org.sigpath.task.navigator
Class TSaveBase

java.lang.Object
  org.sigpath.task.navigator.TSaveBase

Direct Known Subclasses:

TSaveChange_log, TSaveComplex, TSaveConcentrationMeasurement, TSaveCustomKinetic, TSaveEnzymaticReaction, TSaveKinetic, TSaveModel, TSaveModifiedChemical, TSaveNamedChemical, TSaveNamedChemicalInteraction, TSaveOrganism, TSavePathway, TSavePending_list, TSaveProtein, TSaveReaction, TSaveRef, TSaveSmallMolecule, TSaveUserComment

public class TSaveBase
extends Object

Navigator Base Class for Saving SigPath Entities to Memory store. Contains Methods that require Entity Manager, Factory

Field Summary

protected NavigatorEntityManager	navigatorEntityManager
protected HashMap	tempIDtoSPIDMap

Constructor Summary

TSaveBase(NavigatorEntityManager navigatorEntityManager, HashMap tempIDtoSPIDMap)

Method Summary

protected Kinetic	createKinetic(Kinetic castorKinetic)
protected Chemical	createModifiedChemical(ModifiedChemical castorModChem)
protected PendingList	createPendingList(Pending_list castorInstance)
protected Set	getExcludedReactions(ExcludedReactions castorExcRxn)
protected Model	getPreviousVersion(PreviousVersion castorPV)
protected Chemical	getReactionEnzyme(Enzyme castorEnzyme)
protected Collection	getReactionLeftSide(Left castorLeft) Get Left datamodel Chemicals from memory store.
protected Collection	getReactionRightSide(Right castorRight) Get Right datamodel Chemicals from memory store.
protected User	getUser(String createdBy)
protected void	postProcessConcentrationMeasurement(Concentration_measurement castorInstance, ConcentrationMeasurement jdoInstance) This method sets the 1) concentration (value and unit) 2) chemical for ConcentrationMeasurement.
protected void	postProcessEnzymaticReaction(EnzymaticReaction castorEnzymatic, EnzymaticReaction jdoEnzymatic) This method 1) sets the involved-in property of the enzyme.
protected void	postProcessModel(Model castorModel, Model jdoModel) Sets model concentration.
protected void	postProcessNamedChemicalInteraction(NamedChemicalInteraction castorInstance, NamedChemicalInteraction jdoInstance) This method sets the source, target, left and right values.
protected void	postProcessPendingList(Pending_list castorInstance, PendingList jdoInstance) This method sets the PendingItems.
protected void	postProcessReaction(Reaction castorInstance, Reaction jdoInstance) This method sets involved-in value for the reaction.
protected void	setChangeLog(SigPathEntity spe, Change_log castorChange_log)
protected void	setComplexMonomers(Complex jdoComplex, Molecule[] castorMols) Adds monomers to datamodel complex.
protected void	setConcentrationUnit(Model jdoInstance, TargetUnit castorTargetUnit) This method transfers concentration unit from castor to datamodel.
protected void	setConstantsDeclaration(KineticCustom jdoKineticCustom, ParametersBindingsDeclaration castorPBD) Sets the binding declarations (BindingSet) for constants
protected void	setCustomKinetic(Kinetic jdoKinetic, CustomKinetic castorCK) Used by TSaveKinetic to set custom kinetic info.
protected void	setEnzymaticParameters(EnzymaticReaction jdoInstance, EnzymaticParameters castorParameters) This method transfers parameters from castor to datamodel.
protected void	setFormula(KineticCustom jdoKineticCustom, Formula castorFormula)
protected void	setKinetic(KineticInteraction jdoKInt, KineticRef castorKineticRef)
protected void	setKineticBindings(KineticInteraction jdoKInt, KineticBindings castorKB)
protected void	setModelCompartments(Model jdoModel, ModelCompartments castorCompartments)
protected void	setModelReactions(Model jdoModel, ModelReaction[] castorModelRxns)
protected void	setPathwayReactions(Pathway jdoPathway, InteractionRef[] castorInteractionRefs)
protected void	setReactionModifiers(Reaction jdoReaction, Modifiers castorModifiers) Sets jdo Modifiers from castor.
protected void	setReactionParameters(Reaction jdoInstance, Parameters castorParameters) This method transfers parameters from castor to datamodel.
protected void	setRefUnit(KineticCustom jdoKineticCustom, UnitType castorUnitType) Sets the unit
protected void	setSpeciesDeclaration(KineticCustom jdoKineticCustom, SpeciesBindingsDeclaration castorSBD) Sets the binding declarations (BindingSet) for species
protected void	setSubstrateProduct(EnzymaticReaction jdoEnzymatic, Reaction castorReaction)

Methods inherited from class java.lang.Object

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

Field Detail

navigatorEntityManager

protected NavigatorEntityManager navigatorEntityManager

tempIDtoSPIDMap

protected HashMap tempIDtoSPIDMap

Constructor Detail

TSaveBase

public TSaveBase(NavigatorEntityManager navigatorEntityManager,
                 HashMap tempIDtoSPIDMap)

Method Detail

getReactionLeftSide

protected Collection getReactionLeftSide(Left castorLeft)

Get Left datamodel Chemicals from memory store.

Parameters:

castorLeft -

Returns:

Collection

getReactionRightSide

protected Collection getReactionRightSide(Right castorRight)

Get Right datamodel Chemicals from memory store.

