com.banda.chemistry.business

Class ArtificialChemistryUtil

java.lang.Object

com.banda.chemistry.business.ArtificialChemistryUtil

public class ArtificialChemistryUtil
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
static com.banda.core.PairComparator<AcCompartment,AcSpecies>	compartmentSpeciesComparator

Method Summary

Methods

Modifier and Type	Method and Description
void	addInteractions(AcInteractionSeries targetInteractionSeries, AcInteractionSeries sourceInteractionSeries)
void	addReactions(AcReactionSet reactionSet, AcReactionSet additionalReactionSet)
String	createFoldExpression(Collection<AcSpeciesReactionAssociation> speciesAssociations, AcCollectiveSpeciesReactionAssociationType collectiveSpeciesReactionAssociationType, boolean wrapIfNeeded)
String	createFoldOrderedExpression(Collection<AcSpeciesReactionAssociation> speciesAssociations, String operation, boolean wrapIfNeeded)
Set<AcSpecies>	filterOutSpecies(Collection<AcReaction> reactions, Collection<AcSpecies> species, AcSpeciesAssociationType type)
String	getDNAStrandSpeciesSetAsString(AcDNAStrandSpeciesSet speciesSet, String separator)
String	getEvaluationFunctionAsString(AcEvaluation evaluation)
String	getEvolFunctionAsString(AcParameter parameter)
String	getFunctionAsString(com.banda.function.domain.Function<?,?> function, AcReactionSet reactionSet)
<M extends AcVariable<?>> Map<Integer,M>	getIndexVariableMap(AcVariableSetIF<M> variableSet)
static ArtificialChemistryUtil	getInstance()
<M extends AcVariable<?>> Collection<String>	getItemsWithStoichiometry(AcVariableSetIF<M> magnitudeSet, Double[] stoichiometricVector)
Map<String,AcReaction>	getLabelReactionMap(AcReactionSet reactionSet)
<M extends AcVariable<?>> Map<String,M>	getLabelVariableMap(AcVariableSetIF<M> variableSet)
String	getLatexTable(AcReactionSet reactionSet, boolean includeRates)
Collection<AcInteractionVariable>	getNewInteractionVariables(AcInteractionSeries interactionSeries, AcInteractionSeries sourceInteractionSeries)
Collection<AcSpecies>	getNewSpecies(AcReactionSet reactionSet, AcReactionSet additionalReactionSet)
Map<Integer,String>	getOrderedVariableLabelMap(AcVariableSetIF<?> variableSet)
Collection<String>	getProductsAsString(AcReaction reaction)
String	getRateFunctionAsString(AcReaction reaction, boolean forwardFlag)
Collection<String>	getReactantsAsString(AcReaction reaction)
Set<AcSpecies>	getReferencedSpecies(AcReactionSet reactionSet)
Set<AcSpecies>	getReferencedSpecies(AcTranslation rangeTranslation)
Set<AcSpecies>	getReferencedSpecies(AcTranslationSeries translationSeries)
Set<Integer>	getReferencedSpeciesIndeces(AcTranslationSeries translationSeries)
String	getSettingFunctionAsString(AcInteractionVariableAssignment variableAssignment)
String	getSettingFunctionAsString(AcSpeciesInteraction speciesAction)
Collection<AcSpecies>	getSpecies(Collection<AcSpeciesReactionAssociation> assocs)
com.banda.core.Pair<Collection<AcSpeciesInteraction>,Collection<AcInteractionVariableAssignment>>	getSpeciesAndInteractionVariablesToRemove(AcInteractionSeries interactionSeries, AcInteractionSeries sourceInteractionSeries)
Set<AcSpeciesReactionAssociation>	getSpeciesAssociations(AcSpeciesSet speciesSet, Double[] stoichiometricVector)
