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PREV NEXT | FRAMES NO FRAMES |
Packages that use Interval | |
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sbrt.ext.cplex | Provides a class that allows communication with CPLEX. |
sbrt.ext.glpk | Provides a class that allows communication with GLPK. |
sbrt.kernel.fba | Provides classes and interfaces for creating objects relevant to Flux Balance Analysis. |
sbrt.kernel.fba.analysis | Provides classes and interfaces for analyzing Flux Balance Analysis data. |
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.kernel.math | Provides classes and interfaces for creating objects relevant to mathematics. |
sbrt.kernel.math.algebra | Provides classes and interfaces for creating objects relevant to algebra. |
sbrt.kernel.math.geom | Provides classes and interfaces for creating objects relevant to computational geometry. |
sbrt.kernel.math.optimization | Provides classes and interfaces for creating objects relevant to solving optimization problems. |
sbrt.kernel.utilities.proc | Provides classes and interfaces for performing utility 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. |
sbrt.shell.text.math | Provides classes and interfaces for defining formats for mathematical objects. |
Uses of Interval in sbrt.ext.cplex |
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Methods in sbrt.ext.cplex with parameters of type Interval | ||
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|
CplexSolver.setColumnConstraint(T column,
Interval c)
Sets the constraint on the provided column variable. |
|
void |
CplexSolver.setConstraint(LinearComb<? extends C> linComb,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
|
void |
CplexSolver.setConstraint(MathExpr<? extends C> expression,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
|
void |
CplexSolver.setConstraint(QuadraticExpr<? extends C> expr,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
|
|
CplexSolver.setRowConstraint(T row,
Interval c)
Sets the constraint for the provided row variable. |
Method parameters in sbrt.ext.cplex with type arguments of type Interval | |
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void |
CplexSolver.setColumnConstraints(java.util.Map<? extends C,Interval> constraints)
Sets the constraints for the provided column variables. |
void |
CplexSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> exprConstraints)
Sets constraints on the provided mathematical expressions of column variables. |
void |
CplexSolver.setRowConstraints(java.util.Map<? extends R,Interval> rowConstraints)
Sets the constraints for the provided row variables. |
Uses of Interval in sbrt.ext.glpk |
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Methods in sbrt.ext.glpk with parameters of type Interval | ||
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|
GlpkSolver.setColumnConstraint(Y column,
Interval c)
Sets the constraint on the provided column variable. |
|
void |
GlpkSolver.setConstraint(LinearComb<? extends C> expression,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
|
void |
GlpkSolver.setConstraint(MathExpr<? extends C> expression,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
|
|
GlpkSolver.setRowConstraint(X row,
Interval c)
Sets the constraint for the provided row variable. |
Method parameters in sbrt.ext.glpk with type arguments of type Interval | |
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void |
GlpkSolver.setColumnConstraints(java.util.Map<? extends C,Interval> columnConstraints)
Sets the constraints for the provided column variables. |
void |
GlpkSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> expressionConstraints)
Sets constraints on the provided mathematical expressions of column variables. |
void |
GlpkSolver.setRowConstraints(java.util.Map<? extends R,Interval> rowConstraints)
Sets the constraints for the provided row variables. |
Uses of Interval in sbrt.kernel.fba |
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Fields in sbrt.kernel.fba declared as Interval | |
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static Interval |
MixedFluxomeV1.IRREV
The constraint used by default for irreversible internal reactions and sink reactions: [0, Infinity). |
static Interval |
MixedFluxomeV1.OFF
The constraint used by default for source reactions and reversible exchange reactions: [0, 0]. |
static Interval |
IrrevRxnFluxomeV1.OFF
The constraint used by default for all source reactions: [0, 0]. |
static Interval |
IrrevRxnFluxomeV1.ON
The constraint used by default for all internal and sink reactions: [0, Infinity). |
static Interval |
MixedFluxomeV1.REV
The constraint used by default for reversible internal reactions: (-Infinity, Infinity). |
