jp.sbi.celldesigner.plugin

Class PluginSBaseConverter

java.lang.Object

jp.sbi.celldesigner.plugin.PluginSBaseConverter

public final class PluginSBaseConverter
extends java.lang.Object

PluginSBaseConverter

Author:

The Systems Biology Institute

Constructor Summary

Constructors

Constructor and Description
PluginSBaseConverter()

Method Summary

Modifier and Type	Method and Description
static PluginAntiSenseRNA	convertToPluginAntiSenseRNA(jp.sbi.celldesigner.sbmlExtension.AntiSenseRNA target) Converts AntiSenseRNA to PluginAntiSenseRNA
static PluginCompartment	convertToPluginCompartment(org.sbml.libsbml.Compartment compartment, jp.sbi.celldesigner.sbmlExtension.CompartmentAnnotation annotation) Converts Compartment to PluginCompartment
static PluginCompartmentType	convertToPluginCompartmentType(org.sbml.libsbml.CompartmentType compartmentType) Converts CompartmentType to PluginCompartmentType
static PluginConstraint	convertToPluginConstraint(org.sbml.libsbml.Constraint constraint) Converts Constraint to PluginConstraint
static PluginEvent	convertToPluginEvent(org.sbml.libsbml.Event event) Converts Event to PluginEvent
static PluginEventAssignment	convertToPluginEventAssignment(org.sbml.libsbml.EventAssignment event, PluginEvent parent) Converts EventAssignment to PluginEventAssignment
static PluginFunctionDefinition	convertToPluginFunctionDefinition(org.sbml.libsbml.FunctionDefinition function) Converts FunctionDefinition to PluginFunctionDefinition
static PluginGene	convertToPluginGene(jp.sbi.celldesigner.sbmlExtension.Gene target) Converts Gene to PluginGene
static PluginInitialAssignment	convertToPluginInitialAssignment(org.sbml.libsbml.InitialAssignment initialAssignment) Converts InitialAssignment to PluginInitialAssignment
static PluginKineticLaw	convertToPluginKineticLaw(org.sbml.libsbml.KineticLaw law, PluginReaction parent) Converts KineticLaw to PluginKineticLaw
static PluginModel	convertToPluginModel(org.sbml.libsbml.Model model) Converts Model to PluginModel
static PluginModel	convertToPluginModel(org.sbml.libsbml.Model model, jp.sbi.celldesigner.SBModel sbModel) Converts Model to PluginModel
static PluginModifierSpeciesReference	convertToPluginModifierSpeciesReference(org.sbml.libsbml.ModifierSpeciesReference ref, PluginReaction parent, jp.sbi.celldesigner.ReactionLink link, jp.sbi.celldesigner.sbmlExtension.SpeciesReferenceAnnotation anno, PluginSpecies psp) Convers ModifierSpeciesReference to PluginModifierSpeciesReference
static PluginParameter	convertToPluginParameter(org.sbml.libsbml.Parameter param, PluginKineticLaw parent) Converts Parameter to PluginParameter
static PluginParameter	convertToPluginParameter(org.sbml.libsbml.Parameter param, PluginModel parent) Converts Parameter to PluginParameter
static PluginProtein	convertToPluginProtein(jp.sbi.celldesigner.sbmlExtension.Protein target) Converts Protein to PluginProtein
static PluginReaction	convertToPluginReaction(org.sbml.libsbml.Reaction reaction, jp.sbi.celldesigner.sbmlExtension.ReactionAnnotation annotation) Converts Reaction to PluginReaction
static PluginRNA	convertToPluginRNA(jp.sbi.celldesigner.sbmlExtension.RNA target) Converts RNA to PluginRNA
static PluginRule	convertToPluginRule(org.sbml.libsbml.Rule rule, PluginModel parent) Converts Rule to PluginRule
static PluginSBase	convertToPluginSBase(org.sbml.libsbml.SBase sbase) Converts SBase to PluginSBase
static PluginSpecies	convertToPluginSpecies(org.sbml.libsbml.Species species, jp.sbi.celldesigner.sbmlExtension.SpeciesAnnotation annotation) Converts Species to PluginSpecies
static PluginSpeciesAlias	convertToPluginSpeciesAlias(jp.sbi.celldesigner.SpeciesAlias alias, PluginSpecies parent) Convers SpeciesAlias to PluginSpeciesAlias
static PluginSpeciesReference	convertToPluginSpeciesReference(org.sbml.libsbml.SpeciesReference ref, PluginReaction parent, jp.sbi.celldesigner.sbmlExtension.SpeciesReferenceAnnotation anno, PluginSpecies psp) Converts SpeciesReference to PluginSpeciesReference
static PluginSpeciesType	convertToPluginSpeciesType(org.sbml.libsbml.SpeciesType speciesType) Converts SpeciesType to PluginSpeciesType
static PluginUnit	convertToPluginUnit(org.sbml.libsbml.Unit unit, PluginUnitDefinition parent) Converts Unit to PluginUnit
static PluginUnitDefinition	convertToPluginUnitDefinition(org.sbml.libsbml.UnitDefinition unit) Converts UnitDefinition to PluginUnitDefinition

