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Packages that use Fluxome | |
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sbrt.kernel.fba | Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. |
sbrt.kernel.fba.comp | Provides classes and interfaces for performing Flux Balance Analysis computations. |
sbrt.kernel.fba.proc | Provides classes and interfaces for executing Flux Balance Analysis processes. |
sbrt.shell.io.fba | Provides classes and interfaces for reading and writing files relevant to Flux Balance Analysis. |
sbrt.shell.mng.fba | Provides classes and interfaces for creating Flux Balance Analysis process managers. |
sbrt.shell.text.fba | Provides classes and interfaces for defining formats for objects relevant to Flux Balance Analysis. |
Uses of Fluxome in sbrt.kernel.fba |
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Subinterfaces of Fluxome in sbrt.kernel.fba | |
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interface |
CatalyzedFluxome
This interface is used to represent fluxomes with catalyzed reactions. |
interface |
IrrevRxnFluxome
This interface is used to represent fluxomes that contain only irreversible reactions. |
interface |
MixedFluxome
This interface is used to represent fluxomes that contain multiple types of chemical reactions. |
Classes in sbrt.kernel.fba that implement Fluxome | |
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class |
IrrevRxnFluxomeV1
This class is a concrete implementation of IrrevRxnFluxome . |
class |
MixedFluxomeV1
This class is a concrete implementation of MixedFluxome . |
Methods in sbrt.kernel.fba that return Fluxome | |
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Fluxome |
Fluxome.replaceConstraints(FluxConstraints constraints,
double constraintTolerance)
Returns a copy of this fluxome, but with all constraints replaced by those provided. |
Uses of Fluxome in sbrt.kernel.fba.comp |
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Classes in sbrt.kernel.fba.comp with type parameters of type Fluxome | |
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class |
AbstractCvComputer<F extends Fluxome>
This abstract class is a skeleton implementation of FluxCvComputer. |
class |
AbstractFluxIntervalComputer<F extends Fluxome>
This abstract class is a skeleton implemenation of FluxIntervalComputer. |
class |
CdHarFluxComp<F extends Fluxome>
This class is used to compute randomly distributed vectors within flux space. |
interface |
CycleComputer<F extends Fluxome>
This interface is used to represent algorithms for identifying steady state cycles in stoichiometric networks. |
class |
FbaOptimizer<F extends Fluxome>
This class is the workhorse of all Flux Balance Analysis optimizations. |
interface |
FluxCvComputer<F extends Fluxome>
This interface is used to represent a flux constraint variation computer. |
interface |
FluxIntervalComputer<F extends Fluxome>
This interface is used to represent flux interval computers. |
interface |
FluxomeReducer<T extends Fluxome>
This interface is used to represent algorithms that reduce the size of fluxomes. |
class |
InitialPointComputer<F extends Fluxome>
This class is used to compute initial points for coordinate-direction hit-and-run random flux vector algorithms. |
class |
RxnDeletionComputer<F extends Fluxome>
This class is used to compute the effect of deleting reactions in a fluxome. |
class |
SimpleFluxIntervalComputer<F extends Fluxome>
This class is used to compute flux intervals in the simplest possible way. |
Methods in sbrt.kernel.fba.comp with parameters of type Fluxome | |
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static java.util.Collection<java.util.Set<java.lang.String>> |
RedundRxnRemover.getEquivRxns(Fluxome fluxome)
Returns the equivalent reactions contained in the provided fluxome. |
static LinearSystemSolution<java.lang.String> |
FbaSolver.solve(Fluxome fluxome,
LinearSystemSolver<java.lang.String> solver)
Solves Sv = 0, where S is the stoichiometry matrix of the provided fluxome and v is the vector of fluxes. |
Uses of Fluxome in sbrt.kernel.fba.proc |
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Classes in sbrt.kernel.fba.proc with type parameters of type Fluxome | |
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class |
AbstractCvFbaOptProcess<F extends Fluxome,R>
This class is used to represent constraint-variation Flux Balance Analysis processes. |
class |
CdHarFluxVectorProcess<F extends Fluxome>
This class is used to perform coordinate direction hit-and-run flux vector processes. |
class |
CvFbaOptProcess<F extends Fluxome>