Methods in sbrt.kernel.fba that return Interval | |
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Interval |
FluxConstraints.getConstraint(MathExpr<java.lang.String> rxnExpr)
Returns the constraint of the provided mathematical expression of reaction names. |
Interval |
FluxConstraints.getConstraint(java.lang.String rxnName)
Returns the flux constraint for the provided reaction. |
Interval |
MixedFluxomeV1.getFluxConstraint(java.lang.String reactionName)
Returns the flux constraint for the provided reaction. |
Interval |
Fluxome.getFluxConstraint(java.lang.String reactionName)
Returns the flux constraint for the reaction with the provided name. |
Interval |
IrrevRxnFluxomeV1.getFluxConstraint(java.lang.String reactionName)
Returns the flux constraint for the provided reaction. |
Interval |
MixedFluxomeV1.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the constraint associated with the expression provided. |
Interval |
Fluxome.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the constraint corresponding to the provided mathematical expression of reaction names. |
Interval |
IrrevRxnFluxomeV1.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the constraint associated with the expression provided. |
Methods in sbrt.kernel.fba that return types with arguments of type Interval | |
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UnmodifiableMap<MathExpr<java.lang.String>,Interval> |
FluxConstraints.getExprConstraints()
Returns the constraints for mathematical expressions of fluxes. |
java.util.Map<java.lang.String,Interval> |
MixedFluxomeV1.getFluxConstraints()
Returns the constraints on each flux in this fluxome. |
UnmodifiableMap<java.lang.String,Interval> |
FluxConstraints.getFluxConstraints()
Returns the flux constraints for single reactions. |
java.util.Map<java.lang.String,Interval> |
IrrevRxnFluxomeV1.getFluxConstraints()
Returns the constraints on each flux in this fluxome. |
Methods in sbrt.kernel.fba with parameters of type Interval | |
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boolean |
MixedFluxomeV1.isValid(Interval c,
java.lang.String rxnName,
double tolerance)
Indicates if the provided interval is a valid flux constraint for the reaction having the provided name. |
boolean |
Fluxome.isValid(Interval constraint,
java.lang.String rxnName,
double tolerance)
Indicates if the provided interval is a valid flux constraint for the reaction with the provided name. |
boolean |
IrrevRxnFluxomeV1.isValid(Interval c,
java.lang.String rxnName,
double tolerance)
Indicates if the provided interval is a valid flux constraint for the reaction having the provided name. |
Constructor parameters in sbrt.kernel.fba with type arguments of type Interval | |
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FluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Constructs a set of FBA constraints from the provided argument. |
|
FluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints,
java.util.Map<? extends MathExpr<java.lang.String>,Interval> exprConstraints)
Constructs a set of FBA constraints from the provided arguments. |
|
FluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints,
java.util.Map<? extends MathExpr<java.lang.String>,Interval> exprConstraints)
Constructs a set of FBA constraints from the provided arguments. |
Uses of Interval in sbrt.kernel.fba.analysis |
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Method parameters in sbrt.kernel.fba.analysis with type arguments of type Interval | |
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java.util.Set<java.lang.String> |
FluxIntervalAnalyzer.getAlwaysActive(java.util.Map<java.lang.String,Interval> fluxIntervals,
double zeroCutoff)
Returns the always-active fluxes in the provided map. |
java.util.Set<java.lang.String> |
FluxIntervalAnalyzer.getNeverActive(java.util.Map<java.lang.String,Interval> fluxIntervals,
double zeroCutoff)
Returns the never-active fluxes in the provided map. |
java.util.Set<java.lang.String> |
FluxIntervalAnalyzer.getPotentiallyActive(java.util.Map<java.lang.String,Interval> fluxIntervals,
double zeroCutoff)
Returns the potentially-active fluxes in the provided map. |
int |
FluxIntervalAnalyzer.lowerBoundsEqualZero(java.util.Collection<Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose lower bound equals zero. |
int |
FluxIntervalAnalyzer.lowerBoundsEqualZero(java.util.Map<?,Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose lower bound equals zero. |
int |
FluxIntervalAnalyzer.lowerBoundsGreaterThanZero(java.util.Collection<Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose lower bounds are greater than zero. |
int |
