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Packages that use IrrevRxn | |
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sbrt.kernel.fba | Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. |
sbrt.kernel.fba.proc | Provides classes and interfaces for executing Flux Balance Analysis processes. |
sbrt.shell.text.chem | Provides classes and interfaces for defining formats for chemistry related objects. |
sbrt.shell.text.fba | Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. |
Uses of IrrevRxn in sbrt.kernel.fba |
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Methods in sbrt.kernel.fba that return IrrevRxn | |
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IrrevRxn |
IrrevRxnFluxome.getInternalRxn(java.lang.String rxnName)
Returns the internal reaction in this fluxome with the provided name. |
IrrevRxn |
IrrevRxnFluxomeV1.getInternalRxn(java.lang.String reactionName)
Returns the internal reaction in this fluxome with the provided name. |
Methods in sbrt.kernel.fba that return types with arguments of type IrrevRxn | ||
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java.util.Map<java.lang.String,IrrevRxn> |
IrrevRxnFluxomeV1.getCatalyzedRxns(java.lang.String catalyst)
Returns all of the internal reactions contained in this fluxome that are catalyzed by the provided catalyst. |
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static
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RxnComparer.getEquivIrrevRxns(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns the reactions in the provided map that are stoichiometrically equivalent to the reaction in the map with the provided map key. |
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java.util.Map<java.lang.String,IrrevRxn> |
IrrevRxnFluxome.getInternalRxns()
Returns all of the internal reactions in this fluxome. |
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java.util.Map<java.lang.String,IrrevRxn> |
IrrevRxnFluxomeV1.getInternalRxns()
Returns all of the internal reactions in this fluxome. |
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java.util.Map<java.lang.String,IrrevRxn> |
IrrevRxnFluxome.getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the internal reactions with the provided names. |
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java.util.Map<java.lang.String,IrrevRxn> |
IrrevRxnFluxomeV1.getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the internal reactions whose names appear in the provided collection of reaction names. |
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static
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RxnComparer.getReverseIrrevRxns(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns all of the reactions in the provided map that are the reverse of the reaction specified by the provided key. |
Methods in sbrt.kernel.fba with parameters of type IrrevRxn | |
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static boolean |
RxnComparer.equivIrrevRxns(IrrevRxn rxn1,
IrrevRxn rxn2)
Indicates if the provided irreversible reactions are stoichiometrically equivalent. |
static boolean |
RxnComparer.reverseIrrevRxns(IrrevRxn rxn1,
IrrevRxn rxn2)
Indicates if the provided chemical reactions are the reverse of each other. |
Method parameters in sbrt.kernel.fba with type arguments of type IrrevRxn | ||
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static
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RxnComparer.getEquivIrrevRxnIds(java.util.Map<T,IrrevRxn> rxns)
Returns a collection of sets of the names of stoichiometrically equivalent reactions contained in the provided map. |
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static
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RxnComparer.getEquivIrrevRxnIds(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns the keys in the provided map that correspond to reactions that are stoichiometrically equivalent to the reaction in the map with the specified map key. |
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static
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RxnComparer.getEquivIrrevRxns(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns the reactions in the provided map that are stoichiometrically equivalent to the reaction in the map with the provided map key. |
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static
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RxnComparer.getReverseIrrevRxnIds(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns all of the keys in the provided map that correspond to reactions that are the reverse of the reaction specified by the provided key. |
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static
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RxnComparer.getReverseIrrevRxns(T rxnId,
java.util.Map<T,IrrevRxn> rxns)
Returns all of the reactions in the provided map that are the reverse of the reaction specified by the provided key. |
Constructor parameters in sbrt.kernel.fba with type arguments of type IrrevRxn | |
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IrrevRxnFluxomeV1(java.util.Map<java.lang.String,IrrevRxn> internalRxns,
java.util.Map<java.lang.String,SourceRxn> sourceRxns,
java.util.Map<java.lang.String,SinkRxn> sinkRxns)
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions. |
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IrrevRxnFluxomeV1(java.util.Map<java.lang.String,IrrevRxn> internalRxns,
java.util.Map<java.lang.String,SourceRxn> sourceRxns,
java.util.Map<java.lang.String,SinkRxn> sinkRxns,
java.util.Map<java.lang.String,Or<And<java.lang.String>>> catalysts)
Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions and catalysts. |
Uses of IrrevRxn in sbrt.kernel.fba.proc |
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Methods in sbrt.kernel.fba.proc that return types with arguments of type IrrevRxn | |
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java.util.Map<java.lang.String,IrrevRxn> |
RevRxnBreakerProcess.breakRxn(java.lang.String rxnId,
RevRxn rxn)
Breaks a reversible reaction into a pair of irreversible reactions. |
Uses of IrrevRxn in sbrt.shell.text.chem |
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Methods in sbrt.shell.text.chem that return IrrevRxn | |
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IrrevRxn |
IrrevRxnFormatV1.parse(java.lang.String reaction)
Parses the provided string and returns its corresponding irreversible reaction. |
Methods in sbrt.shell.text.chem with parameters of type IrrevRxn | |
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java.lang.String |
IrrevRxnFormatV1.format(IrrevRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
Uses of IrrevRxn in sbrt.shell.text.fba |
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Methods in sbrt.shell.text.fba with parameters of type IrrevRxn | |
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java.lang.String |
RxnFormatV1.format(IrrevRxn rxn)
Returns a formatted string representation of the provided irreversible reaction. |
java.lang.String |
IrrevRxnFormatV2.format(IrrevRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
java.lang.String |
IrrevRxnFormatV1.format(IrrevRxn rxn)
Returns a formatted string representation of the provided irreversible chemical reaction. |
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