This class is used to perform constraint-variation FBA optimization processes. |
class |
CvFluxIntervalProcess<F extends Fluxome>
This class is used to perform constraint variation flux interval processes. |
class |
CvObjectiveFunctionProcess<F extends Fluxome>
This class is used to perform constraint-variation objective function processes. |
class |
CvRxnDeletionProcess<F extends Fluxome>
This class is used to perform constraint-variation reaction deletion processes. |
class |
CycleIdProcess<F extends Fluxome>
This class is used to execute steady state cycle identification processes. |
class |
FbaOptProcess<F extends Fluxome>
This class is used to perform a basic Flux Balance Analysis optimization. |
class |
FbaProcess<F extends Fluxome,R>
This abstract class is used to represent Flux Balance Analysis processes. |
class |
FbaSolverProcess<F extends Fluxome>
This class is used to solve the equation Sv = 0. |
class |
FluxActivityProcess<F extends Fluxome>
This class is used to analyze the activity of fluxes. |
class |
FluxIntervalProcess<F extends Fluxome>
This class is used to perform flux interval computations. |
class |
FluxomeReducerProcess<T extends Fluxome>
This class is used to execute fluxome reduction processes. |
class |
FluxPlasticityProcess<F extends Fluxome>
This class is used to analyze the plasticity of fluxes. |
class |
InitialPointGenerator<F extends Fluxome>
This class is used to execute initial point generators. |
class |
ObjFunAnalysis<F extends Fluxome>
This class is used to perform objective function analyses. |
class |
RandConstGeneratorV1<F extends Fluxome>
This class is used to generate random flux constraints. |
class |
RandomObjectiveGenerator<F extends Fluxome>
This class is used to generate random objective functions. |
class |
RxnDeletionProcess<F extends Fluxome>
This class is used to perform reaction deletion processes. |
class |
SvCdHarFluxVectorProcess<F extends Fluxome>
This class is used to perform space variation coordinate direction hit-and-run flux vector processes. |
class |
SvInitialPointProcess<F extends Fluxome>
This class is used to perform flux space variation initial point processes. |
Methods in sbrt.kernel.fba.proc that return Fluxome | |
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Fluxome |
RedundRxnRemoverProcess.getFluxome()
Returns the fluxome for which redundant reactions are to be removed. |
Method parameters in sbrt.kernel.fba.proc with type arguments of type Fluxome | |
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void |
RedundRxnRemoverProcess.run(ResultsManager<Fluxome> resultsManager)
Adds the information gathered about the fluxome to the provided results manager. |
Uses of Fluxome in sbrt.shell.io.fba |
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Classes in sbrt.shell.io.fba with type parameters of type Fluxome | |
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class |
CofoofSource<F extends Fluxome>
This class is used to provide a source of column-oriented FBA optimization output files. |
class |
ColumnOrFbaOptOutputFile<F extends Fluxome>
This class is used to write column-oriented output files containing FBA optimization data. |
interface |
FbaOptOutputFile<F extends Fluxome>
This interface is used to represent FBA optimization output files. |
class |
RofoofSource<F extends Fluxome>
This class is used to provide a source of row-oriented FBA optimization output files. |
class |
RowOrFbaOptOutputFile<F extends Fluxome>
This class is used to write row-oriented output files containing FBA optimization data. |
class |
SerFbaOptOutputFile<F extends Fluxome>
This class is used to write output files containing FBA optimization data as serialized maps. |
class |
SfoofSource<F extends Fluxome>
This class is used to provide a source of serialized FBA optimization output files. |
Methods in sbrt.shell.io.fba that return Fluxome | |
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Fluxome |
FluxCapInputFile.getFluxome()
Returns the fluxome used to verify reaction names. |
Methods in sbrt.shell.io.fba with parameters of type Fluxome | |
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static FluxConstraints |
FluxIntervalInputFile.convertConstraints(java.util.Map<LinearComb<java.lang.String>,Interval> intervals,
Fluxome fluxome,
double tolerance)
Converts the provided intervals into a FluxConstraints object. |
static void |
FluxIntervalInputFile.verifyFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConsts,
Fluxome fluxome,
double tolerance)
Verifies that the provided constraints are legitimate for the provided fluxome. |