Methods inherited from class java.lang.Object

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

Constructor Detail

PluginSBaseConverter

public PluginSBaseConverter()

Method Detail

convertToPluginSpeciesAlias

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

Convers SpeciesAlias to PluginSpeciesAlias

Parameters:

alias - SpeciesAlias

parent - PluginSpecies

Returns:

PluginSpeciesAlias

convertToPluginSBase

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

Converts SBase to PluginSBase

Parameters:

sbase - SBase

Returns:

PluginSBase

convertToPluginModel

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

Converts Model to PluginModel

Parameters:

model - Model

Returns:

converted PluginModel

convertToPluginModel

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

Converts Model to PluginModel

Parameters:

model - Model

sbModel - SBModel

Returns:

converted PluginModel

convertToPluginProtein

public static final PluginProtein convertToPluginProtein(jp.sbi.celldesigner.sbmlExtension.Protein target)

Converts Protein to PluginProtein

Parameters:

target - Protein

Returns:

converted PluginProtein

convertToPluginGene

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

Converts Gene to PluginGene

Parameters:

target - Gene

Returns:

converted PluginGene

convertToPluginAntiSenseRNA

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

Converts AntiSenseRNA to PluginAntiSenseRNA

Parameters:

target - AntiSenseRNA

Returns:

converted PluginAntiSenseRNA

convertToPluginRNA

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

Converts RNA to PluginRNA

Parameters:

target - RNA

Returns:

converted PluginRNA

convertToPluginSpecies

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

Converts Species to PluginSpecies

Parameters:

species - Species

annotation - SpeciesAnnotation

Returns:

convereted PluginSpecies

convertToPluginReaction

public static final 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 static final 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

convertToPluginEvent

public static final PluginEvent convertToPluginEvent(org.sbml.libsbml.Event event)

Converts Event to PluginEvent

Parameters:

event - Event

Returns:

converted PluginEvent

convertToPluginEventAssignment

public static final PluginEventAssignment convertToPluginEventAssignment(org.sbml.libsbml.EventAssignment event,
                                                                         PluginEvent parent)

Converts EventAssignment to PluginEventAssignment

Parameters:

event - EventAssignment

parent - PluginEvent

Returns:

converted PluginEventAssignment

convertToPluginKineticLaw

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

Converts KineticLaw to PluginKineticLaw

Parameters:

law - KineticLaw

parent - PluginReaction

Returns:

converted PluginKineticLaw

convertToPluginParameter

public static final PluginParameter convertToPluginParameter(org.sbml.libsbml.Parameter param,
                                                             PluginKineticLaw parent)

Converts Parameter to PluginParameter

Parameters:

param - Parameter

parent - PluginKineticLaw

Returns:

converted PluginParameter

convertToPluginParameter

public static final PluginParameter convertToPluginParameter(org.sbml.libsbml.Parameter param,
                                                             PluginModel parent)

