Uses of Class
sbrt.kernel.math.Interval

Packages that use Interval
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
 

Methods in sbrt.ext.cplex with parameters of type Interval
<T extends C>
void
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.
<T extends R>
void
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
 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
 

Methods in sbrt.ext.glpk with parameters of type Interval
<Y extends C>
void
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.
<X extends R>
void
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
 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
 

Fields in sbrt.kernel.fba declared as Interval
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
 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
 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
 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
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
 

Method parameters in sbrt.kernel.fba.analysis with type arguments of type Interval
 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
 

Methods in sbrt.kernel.fba.comp that return Interval
 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
 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
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
 

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
 

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
<V> java.util.Set<IntervalComparer.Diff<V>>
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.
<V> java.util.Set<IntervalComparer.Diff<V>>
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
 

Method parameters in sbrt.kernel.math.algebra with type arguments of type Interval
static
<V> LinearSystemSolution<V>
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
<V> HashConvexPolytope<V>
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
 

Methods in sbrt.kernel.math.optimization with parameters of type Interval
<Y extends C>
void
ProgramSolver.setColumnConstraint(Y column, Interval c)
          Sets the constraint on the provided column variable.
 void LinearProgramSolver.setConstraint(LinearComb<? extends C> expression, Interval c)
          Sets a constraint on the provided linear combination of column variables.
 void ProgramSolver.setConstraint(MathExpr<? extends C> expression, Interval c)
          Sets a constraint on the provided mathematical expression of column variables.
 void QuadraticProgramSolver.setConstraint(QuadraticExpr<? extends C> expression, Interval c)
          Sets a constraint on the provided quadratic expression of column variables.
<X extends R>
void
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
 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
 

Method parameters in sbrt.kernel.utilities.proc with type arguments of type Interval
 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
 

Method parameters in sbrt.shell.io.fba with type arguments of type Interval
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
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
 

Methods in sbrt.shell.mng.fba that return Interval
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
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
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
 

Methods in sbrt.shell.text.fba that return Interval
 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
 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
 

Methods in sbrt.shell.text.math that return Interval
 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
 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.