String	getSpeciesAsString(Collection<? extends AcSpecies> species, String separator)
<M extends AcVariable<?>> Collection<String>	getSpeciesLabels(Collection<AcSpeciesReactionAssociation> speciesAssociations)
<M extends AcVariable<?>> Collection<String>	getSpeciesLabelsWithStoichiometry(Collection<AcSpeciesReactionAssociation> speciesAssociations)
String	getTranslationFunctionAsString(AcTranslationItem translationItem)
Collection<AcSpecies>	getTranslationFunctionReferencedSpecies(AcTranslationItem translationItem)
Collection<AcTranslationVariable>	getTranslationFunctionReferencedVariables(AcTranslationItem translationItem)
Set<Integer>	getVariableIndeces(AcVariableSetIF<? extends AcVariable<?>> variableSet)
Set<Integer>	getVariableIndeces(Collection<? extends AcVariable<?>> variables)
Set<String>	getVariableLabels(AcVariableSetIF<? extends AcVariable<?>> variableSet)
Set<String>	getVariableLabels(Collection<? extends AcVariable<?>> variables)
String	getVariableLabelsAsString(Collection<? extends AcVariable<?>> variables)
String	getVariableLabelsAsString(Collection<? extends AcVariable<?>> variables, String separator)
String	getVariablePlaceholder(AcSpeciesReactionAssociation speciesAssoc)
String	replaceIndexPlaceholdersWithVariableLabels(com.banda.function.domain.Function<?,?> function, AcVariableSetIF<?> variableSet)
String	replaceIndexPlaceholdersWithVariableLabels(com.banda.function.domain.Function<?,?> function, AcVariableSetIF<?> variableSet1, AcVariableSetIF<?> variableSet2)
String	replaceIndexPlaceholdersWithVariableLabels(com.banda.function.domain.Function<?,?> function, Collection<? extends AcVariable<?>> acVariables)
String	replaceSpeciesAndParamaterLabelsWithIndexPlaceholders(String formula, AcSpeciesSet speciesSet)
void	replaceSpeciesSet(AcInteractionSeries interactionSeries, AcSpeciesSet newSpeciesSet)
void	replaceSpeciesSet(AcReactionSet reactionSet, AcSpeciesSet newSpeciesSet)
String	replaceVariableLabelsWithIndexPlaceholders(String formula, AcVariableSetIF<?> variableSet)
String	replaceVariableLabelsWithIndexPlaceholders(String formula, Set<Integer> referencedVariableIndeces, Collection<? extends AcVariable<?>> acVariables)
void	setEvaluationFunctionFromString(String formula, AcEvaluation evaluation)
void	setEvolFunctionFromString(String formula, AcParameter parameter)
void	setRateFunctionFromString(String formula, AcReaction reaction, boolean forwardFlag)
void	setSettingFunctionFromString(String formula, AcInteractionVariableAssignment variableAssignment)
void	setSettingFunctionFromString(String formula, AcSpeciesInteraction speciesAction)
void	setSpeciesAssociationsFromString(String speciesAssociationsString, AcSpeciesAssociationType assocType, AcReaction reaction)
void	setTranslationFunctionFromString(String formula, AcTranslationItem translationItem)
void	updateSpeciesAssociations(Collection<AcSpeciesReactionAssociation> newSpeciesAssociations, AcSpeciesAssociationType assocType, AcReaction reaction)
void	updateSpeciesAssociations(String speciesAssociationsString, AcSpeciesAssociationType assocType, AcReaction reaction)
String	wrapIfNeeded(String expression, Collection<AcSpeciesReactionAssociation> speciesAssociations)

