Uses of Interface
sbrt.kernel.fba.ChemRxn

Packages that use ChemRxn
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.mng.fba Provides classes and interfaces for creating Flux Balance Analysis process managers. 
sbrt.shell.proc.fba Provides classes for converting FBA-related files of different formats. 
sbrt.shell.text.fba Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. 
 

Uses of ChemRxn in sbrt.kernel.fba
 

Subinterfaces of ChemRxn in sbrt.kernel.fba
 interface ExchangeRxn
          This interface is used to represent exchange reactions.
 

Classes in sbrt.kernel.fba that implement ChemRxn
 class AbstractExchangeRxn
          This class is a skeleton implementation of ExchangeRxn.
 class AbstractRxn
          This class is a skeleton implementation of ChemicalRxn.
 class IrrevRxn
          This class is used to represent irreversible chemical reactions.
 class RevExchRxn
          This class is used to represent reversible exchange reactions, that is, exchange reactions that can both supply and consume chemical species to and from a chemical system.
 class RevRxn
          This class is used to represent reversible chemical reactions.
 class SinkRxn
          This class is used to represent exchange reactions that transport chemicals from a chemical system to its surroundings.
 class SourceRxn
          This class is used to represent exchange reactions that transport chemicals to a chemical system from its surroundings.
 

Methods in sbrt.kernel.fba that return ChemRxn
 ChemRxn MixedFluxomeV1.getInternalRxn(java.lang.String reactionName)
          Returns the internal reaction in this fluxome with the provided name.
 ChemRxn MixedFluxome.getInternalRxn(java.lang.String rxnName)
          Returns the internal reaction in this fluxome with the provided name.
 ChemRxn MixedFluxomeV1.getRxn(java.lang.String reactionName)
          Returns the chemical reaction in this fluxome with the provided name.
 ChemRxn Fluxome.getRxn(java.lang.String reactionName)
          Returns the chemical reaction in this fluxome with the provided name.
 ChemRxn IrrevRxnFluxomeV1.getRxn(java.lang.String reactionName)
          Returns the chemical reaction in this fluxome with the provided name.
 

Methods in sbrt.kernel.fba that return types with arguments of type ChemRxn
 java.util.Map<java.lang.String,ChemRxn> MixedFluxomeV1.getCatalyzedRxns(java.lang.String catalyst)
          Returns all of the internal reactions contained in this fluxome that are catalyzed by the provided catalyst.
 java.util.Map<java.lang.String,? extends ChemRxn> CatalyzedFluxome.getCatalyzedRxns(java.lang.String catalyst)
          Returns the chemical reactions contained in this fluxome that are catalyzed by the provided catalyst.
 java.util.Map<java.lang.String,ChemRxn> MixedFluxomeV1.getInternalRxns()
          Returns all of the internal reactions in this fluxome.
 java.util.Map<java.lang.String,? extends ChemRxn> Fluxome.getInternalRxns()
          Returns the set of all internal chemical reactions contained in this fluxome.
 java.util.Map<java.lang.String,ChemRxn> MixedFluxome.getInternalRxns()
          Returns all of the internal reactions in this fluxome.
 java.util.Map<java.lang.String,ChemRxn> MixedFluxomeV1.getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the internal reactions whose names appear in the provided collection of reaction names.
 java.util.Map<java.lang.String,ChemRxn> MixedFluxome.getInternalRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the internal reactions with the provided names.
 java.util.Map<java.lang.String,ChemRxn> MixedFluxomeV1.getRxns()
          Returns all chemical reactions contained in this fluxome.
 java.util.Map<java.lang.String,ChemRxn> Fluxome.getRxns()
          Returns the set of all chemical reactions contained in this fluxome.
 java.util.Map<java.lang.String,ChemRxn> IrrevRxnFluxomeV1.getRxns()
          Returns all chemical reactions contained in this fluxome.
 java.util.Map<java.lang.String,ChemRxn> MixedFluxomeV1.getRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the chemical reactions with the provided names.
 java.util.Map<java.lang.String,ChemRxn> Fluxome.getRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the chemical reactions with the provided names.
 java.util.Map<java.lang.String,ChemRxn> IrrevRxnFluxomeV1.getRxns(java.util.Collection<java.lang.String> rxnNames)
          Returns the chemical reactions with the provided names.
 

Methods in sbrt.kernel.fba with parameters of type ChemRxn
static boolean RxnComparer.equivChemRxns(ChemRxn rxn1, ChemRxn rxn2)
          Indicates if the provided chemical reactions are stoichiometrically equivalent.
static boolean RxnComparer.reverseChemRxns(ChemRxn rxn1, ChemRxn rxn2)
          Indicates if the provided chemical reactions are the reverse of each other.
 

