Uses of Interface
sbrt.kernel.math.MathExpr

Packages that use MathExpr
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.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.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.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 MathExpr in sbrt.ext.cplex
 

Methods in sbrt.ext.cplex with parameters of type MathExpr
 void CplexSolver.setConstraint(MathExpr<? extends C> expression, Interval c)
          Sets a constraint on the provided mathematical expression of column variables.
 void CplexSolver.setObjectiveFunction(MathExpr<? extends C> objective)
          Sets the objective function to the provided mathematical expression of column variables.
 void CplexSolver.setObjectiveFunction(MathExpr<? extends C> objective, OptSense sense)
          Sets the objective function and optimization sense to the provided values.
 

Method parameters in sbrt.ext.cplex with type arguments of type MathExpr
 void CplexSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> exprConstraints)
          Sets constraints on the provided mathematical expressions of column variables.
 

Uses of MathExpr in sbrt.ext.glpk
 

Methods in sbrt.ext.glpk with parameters of type MathExpr
 void GlpkSolver.setConstraint(MathExpr<? extends C> expression, Interval c)
          Sets a constraint on the provided mathematical expression of column variables.
 void GlpkSolver.setObjectiveFunction(MathExpr<? extends C> expression)
          Sets the objective function to the provided mathematical expression of column variables.
 void GlpkSolver.setObjectiveFunction(MathExpr<? extends C> expression, OptSense sense)
          Sets the objective function and optimization sense to the provided values.
 

Method parameters in sbrt.ext.glpk with type arguments of type MathExpr
 void GlpkSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> expressionConstraints)
          Sets constraints on the provided mathematical expressions of column variables.
 

Uses of MathExpr in sbrt.kernel.fba
 

Methods in sbrt.kernel.fba that return types with arguments of type MathExpr
 UnmodifiableMap<MathExpr<java.lang.String>,Interval> FluxConstraints.getExprConstraints()
          Returns the constraints for mathematical expressions of fluxes.
 

Methods in sbrt.kernel.fba with parameters of type MathExpr
 Interval FluxConstraints.getConstraint(MathExpr<java.lang.String> rxnExpr)
          Returns the constraint of the provided mathematical expression of reaction names.
 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.
 

Constructor parameters in sbrt.kernel.fba with type arguments of type MathExpr
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 MathExpr in sbrt.kernel.fba.comp
 

Methods in sbrt.kernel.fba.comp with type parameters of type MathExpr
<V,E extends MathExpr<V>>
java.util.Map<E,java.lang.Double>
FbaOptimizer.getMaxima(java.util.Collection<E> objectives)
          Computes the maximum value of each provided objective function.
<V,E extends MathExpr<V>>
java.util.Map<E,java.lang.Double>
FbaOptimizer.getMinima(java.util.Collection<E> objectives)
          Computes the minimum value of each provided objective function.
 

Methods in sbrt.kernel.fba.comp that return MathExpr
 MathExpr<java.lang.String> FluxCapException.getFluxCap()
          Returns the invalid flux cap.
 MathExpr<java.lang.String> RxnDeletionComputer.getObjectiveFunction()
          Returns the current objective function.
 MathExpr<?> FbaOptException.getObjFunction()
          Returns the objective function whose optimal value could not be found.
 

Methods in sbrt.kernel.fba.comp that return types with arguments of type MathExpr
 java.util.Map<MathExpr<?>,Interval> FbaOptimizer.getColExprConstraints()
          Returns all current constraints on mathematical expressions of column variables.
 java.util.Set<MathExpr<?>> FbaOptimizer.getColExprs()
          Returns the set of all mathematical expressions of column 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<MathExpr<java.lang.String>,Interval> FbaOptimizer.getRxnExprConstraints()
          Returns all current constraints on mathematical expressions of reaction names.
 java.util.Set<MathExpr<java.lang.String>> FbaOptimizer.getRxnExprs()
          Returns the set of all mathematical expressions of reaction names.
 

