public class SBMLInitialAssignmentConverter extends SBMLConverter
This class of objects is defined by libSBML only and has no direct equivalent in terms of SBML components. It is a class used in the implementation of extra functionality provided by libSBML.
This is an SBML converter for replacing InitialAssignment
objects
(when possible) by setting the initial value attributes on the model
objects being assigned. In other words, for every object that is
the target of an initial assignment in the model, it evaluates the
mathematical expression of the assignment to get a numerical value,
and then sets the corresponding attribute of the object to the
value. The effects for different kinds of SBML components are
as follows:
Component | Effect |
---|---|
Compartment | Sets the value of the size attribute. |
Species | Sets the value of either the initialAmount
or the initialConcentration attributes, depending
on the value of the Species object's
hasOnlySubstanceUnits attribute. |
Parameter | Sets the value of the value attribute. |
SpeciesReference | Sets the value of the stoichiometry attribute
in the Reaction object where the SpeciesReference object appears. |
Constructor and Description |
---|
SBMLInitialAssignmentConverter()
Creates a new
SBMLInitialAssignmentConverter object. |
SBMLInitialAssignmentConverter(SBMLInitialAssignmentConverter obj)
Copy constructor creates a copy of an
SBMLInitialAssignmentConverter
object. |
Modifier and Type | Method and Description |
---|---|
SBMLConverter |
cloneObject()
Creates and returns a deep copy of this
SBMLInitialAssignmentConverter
object. |
int |
convert()
Perform the conversion.
|
void |
delete()
Explicitly deletes the underlying native object.
|
ConversionProperties |
getDefaultProperties()
Returns the default properties of this converter.
|
static void |
init()   |
boolean |
matchesProperties(ConversionProperties props)
Returns
true if this converter object's properties match the given
properties. |
getDocument, getProperties, getTargetNamespaces, setDocument, setProperties, swigReleaseOwnership, swigTakeOwnership
public SBMLInitialAssignmentConverter()
SBMLInitialAssignmentConverter
object.public SBMLInitialAssignmentConverter(SBMLInitialAssignmentConverter obj)
SBMLInitialAssignmentConverter
object.
obj
- the SBMLInitialAssignmentConverter
object to copy.public SBMLConverter cloneObject()
SBMLInitialAssignmentConverter
object.
cloneObject
 in class SBMLConverter
public int convert()
This method causes the converter to do the actual conversion work,
that is, to convert the SBMLDocument
object set by
SBMLConverter.setDocument(SBMLDocument doc)
and
with the configuration options set by
SBMLConverter.setProperties(ConversionProperties props)
.
convert
 in class SBMLConverter
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 SBMLInitialAssignmentConverter.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 SBMLInitialAssignmentConverter.delete()
themselves.
delete
 in class SBMLConverter
public ConversionProperties getDefaultProperties()
A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method returns the default property settings for this converter. It is meant to be called in order to discover all the settings for the converter object.
getDefaultProperties
 in class SBMLConverter
ConversionProperties
object describing the default properties
for this converter.SBMLConverter.setProperties(ConversionProperties props)
,
SBMLConverter.matchesProperties(ConversionProperties props)
public static void init()
public boolean matchesProperties(ConversionProperties props)
true
if this converter object's properties match the given
properties.
A typical use of this method involves creating a ConversionProperties
object, setting the options desired, and then calling this method on
an SBMLInitialAssignmentConverter
object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry.getConverterFor(ConversionProperties props)
to search across all registered converters for one matching particular
properties.
matchesProperties
 in class SBMLConverter
props
- the properties to match.
true
if this converter's properties match, false
otherwise.