public class CobraToFbcConverter 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 converter takes a model in &ldquofbc&rdquo Version 2 format and converts it to COBRA format.
CobraToFbcConverter
is enabled by creating a ConversionProperties
object
with the option 'convert cobra'
(literally that full string,
including the spaces), and passing this properties object to
SBMLDocument.convert(ConversionProperties)
. The converter
offers two options:
'checkCompatibility':
whether to check the SBML Level/Version
compatibility
'removeUnits':
whether to remove unit definitions
The use of all the converters follows a similar approach. First, one
creates a ConversionProperties
object and calls
ConversionProperties.addOption(ConversionOption)
on this object with one arguments: a text string that identifies the desired
converter. (The text string is specific to each converter consult the
documentation for a given converter to find out how it should be enabled.)
Next, for some converters, the caller can optionally set some
converter-specific properties using additional calls to
ConversionProperties.addOption(ConversionOption)
.
Many converters provide the ability to
configure their behavior to some extent this is realized through the use
of properties that offer different options. The default property values
for each converter can be interrogated using the method
SBMLConverter.getDefaultProperties()
on the converter class in question .
Finally, the caller should invoke the method
SBMLDocument.convert(ConversionProperties)
with the ConversionProperties
object as an argument.
The following code fragment illustrates an example using
SBMLReactionConverter
, which is invoked using the option string
'replaceReactions':
ConversionProperties
props = newConversionProperties
() if (props != null) { props.addOption('replaceReactions') } else { // Deal with error. }
In the case of SBMLReactionConverter
, there are no options to affect
its behavior, so the next step is simply to invoke the converter on
an SBMLDocument
object. Continuing the example code:
// Assume that the variable 'document' has been set to an SBMLDocument
object.
status = document.convert(config)
if (status != libsbml.LIBSBML_OPERATION_SUCCESS)
{
// Handle error somehow.
System.out.println('Error: conversion failed due to the following:')
document.printErrors()
}
Here is an example of using a converter that offers an option. The
following code invokes SBMLStripPackageConverter
to remove the
SBML Level 3 Layout package from a model. It sets the name
of the package to be removed by adding a value for the option named
'package'
defined by that converter:
ConversionProperties
config = newConversionProperties
() if (config != None) { config.addOption('stripPackage') config.addOption('package', 'layout') status = document.convert(config) if (status != LIBSBML_OPERATION_SUCCESS) { // Handle error somehow. System.out.println('Error: unable to strip theLayout
package') document.printErrors() } } else { // Handle error somehow. System.out.println('Error: unable to createConversionProperties
object') }
LibSBML provides a number of built-in converters by convention, their names end in Converter. The following are the built-in converters provided by libSBML 5.12.0 :
CobraToFbcConverter
CompFlatteningConverter
FbcToCobraConverter
FbcV1ToV2Converter
FbcV2ToV1Converter
SBMLFunctionDefinitionConverter
SBMLIdConverter
SBMLInferUnitsConverter
SBMLInitialAssignmentConverter
SBMLLevel1Version1Converter
SBMLLevelVersionConverter
SBMLLocalParameterConverter
SBMLReactionConverter
SBMLRuleConverter
SBMLStripPackageConverter
SBMLUnitsConverter
Constructor and Description |
---|
CobraToFbcConverter()
Creates a new
CobraToFbcConverter object. |
CobraToFbcConverter(CobraToFbcConverter orig)
Copy constructor creates a copy of an
CobraToFbcConverter
object. |
Modifier and Type | Method and Description |
---|---|
boolean |
checkCompatibility()
Returns
true if the option property to check Level and Version of the
source document ('checkCompatibility' ) is true. |
SBMLConverter |
cloneObject()
Creates and returns a deep copy of this
CobraToFbcConverter object. |
int |
convert()
Perform the conversion.
|
void |
delete()
Explicitly deletes the underlying native object.
|
ConversionProperties |
getDefaultProperties()
Returns the default properties of this converter.
|
boolean |
matchesProperties(ConversionProperties props)
Returns
true if this converter object's properties match the given
properties. |
getDocument, getName, getProperties, getTargetNamespaces, setDocument, setProperties
public CobraToFbcConverter()
CobraToFbcConverter
object.public CobraToFbcConverter(CobraToFbcConverter orig)
CobraToFbcConverter
object.
orig
- the CobraToFbcConverter
object to copy.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 CobraToFbcConverter.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 CobraToFbcConverter.delete()
themselves.
delete
 in class SBMLConverter
public SBMLConverter cloneObject()
CobraToFbcConverter
object.
cloneObject
 in class SBMLConverter
CobraToFbcConverter
.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 CobraToFbcConverter
object to find out if the object's
property values match the given ones. This method is also used by
SBMLConverterRegistry.getConverterFor(ConversionProperties)
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.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)
and
with the configuration options set by
SBMLConverter.setProperties(ConversionProperties)
.
convert
 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)
,
SBMLConverter.matchesProperties(ConversionProperties)
public boolean checkCompatibility()
true
if the option property to check Level and Version of the
source document ('checkCompatibility'
) is true.
true
if the option 'checkCompatibility'
has been set to
true
, false
otherwise.