Package org.sbml.jsbml.ext.comp.util

Class CompFlatteningConverter

java.lang.Object

org.sbml.jsbml.ext.comp.util.CompFlatteningConverter

public class CompFlatteningConverter
extends java.lang.Object

The CompFlatteningConverter object translates a hierarchical model defined with the SBML Level 3 Hierarchical Model Composition package into a 'flattened' version of the same model. This means the the hierarchical structure is dissolved and all objects are built into a single model that does no longer require the comp package.

Since:

1.0

Author:

Christoph Blessing

Constructor Summary

Constructors

Constructor	Description
CompFlatteningConverter()

Method Summary

Modifier and Type	Method	Description
SBMLDocument	flatten(SBMLDocument document)	Public method to call on a CompflatteningConverter object.
static SBMLDocument	internaliseExternalModelDefinitions(SBMLDocument document)	Collects any ExternalModelDefinitions that might be contained in the given SBMLDocument and transfers them into local ModelDefinitions (recursively, if the external models themselves include external models; in that case, renaming may occur).

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CompFlatteningConverter

public CompFlatteningConverter()

Method Detail

flatten

public SBMLDocument flatten(SBMLDocument document)

Public method to call on a CompflatteningConverter object. Takes a SBML Document and flattens the models of the comp plugin. Returns the SBML Document with a flattend model.

Parameters:

document - SBML Document to flatten

Returns:

SBML Document with flattened model

internaliseExternalModelDefinitions

public static SBMLDocument internaliseExternalModelDefinitions(SBMLDocument document)
                                                        throws java.lang.Exception

Collects any ExternalModelDefinitions that might be contained in the given SBMLDocument and transfers them into local ModelDefinitions (recursively, if the external models themselves include external models; in that case, renaming may occur).
The given SBMLDocument need have its locationURI set!
Opaque URIs (URNs) will not be dealt with in any defined way, resolve them first (make sure all relevant externalModelDefinitions' source-attributes are URLs or relative paths)

Parameters:

document - an SBMLDocument, which might, but need not, contain ExternalModelDefinitions to be transferred into its local ModelDefinitions. The locationURI of the given document need be set (SBMLDocument.isSetLocationURI())!

Returns:

a new SBMLDocument without ExternalModelDefinitions, but containing the same information as the given one

Throws:

java.lang.Exception - if given document's locationURI is not set. Set it with SBMLDocument.setLocationURI(java.lang.String)