public class SBMLConverter extends java.lang.Object
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.
The SBMLConverter
class is the base class for the various SBML
converters: classes of objects that transform or convert SBML documents.
These transformations can involve essentially anything that can be
written algorithmically examples include converting the units of
measurement in a model, or converting from one Level+Version combination
of SBML to another.
LibSBML provides a number of built-in converters, and applications can
create their own by subclassing SBMLConverter
and following the examples
of the existing converters. The following are the built-in converters
in libSBML 5.10.0
:
SBMLFunctionDefinitionConverter
SBMLInitialAssignmentConverter
SBMLLevelVersionConverter
SBMLRuleConverter
SBMLStripPackageConverter
SBMLUnitsConverter
Many converters provide the ability to configure their behavior to some
extent. This is realized through the use of properties that offer
different options. Two related classes implement these features:
ConversionProperties
and ConversionOptions. The default property values
for each converter can be interrogated using the method
SBMLConverter.getDefaultProperties()
on the converter class.
Constructor and Description |
---|
SBMLConverter()
Creates a new
SBMLConverter object. |
SBMLConverter(SBMLConverter c)
Copy constructor creates a copy of an
SBMLConverter object. |
Modifier and Type | Method and Description |
---|---|
SBMLConverter |
cloneObject()
Creates and returns a deep copy of this
SBMLConverter object. |
int |
convert()
Perform the conversion.
|
void |
delete()
Explicitly deletes the underlying native object.
|
ConversionProperties |
getDefaultProperties()
Returns the default properties of this converter.
|
SBMLDocument |
getDocument()
Returns the SBML document that is the subject of the conversions.
|
ConversionProperties |
getProperties()
Returns the current properties in effect for this converter.
|
SBMLNamespaces |
getTargetNamespaces()
Returns the target SBML namespaces of the currently set properties.
|
boolean |
matchesProperties(ConversionProperties props)
Predicate returning
true if this converter's properties matches a
given set of configuration properties. |
int |
setDocument(SBMLDocument doc)
Sets the current SBML document to the given
SBMLDocument object. |
int |
setProperties(ConversionProperties props)
Sets the configuration properties to be used by this converter.
|
void |
swigReleaseOwnership()   |
void |
swigTakeOwnership()   |
public SBMLConverter()
SBMLConverter
object.public SBMLConverter(SBMLConverter c)
SBMLConverter
object.
c
- the SBMLConverter
object to copy.
SBMLConstructorException
- Thrown if the argument orig
is null.
public SBMLConverter cloneObject()
SBMLConverter
object.
SBMLConverter
object.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)
.
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 SBMLConverter.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 SBMLConverter.delete()
themselves.
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. The run-time properties of the converter object can
be adjusted by using the method
SBMLConverter.setProperties(ConversionProperties props)
.
SBMLConverter.setProperties(ConversionProperties props)
,
SBMLConverter.matchesProperties(ConversionProperties props)
public SBMLDocument getDocument()
SBMLDocument
object.public ConversionProperties getProperties()
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 current properties for this converter in other words, the
settings in effect at this moment. To change the property values, you
can use SBMLConverter.setProperties(ConversionProperties props)
.
SBMLConverter.setProperties(ConversionProperties props)
,
SBMLConverter.matchesProperties(ConversionProperties props)
public SBMLNamespaces getTargetNamespaces()
SBML namespaces are used by libSBML to express the Level+Version of
the SBML document (and, possibly, any SBML Level 3 packages in
use). Some converters' behavior is affected by the SBML namespace
configured in the converter. For example, the actions of
SBMLLevelVersionConverter
, the converter for converting SBML documents
from one Level+Version combination to another, are fundamentally
dependent on the SBML namespaces being targeted.
SBMLNamespaces
object that describes the SBML namespaces
in effect.public boolean matchesProperties(ConversionProperties props)
true
if this converter's properties matches a
given set of configuration properties.
props
- the configuration properties to match.
true
if this converter's properties match, false
otherwise.public int setDocument(SBMLDocument doc)
SBMLDocument
object.
doc
- the document to use for this conversion.
SBMLConverter
being used, but the default method can return the
following values:
doc
is 'const', it is immediately cast
to a non-const version, which is then usually changed by the
converter upon a successful conversion. This function is here
solely to preserve backwards compatibility.
public int setProperties(ConversionProperties props)
A given converter exposes one or more properties that can be adjusted in order to influence the behavior of the converter. This method sets the current properties for this converter.
props
- the ConversionProperties
object defining the properties
to set.
SBMLConverter
being used, but the default method can return the
following values:
SBMLConverter.getProperties()
,
SBMLConverter.matchesProperties(ConversionProperties props)
public void swigReleaseOwnership()
public void swigTakeOwnership()