com.banda.chemistry.domain

Class AcReaction

java.lang.Object

com.banda.core.domain.DomainObject<Long>

com.banda.core.domain.TechnicalDomainObject

com.banda.chemistry.domain.AcReaction

All Implemented Interfaces:

KeyHolder<Long>, com.banda.function.domain.FunctionHolder<Double,Double>, Serializable

public class AcReaction
extends TechnicalDomainObject
implements com.banda.function.domain.FunctionHolder<Double,Double>

See Also:

Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AcReaction.ReactionDirection

Nested classes/interfaces inherited from class com.banda.core.domain.DomainObject

DomainObject.DomainObjectKeyComparator<K extends Serializable & Comparable<K>>

Constructor Summary

Constructors

Constructor and Description
AcReaction()

Method Summary

Methods

Modifier and Type	Method and Description
void	addAssociationForSpecies(AcSpecies species, AcSpeciesAssociationType type)
void	addAssociationsForSpecies(Collection<AcSpecies> species, AcSpeciesAssociationType type)
void	addSpeciesAssociation(AcSpeciesReactionAssociation specAssoc)
void	addSpeciesAssociation(AcSpeciesReactionAssociation specAssociation, AcSpeciesAssociationType assocType)
void	addSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssocs)
void	addSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssociations, AcSpeciesAssociationType assocType)
AcCollectiveSpeciesReactionAssociationType	getCollectiveCatalysisType()
AcCollectiveSpeciesReactionAssociationType	getCollectiveInhibitionType()
Double[]	getForwardRateConstants()
int	getForwardRateConstantsNum()
Double[]	getForwardRateConstantsSafe()
com.banda.function.domain.Function<Double,Double>	getForwardRateFunction()
com.banda.function.domain.Function<Double,Double>	getFunction()
AcReactionGroup	getGroup()
Integer	getIndex()
String	getLabel()
AcParameterSet	getParameterSet()
Integer	getPriority()
Double[]	getRateConstants(boolean forwardFlag)
int	getRateConstantsNum(boolean forwardFlag)
com.banda.function.domain.Function<Double,Double>	getRateFunction(boolean forwardFlag)
AcReactionSet	getReactionSet()
Double[]	getReverseRateConstants()
int	getReverseRateConstantsNum()
Double[]	getReverseRateConstantsSafe()
com.banda.function.domain.Function<Double,Double>	getReverseRateFunction()
Integer	getSortOrder()
Set<AcSpeciesReactionAssociation>	getSpeciesAssociations()
List<AcSpeciesReactionAssociation>	getSpeciesAssociations(AcSpeciesAssociationType assocType)
Integer	getSpeciesAssociationsNum(AcSpeciesAssociationType assocType)
AcSpeciesSet	getSpeciesSet()
boolean	hasForwardRateConstants()
boolean	hasGroup()
boolean	hasRateConstants(boolean forwardFlag)
boolean	hasReactionSet()
boolean	hasReverseRateConstants()
boolean	hasReverseRateFunction()
boolean	hasSpeciesAssociations(AcSpeciesAssociationType assocType)
void	initSpeciesAssociations()
boolean	isEnabled()
void	removeFromGroup()
void	removeFromReactionSet()
void	removeSpeciesAssociation(AcSpeciesReactionAssociation specAssoc)
void	removeSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssocs)
void	setCollectiveCatalysisType(AcCollectiveSpeciesReactionAssociationType collectiveCatalysisType)
void	setCollectiveInhibitionType(AcCollectiveSpeciesReactionAssociationType collectiveInhibitionType)
void	setEnabled(boolean enabled)
void	setForwardRateConstant(Double forwardRateConstant)
void	setForwardRateConstants(Double[] forwardRateConstants)
void	setForwardRateFunction(com.banda.function.domain.Function<Double,Double> forwardRateFunction)
void	setFunction(com.banda.function.domain.Function<Double,Double> function)
protected void	setGroup(AcReactionGroup group)
void	setIndex(Integer index)
void	setLabel(String label)
void	setPriority(Integer priority)
void	setRateConstants(Double[] rateConstants, boolean forwardFlag)
void	setRateFunction(com.banda.function.domain.Function<Double,Double> rateFunction, boolean forwardFlag)
protected void	setReactionSet(AcReactionSet reactionSet)
void	setReverseRateConstant(Double reverseRateConstant)
void	setReverseRateConstants(Double[] reverseRateConstants)
void	setReverseRateFunction(com.banda.function.domain.Function<Double,Double> reverseRateFunction)
void	setSortOrder(Integer sortOrder)
void	setSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssociations, AcSpeciesAssociationType assocType)
void	setSpeciesAssociations(Set<AcSpeciesReactionAssociation> speciesAssociations)
String	toString()

Methods inherited from class com.banda.core.domain.TechnicalDomainObject

getId, getKey, getVersion, setId, setKey, setVersion

Methods inherited from class com.banda.core.domain.DomainObject

copyFrom, equals, hashCode

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

AcReaction

public AcReaction()