Constructor parameters in sbrt.kernel.fba with type arguments of type ChemRxn
IrrevRxnFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
          Constructs a new irreversible reaction fluxome from the provided internal and exchange reactions.
IrrevRxnFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns, 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.
MixedFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
          Constructs a new mixed fluxome from the provided internal and exchange reactions.
MixedFluxomeV1(java.util.Map<java.lang.String,? extends ChemRxn> rxns, java.util.Map<java.lang.String,Or<And<java.lang.String>>> catalysts)
          Constructs a new mixed fluxome from the provided internal and exchange reactions and catalysts.
 

Uses of ChemRxn in sbrt.kernel.fba.proc
 

Methods in sbrt.kernel.fba.proc that return types with arguments of type ChemRxn
 java.util.Map<java.lang.String,ChemRxn> RevRxnBreakerProcess.breakRxns(java.util.Map<java.lang.String,ChemRxn> rxns)
          Breaks reversible reactions into pairs of irreversible reactions.
 

Method parameters in sbrt.kernel.fba.proc with type arguments of type ChemRxn
 java.util.Map<java.lang.String,ChemRxn> RevRxnBreakerProcess.breakRxns(java.util.Map<java.lang.String,ChemRxn> rxns)
          Breaks reversible reactions into pairs of irreversible reactions.
 void RevRxnBreakerProcess.run(ResultsManager<java.util.Map<java.lang.String,ChemRxn>> resultsManager)
          Breaks the reversible reactions supplied to this process and adds the result to the provided manager.
 void RevRxnBreakerProcess.setRxns(java.util.Map<java.lang.String,? extends ChemRxn> rxns)
          Sets the reactions for which reversible reactions will be broken.
 

Uses of ChemRxn in sbrt.shell.mng.fba
 

Methods in sbrt.shell.mng.fba that return types with arguments of type ChemRxn
static RomoFile<java.lang.String,ChemRxn> WwFluxomeReducerManager.getOutputFile(java.lang.String fileName)
          Returns a file to which the chemical reactions of a fluxome can be written.
static RomoFile<java.lang.String,ChemRxn> WwFluxomeReducerManager.getOutputFile(java.lang.String fileName, java.io.PrintWriter out)
          Returns a file to which the chemical reactions of a fluxome can be written.
 

Uses of ChemRxn in sbrt.shell.proc.fba
 

Methods in sbrt.shell.proc.fba that return types with arguments of type ChemRxn
 java.util.Map<java.lang.String,ChemRxn> MetatoolInputReader.Results.getCat()
          Returns the reactions that are listed in the -CAT section of the input file.
 

Uses of ChemRxn in sbrt.shell.text.fba
 

Methods in sbrt.shell.text.fba that return ChemRxn
 ChemRxn RevRxnFormatV1.parse(java.lang.String reaction)
          Parses the provided string and returns its corresponding chemical reaction.
 ChemRxn RxnFormatV1.parse(java.lang.String reaction)
          Parses the provided string and returns its corresponding chemical reaction.
 ChemRxn IrrevRxnFormatV2.parse(java.lang.String reaction)
          Parses the provided string and returns its corresponding chemical reaction.
 ChemRxn RevRxnFormatV2.parse(java.lang.String reaction)
          Parses the provided string and returns its corresponding chemical reaction.
 ChemRxn IrrevRxnFormatV1.parse(java.lang.String reaction)
          Parses the provided string and returns its corresponding chemical reaction.
 

Methods in sbrt.shell.text.fba that return types with arguments of type ChemRxn
 PipeListFormat<ChemRxn> IrfFormatV1.getListFormat()
          Returns the format used for lists of reactions.
 PipeListFormat<ChemRxn> MixedFluxomeFormatV1.getListFormat()
          Returns the format used for lists of reactions.
 

Methods in sbrt.shell.text.fba with parameters of type ChemRxn
 java.lang.String RevRxnFormatV1.format(ChemRxn rxn)
          Returns a formatted string representation of the provided irreversible chemical reaction.
 java.lang.String RxnFormatV1.format(ChemRxn rxn)
          Returns a formatted string representation of the provided irreversible chemical reaction.
 java.lang.String IrrevRxnFormatV2.format(ChemRxn rxn)
          Returns a formatted string representation of the provided irreversible chemical reaction.
 java.lang.String RevRxnFormatV2.format(ChemRxn rxn)
          Returns a formatted string representation of the provided irreversible chemical reaction.
 java.lang.String IrrevRxnFormatV1.format(ChemRxn rxn)
          Returns a formatted string representation of the provided irreversible chemical reaction.