Uses of Class
sbrt.kernel.fba.IrrevRxn

Packages that use IrrevRxn
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
 

Methods in sbrt.kernel.fba that return IrrevRxn
 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
 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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Map<T,IrrevRxn>
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.
 java.util.Map<java.lang.String,IrrevRxn> IrrevRxnFluxome.getInternalRxns()
          Returns all of the internal reactions in this fluxome.
 java.util.Map<java.lang.String,IrrevRxn> IrrevRxnFluxomeV1.getInternalRxns()
          Returns all of the internal reactions in this fluxome.
 java.util.Map<java.lang.String,IrrevRxn> IrrevRxnFluxome.getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the internal reactions with the provided names.
 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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Map<T,IrrevRxn>
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
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
static
<T extends java.lang.Comparable<? super T>>
java.util.Collection<java.util.Set<T>>
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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Set<T>
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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Map<T,IrrevRxn>
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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Set<T>
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.
static
<T extends java.lang.Comparable<? super T>>
java.util.Map<T,IrrevRxn>
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
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 IrrevRxn in sbrt.kernel.fba.proc
 

Methods in sbrt.kernel.fba.proc that return types with arguments of type IrrevRxn
 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
 

Methods in sbrt.shell.text.chem that return IrrevRxn
 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
 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
 

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