Constructors in sbrt.shell.io.fba with parameters of type Fluxome | |
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FluxIntervalInputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<LinearComb<java.lang.String>> requiredVariables,
MapFormat<LinearComb<java.lang.String>,Interval> mapFormat,
Fluxome fluxome,
double tolerance)
Constructs a new flux-interval input file. |
Uses of Fluxome in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba with type parameters of type Fluxome | ||
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static
|
FbaOptManager.getMultiColOrOutputFiles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
java.lang.String fileNameSourceName,
F fluxome)
Returns a source of column-oriented FBA optimization output files. |
|
static
|
FbaOptManager.getMultiFileOutput(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
java.lang.String fileNameSourceName,
F fluxome)
Returns a source of FBA optimization output files. |
|
static
|
FbaOptManager.getMultiResultsOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
F fluxome)
Returns an empty output file that is suitable for storing multiple FBA optimization results. |
|
static
|
FbaOptManager.getMultiResultsOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> dataHeaders,
F fluxome)
Returns an empty output file that is suitable for storing multiple FBA optimization results. |
|
static
|
FbaOptManager.getMultiRowOrOutputFiles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
F fluxome)
Returns a source of row-oriented FBA optimization output files. |
|
static
|
FbaOptManager.getMultiSerOutputFiles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
java.util.Iterator<java.lang.String> fileNameSource,
java.lang.String fileNameSourceName,
F fluxome)
Returns a source of serialized FBA optimization output files. |
|
static
|
FbaOptManager.getSingleResultOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
F fluxome)
Returns an empty output file that is suitable for storing a single FBA optimization result. |
|
static
|
FbaOptManager.getSingleResultOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> dataHeaders,
F fluxome)
Returns an empty output file that is suitable for storing a single FBA optimization result. |
Methods in sbrt.shell.mng.fba with parameters of type Fluxome | |
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static java.util.Map<java.lang.String,Or<And<java.lang.String>>> |
FbaManager.getCatalysts(Fluxome fluxome,
java.lang.String fileName)
Returns the reaction-catalyst associations contained in the file with the provided name. |
static java.util.Map<java.lang.String,Or<And<java.lang.String>>> |
FbaManager.getCatalysts(Fluxome fluxome,
java.lang.String fileName,
java.io.PrintWriter out)
Returns the reaction-catalyst associations contained in the file with the provided name. |
static FluxConstraints |
FbaOptManager.getConstraints(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains. |
static FluxConstraints |
RandomFluxVectorManager.getConstraints(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by FbaOptManager.CONSTRAINTS_FILE in the provided manager input and returns the set of flux constraints it contains. |
static FluxConstraints |
FbaOptManager.getConstraints(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the set of constraints contained in the file with the provided name. |
static FluxConstraints |
RandomFluxVectorManager.getConstraints(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the set of constraints contained in the file with the provided name. |
static FluxIntervalInputFile |
IntervalVariationManager.getCvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Returns the constraint variation input with the name denoted by IntervalVariationManager.CV_FILE in the provided manager input. |
static FluxIntervalInputFile |
IntervalVariationManager.getCvInputFile(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the constraint variation input file with the provided name. |
static java.util.List<LinearComb<java.lang.String>> |
FluxCapManager.getCycles(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Opens the file denoted by FluxCapManager.CYCLE_FILE in the provided manager input and returns the list of cycles it contains. |
static java.util.Set<java.lang.String> |
FbaOptManager.getDataHeaders(ManagerInput<java.lang.String,java.lang.String> input,
Fluxome fluxome)
Parses and returns the value for AbstractProcessManager.DATA_HEADERS in the provided manager input. |
static java.util.LinkedHashSet<java.lang.String> |
FbaOptManager.getDataHeaders(java.lang.String dataHeaders,
