public class Cellontro2Sbml extends java.lang.Object implements ICellontro2Sbml
Cellontro2Sbml transforms Xholon runtime models into SBML Level 2 files. The exported file contains SBML compartments, species, and reactions.
TODO Do a better job of exporting partial Cellontro models to SBML. For partial models, create an external compartment that's the actual root compartment. Any species references that are outside the subtree being exported will have this as their compartment. To implement this, possibly store species in a temporary data structure first, so that additional external species can be added while processing the reactions.
TODO Be able to export the kinetics, in addition to the structure.
TODO [February 19, 2007] Be able to export models that only implement IXholon and IXholonClass, rather than requiring that they implement the interface extensions IBioXholon and IBioXholonClass. The following incompatible methods are used in Cellontro2Sbml: getPheneVal() isReversible() getNumReactants() getNumProducts() getNumModifiers() IBioXholonClass.SIZE_ARRAY_GENEVAL
Constructor and Description |
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Cellontro2Sbml()
Constructor.
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Cellontro2Sbml(java.lang.String sbmlFileName,
java.lang.String modelName,
IXholon root)
Constructor.
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Modifier and Type | Method and Description |
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boolean |
initialize(java.lang.String sbmlFileName,
java.lang.String modelName,
IXholon root)
Initialize.
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void |
writeAll()
Write out all parts of the SBML file.
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public Cellontro2Sbml()
public Cellontro2Sbml(java.lang.String sbmlFileName, java.lang.String modelName, IXholon root)
sbmlFileName
- Name of the output SBML XML file.modelName
- Name of the model.root
- Root of the tree that will be written out.public boolean initialize(java.lang.String sbmlFileName, java.lang.String modelName, IXholon root)
ICellontro2Sbml
initialize
in interface ICellontro2Sbml
sbmlFileName
- Name of the output SBML file.modelName
- Name of the model.root
- Root of the composite structure hierarchy to write out.public void writeAll()
ICellontro2Sbml
writeAll
in interface ICellontro2Sbml