jp.sbi.celldesigner.plugin

Class PluginModelBuilder

java.lang.Object

jp.sbi.celldesigner.plugin.PluginModelBuilder

public class PluginModelBuilder
extends java.lang.Object

Author:

The Systems Biology Institute

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	ANNOTATION

Constructor Summary

Constructors

Constructor and Description
PluginModelBuilder(jp.sbi.celldesigner.SBModel value)

Method Summary

Modifier and Type	Method and Description
PluginAntiSenseRNA	convertToPluginAntiSenseRNA(jp.sbi.celldesigner.sbmlExtension.AntiSenseRNA target) Converts AntiSenseRNA to PluginAntiSenseRNA
PluginCompartment	convertToPluginCompartment(org.sbml.libsbml.Compartment compartment, jp.sbi.celldesigner.sbmlExtension.CompartmentAnnotation annotation) Converts Compartment to PluginCompartment
PluginGene	convertToPluginGene(jp.sbi.celldesigner.sbmlExtension.Gene target) Converts Gene to PluginGene
PluginKineticLaw	convertToPluginKineticLaw(org.sbml.libsbml.KineticLaw law, PluginReaction parent) Converts KineticLaw to PluginKineticLaw
PluginModel	convertToPluginModel(org.sbml.libsbml.Model model) Converts Model to PluginModel
PluginModel	convertToPluginModel(org.sbml.libsbml.Model model, jp.sbi.celldesigner.SBModel sbModel) Converts Model to PluginModel
PluginReaction	convertToPluginReaction(org.sbml.libsbml.Reaction reaction, jp.sbi.celldesigner.sbmlExtension.ReactionAnnotation annotation) Converts Reaction to PluginReaction
PluginRNA	convertToPluginRNA(jp.sbi.celldesigner.sbmlExtension.RNA target) Converts RNA to PluginRNA
PluginSBase	convertToPluginSBase(org.sbml.libsbml.SBase sbase) Converts SBase to PluginSBase
PluginSpecies	convertToPluginSpecies(org.sbml.libsbml.Species species, jp.sbi.celldesigner.sbmlExtension.SpeciesAnnotation annotation) Converts Species to PluginSpecies
PluginSpeciesAlias	convertToPluginSpeciesAlias(jp.sbi.celldesigner.SpeciesAlias alias, PluginSpecies parent) Convers SpeciesAlias to PluginSpeciesAlias

Methods inherited from class java.lang.Object

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

Field Detail

ANNOTATION

public static final java.lang.String ANNOTATION

See Also:

Constant Field Values

Constructor Detail

PluginModelBuilder

public PluginModelBuilder(jp.sbi.celldesigner.SBModel value)

Method Detail

convertToPluginSpeciesAlias

public PluginSpeciesAlias convertToPluginSpeciesAlias(jp.sbi.celldesigner.SpeciesAlias alias,
                                                      PluginSpecies parent)

Convers SpeciesAlias to PluginSpeciesAlias

Parameters:

alias - SpeciesAlias

parent - PluginSpecies

Returns:

PluginSpeciesAlias

convertToPluginSBase

public PluginSBase convertToPluginSBase(org.sbml.libsbml.SBase sbase)

Converts SBase to PluginSBase

Parameters:

sbase - SBase

Returns:

converted PluginSBase

convertToPluginModel

public PluginModel convertToPluginModel(org.sbml.libsbml.Model model)

Converts Model to PluginModel

Parameters:

model - Model

Returns:

converted PluginModel

convertToPluginModel

public PluginModel convertToPluginModel(org.sbml.libsbml.Model model,
                                        jp.sbi.celldesigner.SBModel sbModel)

Converts Model to PluginModel

Parameters:

model - Model

sbModel - SBModel

Returns:

converted PluginModel

convertToPluginGene

public PluginGene convertToPluginGene(jp.sbi.celldesigner.sbmlExtension.Gene target)

Converts Gene to PluginGene

Parameters:

target - Gene

Returns:

converted PluginGene

convertToPluginAntiSenseRNA

public PluginAntiSenseRNA convertToPluginAntiSenseRNA(jp.sbi.celldesigner.sbmlExtension.AntiSenseRNA target)

Converts AntiSenseRNA to PluginAntiSenseRNA

Parameters:

target - AntiSenseRNA

Returns:

converted PluginAntiSenseRNA

convertToPluginRNA

public PluginRNA convertToPluginRNA(jp.sbi.celldesigner.sbmlExtension.RNA target)

Converts RNA to PluginRNA

Parameters:

target - RNA

Returns:

converted PluginRNA

convertToPluginSpecies

public PluginSpecies convertToPluginSpecies(org.sbml.libsbml.Species species,
                                            jp.sbi.celldesigner.sbmlExtension.SpeciesAnnotation annotation)

Converts Species to PluginSpecies

Parameters:

species - Species

annotation - SpeciesAnnotation

Returns:

converted PluginSpecies

convertToPluginReaction

public PluginReaction convertToPluginReaction(org.sbml.libsbml.Reaction reaction,
                                              jp.sbi.celldesigner.sbmlExtension.ReactionAnnotation annotation)

Converts Reaction to PluginReaction

Parameters:

reaction - Reaction

annotation - ReactionAnnotation

Returns:

converted PluginReaction

convertToPluginCompartment

public PluginCompartment convertToPluginCompartment(org.sbml.libsbml.Compartment compartment,
                                                    jp.sbi.celldesigner.sbmlExtension.CompartmentAnnotation annotation)

Converts Compartment to PluginCompartment

Parameters:

compartment - Compartment

annotation - CompartmentAnnotation

Returns:

converted PluginCompartment

convertToPluginKineticLaw

public PluginKineticLaw convertToPluginKineticLaw(org.sbml.libsbml.KineticLaw law,
                                                  PluginReaction parent)

Converts KineticLaw to PluginKineticLaw

Parameters:

law - KineticLaw

parent - PluginReaction

Returns:

converted PluginKineticLaw