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Packages that use SinkRxn | |
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sbrt.kernel.fba | Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. |
sbrt.shell.text.fba | Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. |
Uses of SinkRxn in sbrt.kernel.fba |
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Methods in sbrt.kernel.fba that return SinkRxn | |
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SinkRxn |
IrrevRxnFluxome.getSinkRxn(java.lang.String rxnName)
Returns the sink reaction in this fluxome with the provided name. |
SinkRxn |
IrrevRxnFluxomeV1.getSinkRxn(java.lang.String reactionName)
Returns the sink reaction in this fluxome with the provided name. |
Methods in sbrt.kernel.fba that return types with arguments of type SinkRxn | ||
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static
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RxnComparer.getReverseSinkRxns(SourceRxn source,
java.util.Map<T,SinkRxn> rxns)
Returns all of the sink reactions in the provided map that are the reverse of the provided source reaction. |
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java.util.Map<java.lang.String,SinkRxn> |
IrrevRxnFluxome.getSinkRxns()
Returns the set of all sink reactions in this fluxome. |
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java.util.Map<java.lang.String,SinkRxn> |
IrrevRxnFluxomeV1.getSinkRxns()
Returns all of the sinks in this fluxome. |
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java.util.Map<java.lang.String,SinkRxn> |
IrrevRxnFluxome.getSinkRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the sink reactions with the provided names. |
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java.util.Map<java.lang.String,SinkRxn> |
IrrevRxnFluxomeV1.getSinkRxns(java.util.Collection<java.lang.String> rxnNames)
Returns the sink reactions whose names appear in the provided collection of reaction names. |
Methods in sbrt.kernel.fba with parameters of type SinkRxn | ||
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static boolean |
RxnComparer.equivSinkRxns(SinkRxn rxn1,
SinkRxn rxn2)
Indicates if the provided sink reactions are stoichiometrically equivalent. |
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static
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RxnComparer.getReverseSourceRxnIds(SinkRxn sink,
java.util.Map<T,SourceRxn> rxns)
Returns all of the keys in the provided map that correspond to the source reactions that are the reverse of the provided sink reaction. |
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static
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RxnComparer.getReverseSourceRxns(SinkRxn sink,
java.util.Map<T,SourceRxn> rxns)
Returns all of the source reactions in the provided map that are the reverse of the provided sink reaction. |
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static boolean |
RxnComparer.reverseExchangeRxns(SinkRxn rxn1,
SourceRxn rxn2)
Indicates if the provided exchange reactions are the reverse of each other. |
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static boolean |
RxnComparer.reverseExchangeRxns(SourceRxn rxn1,
SinkRxn rxn2)
Indicates if the provided exchange reactions are the reverse of each other. |
Method parameters in sbrt.kernel.fba with type arguments of type SinkRxn | ||
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static
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RxnComparer.getEquivSinkRxnIds(java.util.Map<T,SinkRxn> 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.getReverseSinkRxnIds(SourceRxn source,
java.util.Map<T,SinkRxn> rxns)
Returns all of the keys in the provided map that correspond to the sink reactions that are the reverse of the provided source reaction. |
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static
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RxnComparer.getReverseSinkRxns(SourceRxn source,
java.util.Map<T,SinkRxn> rxns)
Returns all of the sink reactions in the provided map that are the reverse of the provided source reaction. |
Constructor parameters in sbrt.kernel.fba with type arguments of type SinkRxn | |
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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 SinkRxn in sbrt.shell.text.fba |
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Methods in sbrt.shell.text.fba with parameters of type SinkRxn | |
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java.lang.String |
RxnFormatV1.format(SinkRxn rxn)
Returns a formatted string representation of the provided sink reaction. |
java.lang.String |
IrrevRxnFormatV2.format(SinkRxn sink)
Returns a formatted string representation of the provided sink. |
java.lang.String |
IrrevRxnFormatV1.format(SinkRxn sink)
Returns a formatted string representation of the provided sink. |
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