com.banda.chemistry.business

Class AcRateConstantUtil

java.lang.Object

com.banda.chemistry.business.AcRateConstantUtil

public class AcRateConstantUtil
extends Object

Method Summary

Methods

Modifier and Type	Method and Description
static AcRateConstantUtil	getInstance()
Collection<com.banda.core.domain.ValueBound<Double>>	getRateConstantBounds(AcCompartment compartment, Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
Collection<com.banda.core.domain.ValueBound<Double>>	getRateConstantBounds(AcReaction reaction, Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection)
Collection<com.banda.core.domain.ValueBound<Double>>	getRateConstantBounds(AcReactionSet reactionSet, Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
Collection<AcReaction>	getRepresentativeReactions(AcReactionSet reactionSet, Collection<AcReactionGroup> reactionGroupsToOmit)
void	setRandomRateConstants(AcReaction reaction, Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap, boolean forwardFlag)
void	setRandomRateConstants(AcReactionSet reactionSet, Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap)
void	setRandomRateConstantsIfNotSet(AcReactionSet reactionSet, Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap, AcReaction.ReactionDirection reactionDirection)
void	setRateConstants(AcCompartment compartment, Double[] rateAndPermeabilityConstants, AcReaction.ReactionDirection direction, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
void	setRateConstants(AcReactionSet reactionSet, Double[] rateConstants, AcReaction.ReactionDirection direction, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
void	setRateConstantsFromString(String rateConstantsString, AcCompartment compartment, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)
void	setRateConstantsFromString(String rateConstantsString, AcReaction reaction, AcReaction.ReactionDirection reactionDirection)
void	setRateConstantsFromString(String rateConstantsString, AcReactionSet reactionSet, AcReaction.ReactionDirection reactionDirection, Collection<AcReaction> reactionsToOmit, Collection<AcReactionGroup> reactionGroupsToOmit)

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static AcRateConstantUtil getInstance()

getRateConstantBounds

public Collection<com.banda.core.domain.ValueBound<Double>> getRateConstantBounds(AcCompartment compartment,
                                                                         Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap,
                                                                         AcReaction.ReactionDirection reactionDirection,
                                                                         Collection<AcReaction> reactionsToOmit,
                                                                         Collection<AcReactionGroup> reactionGroupsToOmit)

getRateConstantBounds

public Collection<com.banda.core.domain.ValueBound<Double>> getRateConstantBounds(AcReactionSet reactionSet,
                                                                         Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap,
                                                                         AcReaction.ReactionDirection reactionDirection,
                                                                         Collection<AcReaction> reactionsToOmit,
                                                                         Collection<AcReactionGroup> reactionGroupsToOmit)

getRateConstantBounds

public Collection<com.banda.core.domain.ValueBound<Double>> getRateConstantBounds(AcReaction reaction,
                                                                         Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap,
                                                                         AcReaction.ReactionDirection reactionDirection)

setRandomRateConstants

public void setRandomRateConstants(AcReactionSet reactionSet,
                          Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap)

setRandomRateConstantsIfNotSet

public void setRandomRateConstantsIfNotSet(AcReactionSet reactionSet,
                                  Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap,
                                  AcReaction.ReactionDirection reactionDirection)

setRandomRateConstants

public void setRandomRateConstants(AcReaction reaction,
                          Map<AcRateConstantType,com.banda.core.domain.ValueBound<Double>> rateConstantTypeBoundMap,
                          boolean forwardFlag)

getRepresentativeReactions

public Collection<AcReaction> getRepresentativeReactions(AcReactionSet reactionSet,
                                                Collection<AcReactionGroup> reactionGroupsToOmit)

setRateConstants

public void setRateConstants(AcCompartment compartment,
                    Double[] rateAndPermeabilityConstants,
                    AcReaction.ReactionDirection direction,
                    Collection<AcReaction> reactionsToOmit,
                    Collection<AcReactionGroup> reactionGroupsToOmit)

setRateConstants

public void setRateConstants(AcReactionSet reactionSet,
                    Double[] rateConstants,
                    AcReaction.ReactionDirection direction,
                    Collection<AcReaction> reactionsToOmit,
                    Collection<AcReactionGroup> reactionGroupsToOmit)

setRateConstantsFromString

public void setRateConstantsFromString(String rateConstantsString,
                              AcCompartment compartment,
                              AcReaction.ReactionDirection reactionDirection,
                              Collection<AcReaction> reactionsToOmit,
                              Collection<AcReactionGroup> reactionGroupsToOmit)

setRateConstantsFromString

public void setRateConstantsFromString(String rateConstantsString,
                              AcReactionSet reactionSet,
                              AcReaction.ReactionDirection reactionDirection,
                              Collection<AcReaction> reactionsToOmit,
                              Collection<AcReactionGroup> reactionGroupsToOmit)

setRateConstantsFromString

public void setRateConstantsFromString(String rateConstantsString,
                              AcReaction reaction,
                              AcReaction.ReactionDirection reactionDirection)