualns) throws SBMLConstructorException
ListOfQualitativeSpecies
with the given QualPkgNamespaces
object.
qualns
- the QualPkgNamespaces
objectSBMLConstructorException
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 ListOfQualitativeSpecies.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 ListOfQualitativeSpecies.delete()
themselves.
public ListOfQualitativeSpecies cloneObject()
ListOfQualitativeSpecies
object.
cloneObject
 in class ListOf
ListOfQualitativeSpecies
object.public SBase get(long n)
QualitativeSpecies
from the ListOfQualitativeSpecies
.
get
 in class ListOf
n
- the index number of the QualitativeSpecies
to get.
QualitativeSpecies
in this ListOfQualitativeSpecies
.
ListOf.size()
public QualitativeSpecies get(String sid)
QualitativeSpecies
from the ListOfQualitativeSpecies
based on its identifier.
sid
- a string representing the identifier
of the QualitativeSpecies
to get.
QualitativeSpecies
in this ListOfQualitativeSpecies
with the given id or null if no such
QualitativeSpecies
exists.
*
,
ListOf.size()
public SBase remove(long n)
QualitativeSpecies
from this ListOfQualitativeSpecies
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 QualitativeSpecies
to remove.
ListOf.size()
public QualitativeSpecies remove(String sid)
QualitativeSpecies
from this ListOfQualitativeSpecies
with the given identifier
and returns a pointer to it.
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 QualitativeSpecies
to remove.
QualitativeSpecies
removed. As mentioned above, the caller owns the
returned item.public String getElementName()
getElementName
 in class ListOf
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_QUAL_QUALITATIVE_SPECIES
(default).
ListOfQualitativeSpecies.getElementName()
,
SBase.getPackageName()