FluxIntervalAnalyzer.lowerBoundsGreaterThanZero(java.util.Map<?,Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose lower bounds are greater than zero. |
int |
FluxIntervalAnalyzer.rangesEqualZero(java.util.Collection<Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose ranges equal zero. |
int |
FluxIntervalAnalyzer.rangesEqualZero(java.util.Map<?,Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose ranges equal zero. |
int |
FluxIntervalAnalyzer.rangesGreaterThanZero(java.util.Collection<Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose ranges are greater than zero. |
int |
FluxIntervalAnalyzer.rangesGreaterThanZero(java.util.Map<?,Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose ranges are greater than zero. |
int |
FluxIntervalAnalyzer.upperBoundsEqualZero(java.util.Collection<Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose upper bounds equal zero. |
int |
FluxIntervalAnalyzer.upperBoundsEqualZero(java.util.Map<?,Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose upper bounds equal zero. |
int |
FluxIntervalAnalyzer.upperBoundsGreaterThanZero(java.util.Collection<Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose upper bounds are greater than zero. |
int |
FluxIntervalAnalyzer.upperBoundsGreaterThanZero(java.util.Map<?,Interval> intervals,
double zeroCutoff)
Returns the number of provided intervals whose upper bounds are greater than zero. |
Uses of Interval in sbrt.kernel.fba.comp |
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Methods in sbrt.kernel.fba.comp that return Interval | |
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Interval |
FbaOptimizer.getColExprConstraint(MathExpr<?> columnVariableExpr)
Returns the current constraint on the provided expression. |
Interval |
FbaOptimizer.getColumnConstraint(java.lang.Object columnVariable)
Returns the current constraint on the provided column variable. |
Interval |
RxnDeletionComputer.getFluxConstraint(java.lang.String rxnName)
Returns the flux constraint of the reaction with the provided name. |
Interval |
InitialPointComputer.getFluxConstraint(java.lang.String rxnName)
Returns the current flux constraint on the reaction with the provided name. |
Interval |
FluxCvComputer.getFluxConstraint(java.lang.String rxnName)
Returns the current flux constraint for the reaction with the provided name. |
Interval |
AbstractFluxIntervalComputer.getFluxConstraint(java.lang.String rxnName)
Returns the current flux constraint on the reaction with the provided name. |
Interval |
CdHarFluxComp.getFluxConstraint(java.lang.String rxnName)
Returns the current flux constraint on the reaction with the provided name. |
Interval |
FbaOptimizer.getFluxConstraint(java.lang.String reactionName)
Returns the current flux constraint on the reaction with the provided name. |
protected Interval |
AbstractFluxIntervalComputer.getInterval(java.lang.String rxn,
Interval fluxConstraint,
double computedMin,
double computedMax)
Returns the provided minimum and maximum fluxes as an interval. |
Interval |
FbaOptimizer.getRowConstraint(java.lang.Object rowVariable)
Returns the current constraint on the provided row variable. |
Interval |
RxnDeletionComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the constraint on the provided mathematical expression of fluxes. |
Interval |
InitialPointComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
FluxCvComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
AbstractFluxIntervalComputer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
CdHarFluxComp.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
Returns the current constraint on the provided expression. |
Interval |
FbaOptimizer.getRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
Returns the current constraint on the provided expression. |
Methods in sbrt.kernel.fba.comp that return types with arguments of type Interval | |
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java.util.Map<MathExpr<?>,Interval> |
FbaOptimizer.getColExprConstraints()
Returns all current constraints on mathematical expressions of column variables. |
java.util.Map<?,Interval> |
FbaOptimizer.getColumnConstraints()
Returns the current constraints for each column variable in the program matrix. |
java.util.Map<java.lang.String,Interval> |
RxnDeletionComputer.getFluxConstraints()
Returns the set of all constraints on single fluxes. |
java.util.Map<java.lang.String,Interval> |
InitialPointComputer.getFluxConstraints()
Returns all current flux constraints. |
java.util.Map<java.lang.String,Interval> |
FluxCvComputer.getFluxConstraints()
Returns all current flux constraints. |
java.util.Map<java.lang.String,Interval> |