Fluxome fluxome)
Parses the provided data header string and returns the corresponding set. |
static UnmodifiableMap<java.lang.String,java.util.Set<LinearComb<java.lang.String>>> |
MsFluxIntervalManager.getFluxCaps(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the flux caps contained in the file with the name specified by MsFluxIntervalManager.FLUX_CAP_FILE in the provided input. |
static MapInputFile<java.lang.String,Interval> |
FluxPlasticityManager.getFluxIntervalFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the flux interval input with the name denoted by FluxPlasticityManager.FLUX_INTERVAL_FILE in the provided manager input. |
static MapInputFile<java.lang.String,Interval> |
FluxPlasticityManager.getFluxIntervalFile(java.lang.String fileName,
Fluxome fluxome)
Returns the flux interval input file with the provided name. |
static LinearSystemSolution<java.lang.String> |
FbaManager.getFluxomeSolution(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double coeffCutoff)
Opens the file denoted by FbaManager.SYSTEM_SOLUTION_FILE in the provided manager input and returns the linear system solution it contains. |
static java.util.Map<java.lang.String,java.lang.Double> |
CdHarFluxVectorManager.getFluxVector(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by CdHarManager.INITIAL_POINT_FILE in the provided manager input and returns the flux vector it contains. |
static java.util.Map<java.lang.String,java.lang.Double> |
RandomFluxVectorManager.getFluxVector(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by FbaManager.FLUX_VECTOR_FILE in the provided manager input and returns the flux vector it contains. |
static java.util.Map<java.lang.String,java.lang.Double> |
RandomFluxVectorManager.getFluxVector(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the flux vector contained in the file with the provided name. |
static MapOutputFile<java.lang.String,java.lang.Double> |
InitialPointManager.getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single flux vector. |
static MapInputFile<java.lang.String,java.lang.Double> |
FluxActivityManager.getFluxVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the flux vector input file specified by the provided input. |
static MapInputFile<java.lang.String,java.lang.Double> |
FluxActivityManager.getFluxVectorFile(java.lang.String fileName,
FileFormat format,
Fluxome fluxome)
Returns the flux vector input file with the provided name. |
static InputFile<java.util.Set<java.lang.String>> |
RxnDeletionManager.getInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Parses and returns the value for RxnDeletionManager.RXN_DELETION_FILE in the provided manager input. |
static TextInputFile<LinearComb<java.lang.String>> |
ObjectiveFunctionManager.getInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns the file denoted by ObjectiveFunctionManager.OBJ_FUNCT_FILE in the provided manager input. |
static TextInputFile<LinearComb<java.lang.String>> |
ObjectiveFunctionManager.getInputFile(java.lang.String fileName,
FileFormat format,
Fluxome fluxome)
Returns the input file with the provided name. |
static InputFile<java.util.Set<java.lang.String>> |
RxnDeletionManager.getInputFile(java.lang.String fileName,
Fluxome fluxome)
Returns the reaction name input file with the provided name. |
static TextInputFile<LinearComb<java.lang.String>> |
ObjectiveFunctionManager.getInputFile(java.lang.String fileName,
Fluxome fluxome)
Returns the input file with the provided name. |
static FluxIntervalInputFile |
IntervalVariationManager.getIntervalInputFile(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the flux interval input file with the provided name. |
static FluxIntervalInputFile |
IntervalVariationManager.getIntervalInputFile(java.lang.String fileName,
Fluxome fluxome,
MapFormat<LinearComb<java.lang.String>,Interval> mapFormat,
double tolerance)
Returns the flux interval input file with the provided name. |
static FluxConstraints |
InitialPointManager.getIntervals(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Opens the file denoted by InitialPointManager.FLUX_INTERVAL_FILE in the provided manager input and returns the set of flux intervals it contains. |
static FluxConstraints |
InitialPointManager.getIntervals(java.lang.String fileName,
Fluxome fluxome,
double tolerance)
Returns the set of flux intervals contained in the file with the provided name. |
static MapOutputFile<java.lang.String,java.lang.Double> |
CdHarFluxVectorManager.getMultiFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors. |
static MapOutputFile<java.lang.String,java.lang.Double> |
