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public interface CatalyzedFluxome
This interface is used to represent fluxomes with catalyzed reactions.
Method Summary | |
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boolean |
areReqCatalysts(java.util.Collection<java.lang.String> catalysts,
java.lang.String rxnName)
Indicates if the reaction with the provided name could function if each of the catalysts in the provided collection were simultaneously absent. |
int |
catalysts()
Returns the total number of catalysts contained in this fluxome. |
LogicalRelation<?> |
getCatalystRule(java.lang.String rxnName)
Returns the boolean logic rule for catalysts of the reaction with the provided name. |
java.util.Map<java.lang.String,? extends LogicalRelation<?>> |
getCatalystRules()
Returns the boolean logic rules for the catalysts of all reactions in this fluxome. |
java.util.Set<java.lang.String> |
getCatalysts()
Returns the set of all catalysts contained in this fluxome. |
java.util.Set<java.lang.String> |
getCatalyzedRxnNames(java.lang.String catalyst)
Returns the set of names of all chemical reactions contained in this fluxome that are catalyzed by the provided catalyst. |
java.util.Map<java.lang.String,? extends ChemRxn> |
getCatalyzedRxns(java.lang.String catalyst)
Returns the chemical reactions contained in this fluxome that are catalyzed by the provided catalyst. |
boolean |
isCatalyst(java.lang.String s)
Indicates if the provided string is the name of a catalyst contained in this fluxome. |
boolean |
isReqCatalyst(java.lang.String catalyst,
java.lang.String rxnName)
Indicates if the provided catalyst is required for the reaction with the provided name. |
CatalyzedFluxome |
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.Fluxome |
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addedConstraints, areRxnNames, exchangeRxns, getConstraints, getExchangeRxnNames, getExchangeRxns, getFluxConstraint, getInternalRxnNames, getInternalRxns, getRxn, getRxnExprConstraint, getRxnNames, getRxns, getRxns, getSpecies, getStoichMatrix, internalRxns, isExchangeRxnName, isFluxVector, isInternalRxnName, isRxnName, isSpecies, isValid, rxns, species |
Method Detail |
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java.util.Map<java.lang.String,? extends ChemRxn> getCatalyzedRxns(java.lang.String catalyst)
catalyst
- the name of the catalyst whose reactions are to be returned.
java.util.Set<java.lang.String> getCatalyzedRxnNames(java.lang.String catalyst)
catalyst
- the name of the catalyst whose reaction names are to be
returned.
LogicalRelation<?> getCatalystRule(java.lang.String rxnName)
rxnName
- the name of the reaction whose catalyst rule are to be
returned.
java.util.Map<java.lang.String,? extends LogicalRelation<?>> getCatalystRules()
java.util.Set<java.lang.String> getCatalysts()
boolean isCatalyst(java.lang.String s)
s
- the string to test.
true
if the string is a valid catalyst; false
otherwise.int catalysts()
boolean isReqCatalyst(java.lang.String catalyst, java.lang.String rxnName)
catalyst
- the catalyst.rxnName
- the name of the reaction.
true
if the provided catalyst is required by the reaction
with the provided name; false
otherwise.boolean areReqCatalysts(java.util.Collection<java.lang.String> catalysts, java.lang.String rxnName)
catalysts
- the collection of catalysts.rxnName
- the name of the reaction.
true
if the provided catalysts are required for the
specified reaction to function; false
otherwise.
java.lang.IllegalArgumentException
- if rxnName
is not a valid reaction name.CatalyzedFluxome replaceConstraints(FluxConstraints constraints, double constraintTolerance)
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.
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