AbstractFluxIntervalComputer.getFluxConstraints()
Returns all current flux constraints. |
java.util.Map<java.lang.String,Interval> |
CdHarFluxComp.getFluxConstraints()
Returns all current flux constraints. |
java.util.Map<java.lang.String,Interval> |
FbaOptimizer.getFluxConstraints()
Returns all current flux constraints for each reaction in the fluxome used by this optimization computer. |
java.util.Map<java.lang.String,Interval> |
ReverseRxnIntervalComp.getIntervals()
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer. |
java.util.Map<java.lang.String,Interval> |
MsFluxIntervalComputer.getIntervals()
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer. |
java.util.Map<java.lang.String,Interval> |
SimpleFluxIntervalComputer.getIntervals()
Computes and returns the intervals of every flux in the fluxome used to construct this flux interval computer. |
java.util.Map<java.lang.String,Interval> |
FluxIntervalComputer.getIntervals()
Computes and returns the intervals of every flux in the fluxome used by this flux interval computer. |
java.util.Map<java.lang.String,Interval> |
ReverseRxnIntervalComp.getIntervals(java.util.Collection<java.lang.String> rxnNames)
Computes and returns the flux intervals of the reactions with the provided names. |
java.util.Map<java.lang.String,Interval> |
MsFluxIntervalComputer.getIntervals(java.util.Collection<java.lang.String> rxnNames)
Computes and returns the flux intervals of the reactions with the provided names. |
java.util.Map<java.lang.String,Interval> |
SimpleFluxIntervalComputer.getIntervals(java.util.Collection<java.lang.String> rxnNames)
Computes and returns the flux intervals of the reactions with the provided names. |
java.util.Map<java.lang.String,Interval> |
FluxIntervalComputer.getIntervals(java.util.Collection<java.lang.String> rxnNames)
Computes and returns the flux intervals of the reactions with the provided names. |
protected java.util.Map<java.lang.String,Interval> |
AbstractFluxIntervalComputer.getIntervals(java.util.Map<java.lang.String,java.lang.Double> fluxMinima,
java.util.Map<java.lang.String,java.lang.Double> fluxMaxima)
Returns the provided minima and maxima as intervals. |
java.util.Map<?,Interval> |
FbaOptimizer.getRowConstraints()
Returns all the current constraints on row variables. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
RxnDeletionComputer.getRxnExprConstraints()
Returns the set of all constraints on mathematical expressions of fluxes. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
InitialPointComputer.getRxnExprConstraints()
Returns all current flux expression constraints. |
java.util.Map<? extends MathExpr<java.lang.String>,Interval> |
FluxCvComputer.getRxnExprConstraints()
Returns all current flux expression constraints. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
AbstractFluxIntervalComputer.getRxnExprConstraints()
Returns all current flux expression constraints. |
java.util.Map<LinearComb<java.lang.String>,Interval> |
CdHarFluxComp.getRxnExprConstraints()
Returns all current flux expression constraints. |
java.util.Map<MathExpr<java.lang.String>,Interval> |
FbaOptimizer.getRxnExprConstraints()
Returns all current constraints on mathematical expressions of reaction names. |
Methods in sbrt.kernel.fba.comp with parameters of type Interval | |
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protected void |
AbstractCvComputer.checkFluxConstraint(Interval c,
java.lang.String rxnName,
double tolerance)
Ensures the flux constraint is valid for the fluxome provided. |
protected void |
FbaOptimizer.checkFluxConstraint(Interval c,
java.lang.String rxnName,
double tolerance)
Ensures the provided constraint is a valid flux constraint in the fluxome used by this optimization computer. |
protected void |
AbstractCvComputer.checkRxnExprConstraint(Interval c)
Ensures the expression constraint is valid for the fluxome provided. |
protected void |
FbaOptimizer.checkRxnExprConstraint(Interval c)
Ensures the provided constraint is valid for reaction name-expressions for the fluxome used by this optimization computer. |
protected Interval |
AbstractFluxIntervalComputer.getInterval(java.lang.String rxn,
Interval fluxConstraint,
double computedMin,
double computedMax)
Returns the provided minimum and maximum fluxes as an interval. |
void |
FbaOptimizer.setColExprConstraint(MathExpr<?> expr,
Interval c)
Changes the constraint on the provided mathematical expression of column variables. |
void |
FbaOptimizer.setColumnConstraint(java.lang.Object columnVar,
Interval c)
Changes the constraint of the provided column variable. |
void |
RxnDeletionComputer.setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