FbaManager.getMultiFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors. |
static MapOutputFile<java.lang.String,java.lang.Double> |
FbaManager.getMultiFluxVectorOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> rxnNameHeaders,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple flux vectors. |
static ComoFile<java.lang.String,Interval> |
SimpleFluxIntervalManager.getMultiResultsOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux interval results. |
static ComoFile<java.lang.String,Interval> |
SimpleFluxIntervalManager.getMultiResultsOutputFile(java.lang.String fileName,
java.util.Set<java.lang.String> headers,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux interval results. |
static LinearComb<java.lang.String> |
FbaOptManager.getObjFunc(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Parses and returns the value for FbaOptManager.OBJECTIVE_FUNCTION in the provided manager input. |
static MapTextOutputFile<java.lang.String,Interval> |
RandomConstraintsManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux constraints. |
static TextOutputFile<LinearComb<java.lang.String>> |
RandomObjectiveManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing randomly generated objective functions. |
static ComoFile<java.lang.String,java.lang.Double> |
ExtremeCurrentManager.getOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
java.util.Set<java.lang.String> rxnNames)
Returns an output file to which extreme currents can be written. |
static TextOutputFile<LinearComb<java.lang.String>> |
RandomObjectiveManager.getOutputFile(java.lang.String fileName,
FileFormat format,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing randomly generated objective functions. |
static MapTextOutputFile<java.lang.String,Interval> |
RandomConstraintsManager.getOutputFile(java.lang.String fileName,
FileFormat format,
java.util.Set<java.lang.String> headers,
Fluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux constraints. |
static ComoFile<java.lang.String,java.lang.Double> |
ExtremeCurrentManager.getOutputFile(java.lang.String fileName,
java.io.PrintWriter out,
Fluxome fluxome,
java.util.Set<java.lang.String> rxnNames)
Returns an output file to which extreme currents can be written. |
static MapOutputFile<java.lang.String,java.lang.Double> |
InitialPointManager.getPVectorFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single C vector with the name denoted by InitialPointManager.P_VECTOR_FILE_NAME in the provided input. |
static RxnNameExprFormat<LinearComb<java.lang.String>,java.lang.String> |
FbaManager.getRxnNameExprFormat(Fluxome f)
Returns the default reaction name expression format. |
static java.util.Set<java.lang.String> |
FbaManager.getRxnNameHeaders(ManagerInput<java.lang.String,java.lang.String> input,
Fluxome fluxome)
Parses and returns the value for AbstractProcessManager.DATA_HEADERS in the provided manager input. |
static java.util.LinkedHashSet<java.lang.String> |
FbaManager.getRxnNameHeaders(java.lang.String dataHeaders,
Fluxome fluxome)
Parses and returns the set of reaction names contained in the provided string. |
static MapOutputFile<java.lang.String,java.lang.Double> |
FbaManager.getSingleFluxVectorOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single flux vector. |
static MapOutputFile<java.lang.String,java.lang.Double> |
FbaManager.getSingleFluxVectorOutputFile(java.lang.String fileName,
FileFormat fileFormat,
java.util.Set<java.lang.String> rxnNameHeaders,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single flux vector. |
static RomoFile<java.lang.String,Interval> |
SimpleFluxIntervalManager.getSingleResultOutputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single set of flux interval results. |
static RomoFile<java.lang.String,Interval> |
SimpleFluxIntervalManager.getSingleResultOutputFile(java.lang.String fileName,
java.util.Set<java.lang.String> headers,
Fluxome fluxome)
Returns an empty output file that is suitable for storing a single set of flux interval results. |
static FluxIntervalInputFile |
IntervalVariationManager.getSvInputFile(ManagerInput<java.lang.String,java.lang.String> input,
java.io.PrintWriter out,
Fluxome fluxome,
double tolerance)
Returns the space variation input with the name denoted by IntervalVariationManager.FLUX_INTERVAL_FILE in the provided manager input. |
static void |
FbaManager.printFluxomeInfo(Fluxome fluxome,
java.io.PrintWriter out)
Prints basic information about the provided fluxome. |
Uses of Fluxome in sbrt.shell.text.fba |
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Methods in sbrt.shell.text.fba that return Fluxome | |