Converts Parameter to PluginParameter

Parameters:

param - Parameter

parent - PluginModel

Returns:

converted PluginParameter

convertToPluginSpeciesReference

public static final PluginSpeciesReference convertToPluginSpeciesReference(org.sbml.libsbml.SpeciesReference ref,
                                                                           PluginReaction parent,
                                                                           jp.sbi.celldesigner.sbmlExtension.SpeciesReferenceAnnotation anno,
                                                                           PluginSpecies psp)

Converts SpeciesReference to PluginSpeciesReference

Parameters:

ref - SpeciesReference

parent - PluginReaction

anno - SpeciesAnnotation

psp - PluginSpecies

Returns:

converted PluginSpeciesReference

convertToPluginModifierSpeciesReference

public static final PluginModifierSpeciesReference convertToPluginModifierSpeciesReference(org.sbml.libsbml.ModifierSpeciesReference ref,
                                                                                           PluginReaction parent,
                                                                                           jp.sbi.celldesigner.ReactionLink link,
                                                                                           jp.sbi.celldesigner.sbmlExtension.SpeciesReferenceAnnotation anno,
                                                                                           PluginSpecies psp)

Convers ModifierSpeciesReference to PluginModifierSpeciesReference

Parameters:

ref - ModifierSpeciesReference

parent - PluginReaction

link - ReactionLink

anno - SpeciesReferenceAnnotation

psp - PluginSpecies

Returns:

converted PluginModifierSpeciesReference

convertToPluginFunctionDefinition

public static final PluginFunctionDefinition convertToPluginFunctionDefinition(org.sbml.libsbml.FunctionDefinition function)

Converts FunctionDefinition to PluginFunctionDefinition

Parameters:

function - FunctionDefinition

Returns:

converted PluginFunctionDefinition

convertToPluginRule

public static final PluginRule convertToPluginRule(org.sbml.libsbml.Rule rule,
                                                   PluginModel parent)

Converts Rule to PluginRule

Parameters:

rule - Rule

parent - PluginModel

Returns:

converted PluginRule

convertToPluginUnitDefinition

public static final PluginUnitDefinition convertToPluginUnitDefinition(org.sbml.libsbml.UnitDefinition unit)

Converts UnitDefinition to PluginUnitDefinition

Parameters:

unit - UnitDefinition

Returns:

converted PluginUnitDefinition

convertToPluginUnit

public static final PluginUnit convertToPluginUnit(org.sbml.libsbml.Unit unit,
                                                   PluginUnitDefinition parent)

Converts Unit to PluginUnit

Parameters:

unit - Unit

parent - PluginUnitDefinition

Returns:

converted PluginUnit

convertToPluginSpeciesType

public static final PluginSpeciesType convertToPluginSpeciesType(org.sbml.libsbml.SpeciesType speciesType)

Converts SpeciesType to PluginSpeciesType

Parameters:

speciesType - SpeciesType

Returns:

converted PluginSpeciesType

convertToPluginCompartmentType

public static final PluginCompartmentType convertToPluginCompartmentType(org.sbml.libsbml.CompartmentType compartmentType)

Converts CompartmentType to PluginCompartmentType

Parameters:

compartmentType - CompartmentType

Returns:

converted PluginCompartmentType

convertToPluginInitialAssignment

public static final PluginInitialAssignment convertToPluginInitialAssignment(org.sbml.libsbml.InitialAssignment initialAssignment)

Converts InitialAssignment to PluginInitialAssignment

Parameters:

initialAssignment - InitialAssignment

Returns:

converted PluginInitialAssignment

convertToPluginConstraint

public static final PluginConstraint convertToPluginConstraint(org.sbml.libsbml.Constraint constraint)

Converts Constraint to PluginConstraint

Parameters:

constraint - Constraint

Returns:

converted PluginConstraint