Parameters:

castorRight -

Returns:

Collection

setReactionModifiers

protected void setReactionModifiers(Reaction jdoReaction,
                                    Modifiers castorModifiers)

Sets jdo Modifiers from castor.

Parameters:

castorModifiers -

postProcessReaction

protected void postProcessReaction(Reaction castorInstance,
                                   Reaction jdoInstance)

This method sets involved-in value for the reaction.

Parameters:

castorInstance -

jdoInstance -

setComplexMonomers

protected void setComplexMonomers(Complex jdoComplex,
                                  Molecule[] castorMols)

Adds monomers to datamodel complex.

Parameters:

jdoComplex -

castorMols -

getReactionEnzyme

protected Chemical getReactionEnzyme(Enzyme castorEnzyme)

postProcessEnzymaticReaction

protected void postProcessEnzymaticReaction(EnzymaticReaction castorEnzymatic,
                                            EnzymaticReaction jdoEnzymatic)

This method 1) sets the involved-in property of the enzyme. 3) setKineticBindings (this method requires setting substrate value first)

Parameters:

castorEnzymatic -

jdoEnzymatic -

setSubstrateProduct

protected void setSubstrateProduct(EnzymaticReaction jdoEnzymatic,
                                   Reaction castorReaction)

setPathwayReactions

protected void setPathwayReactions(Pathway jdoPathway,
                                   InteractionRef[] castorInteractionRefs)

createModifiedChemical

protected Chemical createModifiedChemical(ModifiedChemical castorModChem)

setKinetic

protected void setKinetic(KineticInteraction jdoKInt,
                          KineticRef castorKineticRef)

setKineticBindings

protected void setKineticBindings(KineticInteraction jdoKInt,
                                  KineticBindings castorKB)

createKinetic

protected Kinetic createKinetic(Kinetic castorKinetic)

setCustomKinetic

protected void setCustomKinetic(Kinetic jdoKinetic,
                                CustomKinetic castorCK)

Used by TSaveKinetic to set custom kinetic info.

Parameters:

jdoKinetic -

castorCK -

setFormula

protected void setFormula(KineticCustom jdoKineticCustom,
                          Formula castorFormula)

setConstantsDeclaration

protected void setConstantsDeclaration(KineticCustom jdoKineticCustom,
                                       ParametersBindingsDeclaration castorPBD)

Sets the binding declarations (BindingSet) for constants

Parameters:

jdoKineticCustom -

castorPBD -

setSpeciesDeclaration

protected void setSpeciesDeclaration(KineticCustom jdoKineticCustom,
                                     SpeciesBindingsDeclaration castorSBD)

Sets the binding declarations (BindingSet) for species

Parameters:

jdoKineticCustom -

castorSBD -

setRefUnit

protected void setRefUnit(KineticCustom jdoKineticCustom,
                          UnitType castorUnitType)

Sets the unit

Parameters:

jdoKineticCustom -

castorUnitType -

postProcessConcentrationMeasurement

protected void postProcessConcentrationMeasurement(Concentration_measurement castorInstance,
                                                   ConcentrationMeasurement jdoInstance)

This method sets the 1) concentration (value and unit) 2) chemical for ConcentrationMeasurement.

Parameters:

castorInstance -

jdoInstance -

setReactionParameters

protected void setReactionParameters(Reaction jdoInstance,
                                     Parameters castorParameters)

This method transfers parameters from castor to datamodel.

Parameters:

jdoInstance -

castorParameters -

setEnzymaticParameters

protected void setEnzymaticParameters(EnzymaticReaction jdoInstance,
                                      EnzymaticParameters castorParameters)

This method transfers parameters from castor to datamodel.

Parameters:

jdoInstance -

castorParameters -

createPendingList

protected PendingList createPendingList(Pending_list castorInstance)

getUser

protected User getUser(String createdBy)

postProcessPendingList

protected void postProcessPendingList(Pending_list castorInstance,
                                      PendingList jdoInstance)

This method sets the PendingItems.

Parameters:

castorInstance -

jdoInstance -

postProcessNamedChemicalInteraction

protected void postProcessNamedChemicalInteraction(NamedChemicalInteraction castorInstance,
                                                   NamedChemicalInteraction jdoInstance)

This method sets the source, target, left and right values.

Parameters:

castorInstance -

jdoInstance -

getExcludedReactions

protected Set getExcludedReactions(ExcludedReactions castorExcRxn)

getPreviousVersion

protected Model getPreviousVersion(PreviousVersion castorPV)

setModelReactions

protected void setModelReactions(Model jdoModel,
                                 ModelReaction[] castorModelRxns)

setConcentrationUnit

protected void setConcentrationUnit(Model jdoInstance,
                                    TargetUnit castorTargetUnit)

This method transfers concentration unit from castor to datamodel.

Parameters:

jdoInstance -

castorTargetUnit -

setModelCompartments

protected void setModelCompartments(Model jdoModel,
                                    ModelCompartments castorCompartments)

postProcessModel

protected void postProcessModel(Model castorModel,
                                Model jdoModel)

Sets model concentration.

Parameters:

castorModel -

jdoModel -

setChangeLog

protected void setChangeLog(SigPathEntity spe,
                            Change_log castorChange_log)