InitialPointComputer.setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
FluxCvComputer.setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
AbstractFluxIntervalComputer.setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
CdHarFluxComp.setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
FbaOptimizer.setFluxConstraint(java.lang.String reactionName,
Interval c)
Changes the flux constraint of the reaction with the provided name. |
void |
FbaOptimizer.setRowConstraint(java.lang.Object rowVariable,
Interval c)
Changes the constraint of the provided row variable. |
void |
CdHarFluxComp.setRxnExprConstraint(LinearComb<java.lang.String> rxnExpr,
Interval c)
Changes the constraint on the provided linear combination of fluxes. |
void |
RxnDeletionComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
InitialPointComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
FluxCvComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
AbstractFluxIntervalComputer.setRxnExprConstraint(MathExpr<java.lang.String> e,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
CdHarFluxComp.setRxnExprConstraint(MathExpr<java.lang.String> rxnExpr,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
void |
FbaOptimizer.setRxnExprConstraint(MathExpr<java.lang.String> expr,
Interval c)
Changes the constraint on the provided mathematical expression of fluxes. |
Method parameters in sbrt.kernel.fba.comp with type arguments of type Interval | |
---|---|
void |
FbaOptimizer.setColExprConstraints(java.util.Map<? extends MathExpr<?>,Interval> exprConstraints)
Changes the constraints on more than one mathematical expression of column variables. |
void |
FbaOptimizer.setColumnConstraints(java.util.Map<?,Interval> columnConstraints)
Changes the constraints on more than one column variable. |
void |
InitialPointComputer.setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Changes the flux constraints on more than one reaction. |
void |
FluxCvComputer.setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Changes the flux constraints on more than one reaction. |
void |
AbstractCvComputer.setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Changes the flux constraints on more than one reaction. |
void |
AbstractFluxIntervalComputer.setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Changes the flux constraints on more than one reaction. |
void |
FbaOptimizer.setFluxConstraints(java.util.Map<java.lang.String,Interval> fluxConstraints)
Changes the flux constraints on more than one reaction. |
void |
FbaOptimizer.setRowConstraints(java.util.Map<?,Interval> rowConstraints)
Changes the constraints on more than one row variable. |
void |
InitialPointComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
FluxCvComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
AbstractCvComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
AbstractFluxIntervalComputer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> constraints)
Changes the constraints on more than one mathematical expression of fluxes. |
void |
FbaOptimizer.setRxnExprConstraints(java.util.Map<? extends MathExpr<java.lang.String>,Interval> exprConstraints)
Changes the constraints on more than one mathematical expression of fluxes. |
Uses of Interval in sbrt.kernel.fba.proc |
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Methods in sbrt.kernel.fba.proc that return Interval | |
---|---|
Interval |
RandConstGeneratorV1.getInactive()
Returns the constraint used for inactive reactions. |
Interval |
RandConstGeneratorV1.getIrrevConstraint()
Returns the constraint used for active irreversible reactions. |
Interval |
RandConstGeneratorV1.getRevConstraint()
Returns the constraint used for active reversible reactions. |
Methods in sbrt.kernel.fba.proc with parameters of type Interval | |
---|---|
void |
RandConstGeneratorV1.setInactive(Interval inactive)
Sets the constraint used for inactive reactions. |
void |
RandConstGeneratorV1.setIrrevConstraint(Interval constraint)
Sets the constraint used for active irreversible reactions. |
void |
RandConstGeneratorV1.setRevConstraint(Interval constraint)
Sets the constraint used for active reversible reactions. |
Method parameters in sbrt.kernel.fba.proc with type arguments of type Interval | |
---|---|
void |
FluxIntervalProcess.run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
Computes the flux intervals of the reactions with the current names and adds them to the provided results manager. |
void |
RandConstGeneratorV1.run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
Generates sets of random flux constraints and adds them to the provided results manager. |
void |
CvFluxIntervalProcess.run(ResultsManager<java.util.Map<java.lang.String,Interval>> resultsManager)
