Uses of Class
sbrt.kernel.fba.SinkRxn

Packages that use SinkRxn
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
 

Methods in sbrt.kernel.fba that return SinkRxn
 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
static
<T extends java.lang.Comparable<? super T>>
java.util.Map<T,SinkRxn>
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.
 java.util.Map<java.lang.String,SinkRxn> IrrevRxnFluxome.getSinkRxns()
          Returns the set of all sink reactions in this fluxome.
 java.util.Map<java.lang.String,SinkRxn> IrrevRxnFluxomeV1.getSinkRxns()
          Returns all of the sinks in this fluxome.
 java.util.Map<java.lang.String,SinkRxn> IrrevRxnFluxome.getSinkRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the sink reactions with the provided names.
 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
static boolean RxnComparer.equivSinkRxns(SinkRxn rxn1, SinkRxn rxn2)
          Indicates if the provided sink reactions are stoichiometrically equivalent.
static
<T extends java.lang.Comparable<? super T>>
java.util.Set<T>
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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Map<T,SourceRxn>
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.
static boolean RxnComparer.reverseExchangeRxns(SinkRxn rxn1, SourceRxn rxn2)
          Indicates if the provided exchange reactions are the reverse of each other.
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
static
<T extends java.lang.Comparable<? super T>>
java.util.Collection<java.util.Set<T>>
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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Set<T>
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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Map<T,SinkRxn>
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
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.
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
 

Methods in sbrt.shell.text.fba with parameters of type SinkRxn
 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.