Methods in sbrt.kernel.fba.comp with parameters of type MathExpr
protected  void FbaOptimizer.checkColExpr(MathExpr<?> e)
          Ensures all the variables in the provided expression are valid column variables.
protected  void AbstractCvComputer.checkRxnExpr(MathExpr<java.lang.String> e)
          Ensures the expression is valid for the fluxome provided.
protected  void FbaOptimizer.checkRxnExpr(MathExpr<java.lang.String> e)
          Ensures all the variables in the provided expression are reaction names.
protected  double AbstractFluxIntervalComputer.getBoundedMax(MathExpr<java.lang.String> rxnNameExpr)
          Computes the maximum value of the provided objective function.
protected  double AbstractFluxIntervalComputer.getBoundedMin(MathExpr<java.lang.String> rxnNameExpr)
          Computes the minimum value of the provided objective function.
 Interval FbaOptimizer.getColExprConstraint(MathExpr<?> columnVariableExpr)
          Returns the current constraint on the provided expression.
 FbaOptimizer.Results FbaOptimizer.getMax(MathExpr<?> objective)
          Returns the results of computing the maximum value of the provided objective function.
 double FbaOptimizer.getMaximum(MathExpr<?> objective)
          Computes the maximum value of the provided objective function.
protected  double AbstractFluxIntervalComputer.getMaximum(MathExpr<java.lang.String> rxnNameExpr)
          Computes the maximum value of the provided objective function.
 FbaOptimizer.Results FbaOptimizer.getMin(MathExpr<?> objective)
          Returns the results of computing the minimum value of the provided objective function.
 double FbaOptimizer.getMinimum(MathExpr<?> objective)
          Computes the minimum value of the provided objective function.
protected  double AbstractFluxIntervalComputer.getMinimum(MathExpr<java.lang.String> rxnNameExpr)
          Computes the minimum value of the provided objective function.
 FbaOptimizer.Results FbaOptimizer.getOptimal(MathExpr<?> objective, OptSense sense)
          Returns the results of computing the optimal value of the provided objective function.
 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.
 void FbaOptimizer.restoreColExprConstraint(MathExpr<?> columnVarExpr)
          Restores the constraint on the provided expression of column variables to the value contained in the fluxome.
 void RxnDeletionComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void InitialPointComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> expr)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void FluxCvComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void AbstractFluxIntervalComputer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExp)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void CdHarFluxComp.restoreRxnExprConstraint(MathExpr<java.lang.String> expr)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void FbaOptimizer.restoreRxnExprConstraint(MathExpr<java.lang.String> rxnNameExpr)
          Restores the constraint on the provided flux expression to the value contained in the fluxome.
 void FbaOptimizer.setColExprConstraint(MathExpr<?> expr, Interval c)
          Changes the constraint on the provided mathematical expression of column variables.
 void RxnDeletionComputer.setObjectiveFunction(MathExpr<java.lang.String> objective)
          Sets the objective function to the provided mathematical expression.
 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 MathExpr
 void FbaOptimizer.restoreColExprConstraints(java.util.Collection<? extends MathExpr<?>> colVarExprs)
          Restores the constraints for the provided column variable expressions to those in the provided fluxome.
 void InitialPointComputer.restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExps)
          Restores the constraints on the provided expressions to the values contained in the fluxome.
 void FluxCvComputer.restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExps)
          Restores the constraints on the provided expressions to the values contained in the fluxome.
 void AbstractCvComputer.restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExps)
          Restores the constraints on the provided expressions to the values contained in the fluxome.
 void AbstractFluxIntervalComputer.restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExps)
          Restores the constraints on the provided expressions to the values contained in the fluxome.
 void FbaOptimizer.restoreRxnExprConstraints(java.util.Collection<? extends MathExpr<java.lang.String>> rxnNameExprs)
          Restores the constraints for the provided reaction name expressions to those in the provided fluxome.
 void FbaOptimizer.setColExprConstraints(java.util.Map<? extends MathExpr<?>,Interval> exprConstraints)
          Changes the constraints on more than one mathematical expression of column variables.
 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.
 

Constructors in sbrt.kernel.fba.comp with parameters of type MathExpr
FbaOptException(MathExpr<?> objectiveFunction, OptSense sense, ProgramSolverStatus status)
          Constructs a new FBA optimization exception.
FbaOptException(MathExpr<?> objectiveFunction, OptSense sense, ProgramSolverStatus status, java.lang.String message)
          Constructs a new FBA optimization exception.
FluxCapException(MathExpr<java.lang.String> fluxCap, java.lang.String reactionName)
          Constructs a new flux cap exception.
FluxCapException(MathExpr<java.lang.String> fluxCap, java.lang.String reactionName, java.lang.Throwable cause)
          Constructs a new flux cap exception.
 