Runs this process and adds the generated results to the provided results manager via its ResultsManager.addData(Object) method. |
void |
FluxPlasticityProcess.setFluxIntervalSource(java.lang.Iterable<java.util.Map<java.lang.String,Interval>> intervalSource)
Sets the flux interval source. |
Uses of Interval in sbrt.kernel.math |
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Methods in sbrt.kernel.math that return Interval | |
---|---|
Interval |
ConstraintViolationException.getBounds()
Returns the constraints that have been violated. |
Interval |
IntervalComparer.Diff.getInterval1()
Returns the "first" interval of the pair of intervals. |
Interval |
IntervalComparer.Diff.getInterval2()
Returns the "second" interval of the pair of intervals. |
Methods in sbrt.kernel.math with parameters of type Interval | |
---|---|
boolean |
IntervalEquiv.areEquiv(Interval value1,
Interval value2)
Indicates if the provided intervals are equivalent. |
Method parameters in sbrt.kernel.math with type arguments of type Interval | ||
---|---|---|
|
IntervalComparer.getDiffs(java.util.Map<? extends V,Interval> m1,
java.util.Map<? extends V,Interval> m2,
double tolerance)
Returns the set of differences between the provided interval vectors. |
|
|
IntervalComparer.getDiffs(java.util.Map<? extends V,Interval> m1,
java.util.Map<? extends V,Interval> m2,
double tolerance)
Returns the set of differences between the provided interval vectors. |
Constructors in sbrt.kernel.math with parameters of type Interval | |
---|---|
ConstraintViolationException(java.lang.Object variable,
Interval bounds,
double violatingValue)
Constructs a new constraint violation exception. |
|
ConstraintViolationException(java.lang.Object variable,
Interval bounds,
java.lang.Number violatingValue)
Constructs a new constraint violation exception. |
Uses of Interval in sbrt.kernel.math.algebra |
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Method parameters in sbrt.kernel.math.algebra with type arguments of type Interval | ||
---|---|---|
static
|
HashLinearSystemSolution.simplify(LinearSystemSolution<V> solution,
java.util.Map<? extends V,Interval> variableBounds,
double tolerance)
Returns a simplified version of the provided linear system solution given the variable bounds. |
Uses of Interval in sbrt.kernel.math.geom |
---|
Methods in sbrt.kernel.math.geom that return Interval | |
---|---|
Interval |
ParallelHyperplanes.getBounds()
Returns the bounding values used to define the inequality. |
Method parameters in sbrt.kernel.math.geom with type arguments of type Interval | ||
---|---|---|
static
|
HashConvexPolytope.make(LinearSystemSolution<V> systemSolution,
java.util.Map<? extends V,Interval> variableBounds,
double tolerance)
Constructs a new convex poltyope from the provided linear system solution and variable bounds. |
Constructors in sbrt.kernel.math.geom with parameters of type Interval | |
---|---|
ParallelHyperplanes(LinearComb<V> hyperplane,
Interval bounds)
Constructs a new pair of bounding parallel hyperplanes. |
Uses of Interval in sbrt.kernel.math.optimization |
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Methods in sbrt.kernel.math.optimization with parameters of type Interval | ||
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ProgramSolver.setColumnConstraint(Y column,
Interval c)
Sets the constraint on the provided column variable. |
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void |
LinearProgramSolver.setConstraint(LinearComb<? extends C> expression,
Interval c)
Sets a constraint on the provided linear combination of column variables. |
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void |
ProgramSolver.setConstraint(MathExpr<? extends C> expression,
Interval c)
Sets a constraint on the provided mathematical expression of column variables. |
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void |
QuadraticProgramSolver.setConstraint(QuadraticExpr<? extends C> expression,
Interval c)
Sets a constraint on the provided quadratic expression of column variables. |
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ProgramSolver.setRowConstraint(X row,
Interval c)
Sets the constraint for the provided row variable. |
Method parameters in sbrt.kernel.math.optimization with type arguments of type Interval | |
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void |
ProgramSolver.setColumnConstraints(java.util.Map<? extends C,Interval> columnConstraints)
Sets the constraints for the provided column variables. |
void |
ProgramSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> expressionConstraints)
Sets constraints on the provided mathematical expressions of column variables. |
