public class ListOfSpecies extends ListOf
The various ListOf___ classes in SBML are merely containers used for
organizing the main components of an SBML model. All are derived from
the abstract class SBase
, and inherit the various attributes and
subelements of SBase
, such as 'metaid' as and 'annotation'. The
ListOf___ classes do not add any attributes of their own.
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. 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
ListOf
Classname, 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 |
---|
ListOfSpecies(long level,
long version)
Creates a new
ListOfSpecies object. |
ListOfSpecies(SBMLNamespaces sbmlns)
Creates a new
ListOfSpecies object. |
Modifier and Type | Method and Description |
---|---|
ListOfSpecies |
cloneObject()
Creates and returns a deep copy of this ListOfSpeciess instance.
|
void |
delete()
Explicitly deletes the underlying native object.
|
Species |
get(long n)
Get a
Species from the ListOfSpecies . |
Species |
get(String sid)
Get a
Species from the ListOfSpecies
based on its identifier. |
String |
getElementName()
Returns the XML element name of this object.
|
int |
getItemTypeCode()
|
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
Species |
remove(long n)
Removes the nth item from this ListOfSpeciess items and returns a pointer to
it.
|
Species |
remove(String sid)
Removes item in this ListOfSpeciess items with the given identifier.
|
append, appendAndOwn, appendFrom, clear, clear, getElementByMetaId, getElementBySId, insert, insertAndOwn, removeFromParentAndDelete, size
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, 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, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, unsetAnnotation, unsetCVTerms, unsetId, unsetMetaId, unsetModelHistory, unsetName, unsetNotes, unsetSBOTerm
public ListOfSpecies(long level, long version) throws SBMLConstructorException
ListOfSpecies
object.
The object is constructed such that it is valid for the given SBML Level and Version combination.
level
- the SBML Level
version
- the Version within the SBML LevelSBMLConstructorException
public ListOfSpecies(SBMLNamespaces sbmlns) throws SBMLConstructorException
ListOfSpecies
object.
The object is constructed such that it is valid for the SBML Level and
Version combination determined by the SBMLNamespaces
object in
sbmlns
.
sbmlns
- an SBMLNamespaces
object that is used to determine the
characteristics of the ListOfSpecies
object to be created.SBMLConstructorException
public ListOfSpecies cloneObject()
cloneObject
 in class ListOf
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 ListOfSpecies.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 ListOfSpecies.delete()
themselves.
public Species get(long n)
Species
from the ListOfSpecies
.
get
 in class ListOf
n
- the index number of the Species
to get.
Species
in this ListOfSpecies
.
ListOf.size()
public Species get(String sid)
Species
from the ListOfSpecies
based on its identifier.
sid
- a string representing the identifier
of the Species
to get.
Species
in this ListOfSpecies
with the given sid
or null
if no such
Species
exists.
ListOfSpecies.get(long n)
,
ListOf.size()
public String getElementName()
For ListOfSpeciess, the XML element name is 'listOfSpeciess'.
getElementName
 in class ListOf
'listOfSpeciess'.
public int getItemTypeCode()
ListOf
(i.e., Species
objects, if the list is non-empty).
LibSBML attaches an identifying code to every
kind of SBML object. These are known as SBML type codes. In
other languages, the set of type codes is stored in an enumeration in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class libsbmlConstants
. The names of the type codes all begin with the
characters SBML_.
getItemTypeCode
 in class ListOf
ListOf
instance, or SBML_UNKNOWN
(default).
ListOfSpecies.getElementName()
public int getTypeCode()
LibSBML attaches an identifying code to every
kind of SBML object. These are known as SBML type codes. In
other languages, the set of type codes is stored in an enumeration in
the Java language interface for libSBML, the type codes are defined as
static integer constants in the interface class libsbmlConstants
. The names of the type codes all begin with the
characters SBML_.
getTypeCode
 in class ListOf
SBML_UNKNOWN
(default).
ListOfSpecies.getElementName()
public Species remove(long n)
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 Species remove(String sid)
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