Uses of MathExpr in sbrt.kernel.fba.proc
 

Methods in sbrt.kernel.fba.proc that return MathExpr
 MathExpr<java.lang.String> CvFbaOptProcess.getObjectiveFunction()
          Returns the current objective function.
 MathExpr<java.lang.String> CatalystDeletionProcess.getObjectiveFunction()
          Returns the current objective function.
 MathExpr<java.lang.String> RxnDeletionProcess.getObjectiveFunction()
          Returns the current objective function.
 MathExpr<java.lang.String> CvRxnDeletionProcess.getObjectiveFunction()
          Returns the current objective function.
 MathExpr<java.lang.String> CvCatalystDeletionProcess.getObjectiveFunction()
          Returns the current objective function.
 

Methods in sbrt.kernel.fba.proc with parameters of type MathExpr
 void CvFbaOptProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
          Sets the objective function to the provided mathematical expression.
 void CatalystDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
          Sets the objective function to the provided mathematical expression.
 void RxnDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
          Sets the objective function to the provided mathematical expression.
 void CvRxnDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
          Sets the objective function to the provided mathematical expression.
 void CvCatalystDeletionProcess.setObjectiveFunction(MathExpr<java.lang.String> objective)
          Sets the objective function to the provided mathematical expression.
 

Method parameters in sbrt.kernel.fba.proc with type arguments of type MathExpr
 void CvObjectiveFunctionProcess.setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
          Sets the objective function input source.
 void ObjFunAnalysis.setObjectiveFunctionSource(java.lang.Iterable<? extends MathExpr<java.lang.String>> objectiveSource)
          Sets the objective function input source.
 

Uses of MathExpr in sbrt.kernel.math
 

Subinterfaces of MathExpr in sbrt.kernel.math
 interface LinearComb<V>
          This interface is used to represent linear combinations.
 interface Polynomial<V>
          This interface is used to represent polynomials.
 interface QuadraticExpr<V>
          This interface is used to represent quadratic expressions.
 

Classes in sbrt.kernel.math that implement MathExpr
 class AbstractLinearComb<V>
          This abstract class is a skeleton implementation of LinearComb.
 class AbstractPolynomial<V>
          This abstract class is a skeleton implementation of Polynomial.
 class HashLinearComb<V>
          This class is a concrete implemenation of LinearComb.
 

Methods in sbrt.kernel.math that return MathExpr
 MathExpr<V> MathExpr.plugInNumbers(java.util.Map<?,java.lang.Double> variableValues)
          Plugs in the provided numerical values to produce a new mathematical expression.
 

Uses of MathExpr in sbrt.kernel.math.optimization
 

Methods in sbrt.kernel.math.optimization with parameters of type MathExpr
 void ProgramSolver.setConstraint(MathExpr<? extends C> expression, Interval c)
          Sets a constraint on the provided mathematical expression of column variables.
 void ProgramSolver.setObjectiveFunction(MathExpr<? extends C> expression)
          Sets the objective function to the provided mathematical expression of column variables.
 void ProgramSolver.setObjectiveFunction(MathExpr<? extends C> expression, OptSense sense)
          Sets the objective function and optimization sense to the provided values.
 

Method parameters in sbrt.kernel.math.optimization with type arguments of type MathExpr
 void ProgramSolver.setConstraints(java.util.Map<? extends MathExpr<? extends C>,Interval> expressionConstraints)
          Sets constraints on the provided mathematical expressions of column variables.
 

Uses of MathExpr in sbrt.kernel.utilities.proc
 

Classes in sbrt.kernel.utilities.proc with type parameters of type MathExpr
 class VariableParticipation<E extends MathExpr<V>,V>
          This class is used to organize a collection of mathematical expressions according to the variables they contain.
 

Uses of MathExpr in sbrt.shell.io.fba
 

Classes in sbrt.shell.io.fba with type parameters of type MathExpr
 class RxnNamExprSetInputFile<E extends MathExpr<S>,S>
          This class is used to read files containing a set of reaction name expressions.
 

Uses of MathExpr in sbrt.shell.text.fba
 

Classes in sbrt.shell.text.fba with type parameters of type MathExpr
 interface RxnNameExprFormat<E extends MathExpr<S>,S>
          This interface is used to represent formats for mathematical expressions of reaction names.
 

Uses of MathExpr in sbrt.shell.text.math
 

Classes in sbrt.shell.text.math with type parameters of type MathExpr
 interface MathExprFormat<E extends MathExpr<V>,V>
          This interface is used to represent formats for linear combinations.