Uses of Class
sbrt.kernel.fba.SourceRxn

Packages that use SourceRxn
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 SourceRxn in sbrt.kernel.fba
 

Methods in sbrt.kernel.fba that return SourceRxn
 SourceRxn IrrevRxnFluxome.getSourceRxn(java.lang.String rxnName)
          Returns the source reaction in this fluxome with the provided name.
 SourceRxn IrrevRxnFluxomeV1.getSourceRxn(java.lang.String reactionName)
          Returns the source reaction in this fluxome with the provided name.
 

Methods in sbrt.kernel.fba that return types with arguments of type SourceRxn
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.
 java.util.Map<java.lang.String,SourceRxn> IrrevRxnFluxome.getSourceRxns()
          Returns the set of all source reactions in this fluxome.
 java.util.Map<java.lang.String,SourceRxn> IrrevRxnFluxomeV1.getSourceRxns()
          Returns all of the sources in this fluxome.
 java.util.Map<java.lang.String,SourceRxn> IrrevRxnFluxome.getSourceRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the source reactions with the provided names.
 java.util.Map<java.lang.String,SourceRxn> IrrevRxnFluxomeV1.getSourceRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the source reactions whose names appear in the provided collection of reaction names.
 

Methods in sbrt.kernel.fba with parameters of type SourceRxn
static boolean RxnComparer.equivSourceRxns(SourceRxn rxn1, SourceRxn rxn2)
          Indicates if the provided source reactions are stoichiometrically equivalent.
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.
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 SourceRxn
static
<T extends java.lang.Comparable<? super T>>
java.util.Collection<java.util.Set<T>>
RxnComparer.getEquivSourceRxnIds(java.util.Map<T,SourceRxn> 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.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.
 

Constructor parameters in sbrt.kernel.fba with type arguments of type SourceRxn
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 SourceRxn in sbrt.shell.text.fba
 

Methods in sbrt.shell.text.fba with parameters of type SourceRxn
 java.lang.String RxnFormatV1.format(SourceRxn rxn)
          Returns a formatted string representation of the provided source reaction.
 java.lang.String IrrevRxnFormatV2.format(SourceRxn source)
          Returns a formatted string representation of the provided source.
 java.lang.String IrrevRxnFormatV1.format(SourceRxn source)
          Returns a formatted string representation of the provided source.