---|---|
Fluxome |
FluxCapFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
CatalystSetFormat.getFluxome()
Returns the fluxome used to verify enzyme names. |
Fluxome |
ConstraintsFileLineFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FluxVectorFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
RxnNameExprFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
ChemSpeciesVerifier.getFluxome()
Returns the fluxome used to create this chemical species verifier. |
Fluxome |
RxnNameExprFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FluxVectorFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
RxnNameOrExprFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FbaOptHeaderParserV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
RxnNameOrExprFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FbaOptHeaderFormatter.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
RxnNameSetFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
ConstraintsFileLineFormatV2.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
RxnNameListFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FbaOptHeaderFormatterV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FbaOptHeaderParser.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FluxomeSolFileLineFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
RxnNameVerifier.getFluxome()
Returns the fluxome used to create this reaction name checker. |
Fluxome |
RxnNameSetFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
RxnNameListFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FluxomeSolutionFileLineFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FluxCapFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FbaOptFileLineFormatV1.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
ConstraintsFileLineFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Fluxome |
FbaOptFileLineFormat.getFluxome()
Returns the fluxome used to verify reaction names. |
Constructors in sbrt.shell.text.fba with parameters of type Fluxome | |
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ChemSpeciesVerifier(Fluxome fluxome)
Constructs a new chemical species verifier for the provided fluxome. |
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ConstraintsFileLineFormatV1(Fluxome fluxome)
Constructs a new contraints file line format. |
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ConstraintsFileLineFormatV2(Fluxome fluxome)
Constructs a new contraints file line format. |
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FbaOptFileLineFormatV1(Fluxome fluxome)
Constructs a new FBA optimization file line format. |
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FbaOptHeaderFormatterV1(Fluxome fluxome)
Constructs a new FBA optimization header formatter. |
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FbaOptHeaderParserV1(Fluxome fluxome)
Constructs a new FBA optimization header parser. |
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FluxCapFormatV1(Fluxome fluxome)
Constructs a new flux cap file line format using the provided fluxome. |
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FluxomeSolFileLineFormatV1(Fluxome fluxome)
Constructs a new fluxome solution file line format. |
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FluxomeSolFileLineFormatV1(Fluxome fluxome,
double coeffCutoff)
Constructs a new fluxome solution file line format. |
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FluxVectorFormatV1(Fluxome fluxome)
Constructs a new flux vector format. |
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RxnNameExprFormatV1(Fluxome fluxome)
Constructs a new reaction name expression format using the provided fluxome. |
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RxnNameExprFormatV1(Fluxome fluxome,
double coeffCutoff)
Constructs a new reaction name expression format using the provided fluxome. |
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RxnNameListFormatV1(Fluxome fluxome)
Constructs a new reaction name list format using the provided fluxome. |
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RxnNameOrExprFormatV1(Fluxome fluxome)
Constructs a new reaction name and expression format. |
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RxnNameSetFormatV1(Fluxome fluxome)
Constructs a new reaction name collection format using the provided fluxome. |
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RxnNameVerifier(Fluxome fluxome)
Constructs a new reaction name checker for the provided fluxome. |
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