Methods inherited from class java.lang.Object

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

Field Detail

compartmentSpeciesComparator

public static final com.banda.core.PairComparator<AcCompartment,AcSpecies> compartmentSpeciesComparator

Method Detail

getInstance

public static ArtificialChemistryUtil getInstance()

replaceIndexPlaceholdersWithVariableLabels

public String replaceIndexPlaceholdersWithVariableLabels(com.banda.function.domain.Function<?,?> function,
                                                AcVariableSetIF<?> variableSet1,
                                                AcVariableSetIF<?> variableSet2)

replaceIndexPlaceholdersWithVariableLabels

public String replaceIndexPlaceholdersWithVariableLabels(com.banda.function.domain.Function<?,?> function,
                                                AcVariableSetIF<?> variableSet)

replaceIndexPlaceholdersWithVariableLabels

public String replaceIndexPlaceholdersWithVariableLabels(com.banda.function.domain.Function<?,?> function,
                                                Collection<? extends AcVariable<?>> acVariables)

replaceVariableLabelsWithIndexPlaceholders

public String replaceVariableLabelsWithIndexPlaceholders(String formula,
                                                AcVariableSetIF<?> variableSet)

replaceSpeciesAndParamaterLabelsWithIndexPlaceholders

public String replaceSpeciesAndParamaterLabelsWithIndexPlaceholders(String formula,
                                                           AcSpeciesSet speciesSet)

replaceVariableLabelsWithIndexPlaceholders

public String replaceVariableLabelsWithIndexPlaceholders(String formula,
                                                Set<Integer> referencedVariableIndeces,
                                                Collection<? extends AcVariable<?>> acVariables)

getItemsWithStoichiometry

public <M extends AcVariable<?>> Collection<String> getItemsWithStoichiometry(AcVariableSetIF<M> magnitudeSet,
                                                                     Double[] stoichiometricVector)

getSpeciesLabelsWithStoichiometry

public <M extends AcVariable<?>> Collection<String> getSpeciesLabelsWithStoichiometry(Collection<AcSpeciesReactionAssociation> speciesAssociations)

getSpeciesLabels

public <M extends AcVariable<?>> Collection<String> getSpeciesLabels(Collection<AcSpeciesReactionAssociation> speciesAssociations)

getSpeciesAssociations

public Set<AcSpeciesReactionAssociation> getSpeciesAssociations(AcSpeciesSet speciesSet,
                                                       Double[] stoichiometricVector)

getFunctionAsString

public String getFunctionAsString(com.banda.function.domain.Function<?,?> function,
                         AcReactionSet reactionSet)

getRateFunctionAsString

public String getRateFunctionAsString(AcReaction reaction,
                             boolean forwardFlag)

getEvolFunctionAsString

public String getEvolFunctionAsString(AcParameter parameter)

getEvaluationFunctionAsString

public String getEvaluationFunctionAsString(AcEvaluation evaluation)

setRateFunctionFromString

public void setRateFunctionFromString(String formula,
                             AcReaction reaction,
                             boolean forwardFlag)

getSettingFunctionAsString

public String getSettingFunctionAsString(AcSpeciesInteraction speciesAction)

setSettingFunctionFromString

public void setSettingFunctionFromString(String formula,
                                AcSpeciesInteraction speciesAction)

getSettingFunctionAsString

public String getSettingFunctionAsString(AcInteractionVariableAssignment variableAssignment)

setSettingFunctionFromString

public void setSettingFunctionFromString(String formula,
                                AcInteractionVariableAssignment variableAssignment)

getTranslationFunctionAsString

public String getTranslationFunctionAsString(AcTranslationItem translationItem)

getTranslationFunctionReferencedSpecies

public Collection<AcSpecies> getTranslationFunctionReferencedSpecies(AcTranslationItem translationItem)

getTranslationFunctionReferencedVariables

public Collection<AcTranslationVariable> getTranslationFunctionReferencedVariables(AcTranslationItem translationItem)

setTranslationFunctionFromString

public void setTranslationFunctionFromString(String formula,
                                    AcTranslationItem translationItem)

setEvolFunctionFromString

public void setEvolFunctionFromString(String formula,
                             AcParameter parameter)

setEvaluationFunctionFromString

public void setEvaluationFunctionFromString(String formula,
                                   AcEvaluation evaluation)

getReactantsAsString

public Collection<String> getReactantsAsString(AcReaction reaction)

getProductsAsString

public Collection<String> getProductsAsString(AcReaction reaction)

getDNAStrandSpeciesSetAsString

public String getDNAStrandSpeciesSetAsString(AcDNAStrandSpeciesSet speciesSet,
                                    String separator)

getSpeciesAsString

public String getSpeciesAsString(Collection<? extends AcSpecies> species,
                        String separator)

setSpeciesAssociationsFromString

public void setSpeciesAssociationsFromString(String speciesAssociationsString,
                                    AcSpeciesAssociationType assocType,
                                    AcReaction reaction)

updateSpeciesAssociations

public void updateSpeciesAssociations(String speciesAssociationsString,
                             AcSpeciesAssociationType assocType,
                             AcReaction reaction)

updateSpeciesAssociations

public void updateSpeciesAssociations(Collection<AcSpeciesReactionAssociation> newSpeciesAssociations,
                             AcSpeciesAssociationType assocType,
                             AcReaction reaction)

getLatexTable

public String getLatexTable(AcReactionSet reactionSet,
                   boolean includeRates)

getLabelVariableMap

public <M extends AcVariable<?>> Map<String,M> getLabelVariableMap(AcVariableSetIF<M> variableSet)