void |
ProgramSolver.setRowConstraints(java.util.Map<? extends R,Interval> rowConstraints)
Sets the constraints for the provided row variables. |
Uses of Interval in sbrt.kernel.utilities.proc |
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Method parameters in sbrt.kernel.utilities.proc with type arguments of type Interval | |
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void |
IntervalComparison.setIntervalSources(java.lang.Iterable<java.util.Map<V,Interval>> source1,
java.lang.Iterable<java.util.Map<V,Interval>> source2)
Sets of the sources of interval vectors. |
void |
IntervalComparison.setIntervalSources(java.lang.Iterable<java.util.Map<V,Interval>> source1,
java.lang.Iterable<java.util.Map<V,Interval>> source2)
Sets of the sources of interval vectors. |
Uses of Interval in sbrt.shell.io.fba |
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Method parameters in sbrt.shell.io.fba with type arguments of type Interval | |
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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. |
Constructor parameters in sbrt.shell.io.fba with type arguments of type Interval | |
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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 Interval in sbrt.shell.mng.fba |
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Methods in sbrt.shell.mng.fba that return Interval | |
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static Interval |
RandomConstraintsManager.getInactive(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for RandomConstraintsManager.INACTIVE in the provided manager input. |
static Interval |
RandomConstraintsManager.getIrrevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for RandomConstraintsManager.IRREV_CONSTRAINT in the provided manager input. |
static Interval |
RandomConstraintsManager.getRevConstraint(ManagerInput<java.lang.String,java.lang.String> input)
Parses and returns the value for RandomConstraintsManager.REV_CONSTRAINT in the provided manager input. |
Methods in sbrt.shell.mng.fba that return types with arguments of type Interval | |
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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 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 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 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 MapTextOutputFile<java.lang.String,Interval> |
RandomConstraintsManager.getOutputFile(java.lang.String fileName,
java.util.Set<java.lang.String> headers,
IrrevRxnFluxome fluxome)
Returns an empty output file that is suitable for storing multiple sets of flux constraints. |
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. |
Method parameters in sbrt.shell.mng.fba with type arguments of type Interval | |
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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. |
Uses of Interval in sbrt.shell.text.fba |
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Methods in sbrt.shell.text.fba that return Interval | |
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Interval |
PalssonRxnNodeParser.getFluxBounds(org.w3c.dom.Node reactionNode)
Returns the flux bounds of the provided reaction node. |
Interval |
BiggRxnNodeParser.getFluxBounds(org.w3c.dom.Node reactionNode)
Returns the flux bounds of the provided reaction node. |
Methods in sbrt.shell.text.fba that return types with arguments of type Interval | |
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PipeListFormat<Interval> |
ConstraintsFileLineFormatV1.getListFormat()
Returns the format used for lists of values. |
PipeListFormat<Interval> |
ConstraintsFileLineFormatV2.getListFormat()
Returns the format used for lists of values. |
Uses of Interval in sbrt.shell.text.math |
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Methods in sbrt.shell.text.math that return Interval | |
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Interval |
IntervalFormatV1.parse(java.lang.String interval)
Parses the provided string and returns its corresponding interval. |
Interval |
BoundedIntervalFormatV1.parse(java.lang.String interval)
Parses the provided string and returns its corresponding interval. |
Methods in sbrt.shell.text.math with parameters of type Interval | |
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java.lang.String |
IntervalFormatV1.format(Interval interval)
Returns a formatted string representation of the provided interval. |
java.lang.String |
BoundedIntervalFormatV1.format(Interval interval)
Returns a formatted string representation of the provided interval. |
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