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public interface MixedFluxome
This interface is used to represent fluxomes that contain multiple types of chemical reactions. These reaction types include: irreversible internal reactions, reversible internal reactions, source reactions, sink reactions, and reversible exchange reactions.
Method Summary | |
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void |
checkRxnName(java.lang.String reactionName)
Ensures the provided string is a valid reaction name. |
void |
checkRxnNames(java.util.Collection<java.lang.String> rxnNames)
Ensures each element of the provided collection is a valid reaction name. |
Or<And<java.lang.String>> |
getCatalystRule(java.lang.String rxnName)
Returns the boolean logic statement for the catalysts of the reaction with the provided name. |
java.util.Map<java.lang.String,Or<And<java.lang.String>>> |
getCatalystRules()
Returns all of the boolean logic statements regarding reaction catalysis. |
ExchangeRxn |
getExchangeRxn(java.lang.String rxnName)
Returns the exchange reaction in this fluxome with the provided name. |
java.util.Map<java.lang.String,ExchangeRxn> |
getExchangeRxns()
Returns all of the exchange reactions contained in this fluxome. |
java.util.Map<java.lang.String,ExchangeRxn> |
getExchangeRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the exchange reactions with the provided names. |
ChemRxn |
getInternalRxn(java.lang.String rxnName)
Returns the internal reaction in this fluxome with the provided name. |
java.util.Map<java.lang.String,ChemRxn> |
getInternalRxns()
Returns all of the internal reactions in this fluxome. |
java.util.Map<java.lang.String,ChemRxn> |
getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the internal reactions with the provided names. |
MixedFluxome |
replaceConstraints(FluxConstraints constraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
Methods inherited from interface sbrt.kernel.fba.CatalyzedFluxome |
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areReqCatalysts, catalysts, getCatalysts, getCatalyzedRxnNames, getCatalyzedRxns, isCatalyst, isReqCatalyst |
Methods inherited from interface sbrt.kernel.fba.Fluxome |
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addedConstraints, areRxnNames, exchangeRxns, getConstraints, getExchangeRxnNames, getFluxConstraint, getInternalRxnNames, getRxn, getRxnExprConstraint, getRxnNames, getRxns, getRxns, getSpecies, getStoichMatrix, internalRxns, isExchangeRxnName, isFluxVector, isInternalRxnName, isRxnName, isSpecies, isValid, rxns, species |
Method Detail |
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void checkRxnNames(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- a collection of strings.
java.lang.IllegalArgumentException
- if any element of this collection
is not a valid reaction name.
java.lang.NullPointerException
- if the collection is null.void checkRxnName(java.lang.String reactionName)
reactionName
- a potential reaction name.
java.lang.IllegalArgumentException
- if the provided string
is not a valid reaction name.java.util.Map<java.lang.String,ChemRxn> getInternalRxns()
getInternalRxns
in interface Fluxome
java.util.Map<java.lang.String,ChemRxn> getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- the names of the reactions to be returned.
java.util.Map<java.lang.String,ExchangeRxn> getExchangeRxns(java.util.Collection<java.lang.String> rxnNames)
rxnNames
- the names of the reactions to be returned.
java.util.Map<java.lang.String,ExchangeRxn> getExchangeRxns()
getExchangeRxns
in interface Fluxome
ChemRxn getInternalRxn(java.lang.String rxnName)
rxnName
- the name of the internal reaction to return.
ExchangeRxn getExchangeRxn(java.lang.String rxnName)
rxnName
- the name of the exchange reaction to return.
MixedFluxome replaceConstraints(FluxConstraints constraints, double constraintTolerance)
replaceConstraints
in interface CatalyzedFluxome
replaceConstraints
in interface Fluxome
constraints
- the new set of flux constraints.constraintTolerance
- the allowed amount by which constraints can violate their
maximum defined intervals. These maximum defined intervals are
implementation-dependent.
Or<And<java.lang.String>> getCatalystRule(java.lang.String rxnName)
getCatalystRule
in interface CatalyzedFluxome
rxnName
- the name of the reaction for which the catalyst rules are to
be returned.
java.util.Map<java.lang.String,Or<And<java.lang.String>>> getCatalystRules()
getCatalystRules
in interface CatalyzedFluxome
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