getIndexVariableMap

public <M extends AcVariable<?>> Map<Integer,M> getIndexVariableMap(AcVariableSetIF<M> variableSet)

getOrderedVariableLabelMap

public Map<Integer,String> getOrderedVariableLabelMap(AcVariableSetIF<?> variableSet)

getVariableIndeces

public Set<Integer> getVariableIndeces(AcVariableSetIF<? extends AcVariable<?>> variableSet)

getVariableIndeces

public Set<Integer> getVariableIndeces(Collection<? extends AcVariable<?>> variables)

getVariableLabels

public Set<String> getVariableLabels(AcVariableSetIF<? extends AcVariable<?>> variableSet)

getVariableLabels

public Set<String> getVariableLabels(Collection<? extends AcVariable<?>> variables)

getVariableLabelsAsString

public String getVariableLabelsAsString(Collection<? extends AcVariable<?>> variables)

getVariableLabelsAsString

public String getVariableLabelsAsString(Collection<? extends AcVariable<?>> variables,
                               String separator)

createFoldExpression

public String createFoldExpression(Collection<AcSpeciesReactionAssociation> speciesAssociations,
                          AcCollectiveSpeciesReactionAssociationType collectiveSpeciesReactionAssociationType,
                          boolean wrapIfNeeded)

createFoldOrderedExpression

public String createFoldOrderedExpression(Collection<AcSpeciesReactionAssociation> speciesAssociations,
                                 String operation,
                                 boolean wrapIfNeeded)

wrapIfNeeded

public String wrapIfNeeded(String expression,
                  Collection<AcSpeciesReactionAssociation> speciesAssociations)

getReferencedSpeciesIndeces

public Set<Integer> getReferencedSpeciesIndeces(AcTranslationSeries translationSeries)

getReferencedSpecies

public Set<AcSpecies> getReferencedSpecies(AcTranslation rangeTranslation)

getReferencedSpecies

public Set<AcSpecies> getReferencedSpecies(AcTranslationSeries translationSeries)

getReferencedSpecies

public Set<AcSpecies> getReferencedSpecies(AcReactionSet reactionSet)

getLabelReactionMap

public Map<String,AcReaction> getLabelReactionMap(AcReactionSet reactionSet)

getVariablePlaceholder

public String getVariablePlaceholder(AcSpeciesReactionAssociation speciesAssoc)

addReactions

public void addReactions(AcReactionSet reactionSet,
                AcReactionSet additionalReactionSet)
                  throws BndChemistryValidationException

Throws:

BndChemistryValidationException

getNewSpecies

public Collection<AcSpecies> getNewSpecies(AcReactionSet reactionSet,
                                  AcReactionSet additionalReactionSet)
                                    throws BndChemistryValidationException

Throws:

BndChemistryValidationException

replaceSpeciesSet

public void replaceSpeciesSet(AcReactionSet reactionSet,
                     AcSpeciesSet newSpeciesSet)
                       throws BndChemistryValidationException

Throws:

BndChemistryValidationException

replaceSpeciesSet

public void replaceSpeciesSet(AcInteractionSeries interactionSeries,
                     AcSpeciesSet newSpeciesSet)
                       throws BndChemistryValidationException

Throws:

BndChemistryValidationException

addInteractions

public void addInteractions(AcInteractionSeries targetInteractionSeries,
                   AcInteractionSeries sourceInteractionSeries)
                     throws BndChemistryValidationException

Throws:

BndChemistryValidationException

getSpeciesAndInteractionVariablesToRemove

public com.banda.core.Pair<Collection<AcSpeciesInteraction>,Collection<AcInteractionVariableAssignment>> getSpeciesAndInteractionVariablesToRemove(AcInteractionSeries interactionSeries,
                                                                                                                                          AcInteractionSeries sourceInteractionSeries)

getNewInteractionVariables

public Collection<AcInteractionVariable> getNewInteractionVariables(AcInteractionSeries interactionSeries,
                                                           AcInteractionSeries sourceInteractionSeries)

getSpecies

public Collection<AcSpecies> getSpecies(Collection<AcSpeciesReactionAssociation> assocs)

filterOutSpecies

public Set<AcSpecies> filterOutSpecies(Collection<AcReaction> reactions,
                              Collection<AcSpecies> species,
                              AcSpeciesAssociationType type)