Method Detail

getSortOrder

public Integer getSortOrder()

setSortOrder

public void setSortOrder(Integer sortOrder)

getSpeciesAssociations

public Set<AcSpeciesReactionAssociation> getSpeciesAssociations()

setSpeciesAssociations

public void setSpeciesAssociations(Set<AcSpeciesReactionAssociation> speciesAssociations)

initSpeciesAssociations

public void initSpeciesAssociations()

addAssociationForSpecies

public void addAssociationForSpecies(AcSpecies species,
                            AcSpeciesAssociationType type)

addSpeciesAssociation

public void addSpeciesAssociation(AcSpeciesReactionAssociation specAssoc)

addSpeciesAssociations

public void addSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssocs)

addAssociationsForSpecies

public void addAssociationsForSpecies(Collection<AcSpecies> species,
                             AcSpeciesAssociationType type)

removeSpeciesAssociation

public void removeSpeciesAssociation(AcSpeciesReactionAssociation specAssoc)

removeSpeciesAssociations

public void removeSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssocs)

hasSpeciesAssociations

public boolean hasSpeciesAssociations(AcSpeciesAssociationType assocType)

getPriority

public Integer getPriority()

setPriority

public void setPriority(Integer priority)

getReactionSet

public AcReactionSet getReactionSet()

setReactionSet

protected void setReactionSet(AcReactionSet reactionSet)

hasReactionSet

public boolean hasReactionSet()

removeFromReactionSet

public void removeFromReactionSet()

getGroup

public AcReactionGroup getGroup()

setGroup

protected void setGroup(AcReactionGroup group)

hasGroup

public boolean hasGroup()

removeFromGroup

public void removeFromGroup()

getForwardRateFunction

public com.banda.function.domain.Function<Double,Double> getForwardRateFunction()

setForwardRateFunction

public void setForwardRateFunction(com.banda.function.domain.Function<Double,Double> forwardRateFunction)

getForwardRateConstants

public Double[] getForwardRateConstants()

getForwardRateConstantsSafe

public Double[] getForwardRateConstantsSafe()

setForwardRateConstants

public void setForwardRateConstants(Double[] forwardRateConstants)

hasForwardRateConstants

public boolean hasForwardRateConstants()

getForwardRateConstantsNum

public int getForwardRateConstantsNum()

setForwardRateConstant

public void setForwardRateConstant(Double forwardRateConstant)

getReverseRateFunction

public com.banda.function.domain.Function<Double,Double> getReverseRateFunction()

setReverseRateFunction

public void setReverseRateFunction(com.banda.function.domain.Function<Double,Double> reverseRateFunction)

hasReverseRateFunction

public boolean hasReverseRateFunction()

getReverseRateConstants

public Double[] getReverseRateConstants()

getReverseRateConstantsSafe

public Double[] getReverseRateConstantsSafe()

setReverseRateConstants

public void setReverseRateConstants(Double[] reverseRateConstants)

hasReverseRateConstants

public boolean hasReverseRateConstants()

getReverseRateConstantsNum

public int getReverseRateConstantsNum()

setReverseRateConstant

public void setReverseRateConstant(Double reverseRateConstant)

getRateConstants

public Double[] getRateConstants(boolean forwardFlag)

hasRateConstants

public boolean hasRateConstants(boolean forwardFlag)

setRateConstants

public void setRateConstants(Double[] rateConstants,
                    boolean forwardFlag)

getRateConstantsNum

public int getRateConstantsNum(boolean forwardFlag)

getRateFunction

public com.banda.function.domain.Function<Double,Double> getRateFunction(boolean forwardFlag)

setRateFunction

public void setRateFunction(com.banda.function.domain.Function<Double,Double> rateFunction,
                   boolean forwardFlag)

getLabel

public String getLabel()

setLabel

public void setLabel(String label)

getIndex

public Integer getIndex()

setIndex

public void setIndex(Integer index)

getSpeciesSet

public AcSpeciesSet getSpeciesSet()

getParameterSet

public AcParameterSet getParameterSet()

isEnabled

public boolean isEnabled()

setEnabled

public void setEnabled(boolean enabled)

getCollectiveCatalysisType

public AcCollectiveSpeciesReactionAssociationType getCollectiveCatalysisType()

setCollectiveCatalysisType

public void setCollectiveCatalysisType(AcCollectiveSpeciesReactionAssociationType collectiveCatalysisType)

getCollectiveInhibitionType

public AcCollectiveSpeciesReactionAssociationType getCollectiveInhibitionType()

setCollectiveInhibitionType

public void setCollectiveInhibitionType(AcCollectiveSpeciesReactionAssociationType collectiveInhibitionType)

getFunction

public com.banda.function.domain.Function<Double,Double> getFunction()

Specified by:

getFunction in interface com.banda.function.domain.FunctionHolder<Double,Double>

setFunction

public void setFunction(com.banda.function.domain.Function<Double,Double> function)

Specified by:

setFunction in interface com.banda.function.domain.FunctionHolder<Double,Double>

getSpeciesAssociations

public List<AcSpeciesReactionAssociation> getSpeciesAssociations(AcSpeciesAssociationType assocType)

addSpeciesAssociation

public void addSpeciesAssociation(AcSpeciesReactionAssociation specAssociation,
                         AcSpeciesAssociationType assocType)

addSpeciesAssociations

public void addSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssociations,
                          AcSpeciesAssociationType assocType)

setSpeciesAssociations

public void setSpeciesAssociations(Collection<AcSpeciesReactionAssociation> specAssociations,
                          AcSpeciesAssociationType assocType)

getSpeciesAssociationsNum

public Integer getSpeciesAssociationsNum(AcSpeciesAssociationType assocType)

toString

public String toString()

Overrides:

toString in class DomainObject<Long>

See Also:

Object.toString()